- galaxy-dev - lists.galaxyproject.org

[hg] galaxy 3576: Fix an eggs bug wherein compatible platform ve...
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/5b793b193cac changeset: 3576:5b793b193cac user: Nate Coraor <nate(a)bx.psu.edu> date: Mon Mar 29 11:48:05 2010 -0400 description: Fix an eggs bug wherein compatible platform versions would match even when python versions differed diffstat: lib/galaxy/eggs/__init__.py | 1 + 1 files changed, 1 insertions(+), 0 deletions(-) diffs (11 lines): diff -r b1165a0614ff -r 5b793b193cac lib/galaxy/eggs/__init__.py --- a/lib/galaxy/eggs/__init__.py Sat Mar 27 14:25:10 2010 -0400 +++ b/lib/galaxy/eggs/__init__.py Mon Mar 29 11:48:05 2010 -0400 @@ -97,6 +97,7 @@ if tmp_dist.platform is not None and \ self.distribution.project_name == tmp_dist.project_name and \ self.distribution.version == tmp_dist.version and \ + self.distribution.py_version == tmp_dist.py_version and \ pkg_resources.compatible_platforms( tmp_dist.platform, pkg_resources.get_platform() ): return file return None

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[hg] galaxy 3575: Change to rgCaCo to output NAs unchanged rathe...
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/b1165a0614ff changeset: 3575:b1165a0614ff user: fubar: ross Lazarus at gmail period com date: Sat Mar 27 14:25:10 2010 -0400 description: Change to rgCaCo to output NAs unchanged rather than fiddling with any p values This fixes an ugly artifact detected in manhatten plots Improved fidelity means downstream apps will need to cope with the awful realities diffstat: test-data/rgCaCotest1_CaCo.xls | 50 +++++++++++----------- test-data/rgtestouts/rgManQQ/Allelep_qqplot.png | 0 test-data/rgtestouts/rgManQQ/Armitagep_qqplot.png | 0 3 files changed, 25 insertions(+), 25 deletions(-) diffs (59 lines): diff -r bda77e05c7c0 -r b1165a0614ff test-data/rgCaCotest1_CaCo.xls --- a/test-data/rgCaCotest1_CaCo.xls Sat Mar 27 11:42:45 2010 -0400 +++ b/test-data/rgCaCotest1_CaCo.xls Sat Mar 27 14:25:10 2010 -0400 @@ -1,26 +1,26 @@ rs Chr Offset Genop log10Genop Armitagep log10Armitagep Allelep log10Allelep Domp log10Domp -rs2283802 22 21784722 1.000 0.000000 1.000 -0.000000 1.000 -0.000000 1.000 0.000000 -rs2267000 22 21785366 1.000 0.000000 0.893 0.049197 0.896 0.047450 1.000 0.000000 -rs16997606 22 21794754 1.000 0.000000 0.512 0.290815 0.540 0.267606 1.000 0.000000 -rs4820537 22 21794810 1.000 0.000000 0.266 0.575935 0.238 0.623423 1.000 0.000000 -rs3788347 22 21797804 1.000 0.000000 0.528 0.276955 0.518 0.285251 1.000 0.000000 -rs756632 22 21799918 1.000 0.000000 0.847 0.072014 0.838 0.076704 1.000 0.000000 -rs4820539 22 21807970 1.000 0.000000 0.663 0.178618 0.669 0.174704 1.000 0.000000 -rs2283804 22 21820335 1.000 0.000000 0.888 0.051636 0.891 0.049927 1.000 0.000000 -rs2267006 22 21820990 1.000 0.000000 0.888 0.051636 0.891 0.049927 1.000 0.000000 -rs4822363 22 21821000 1.000 0.000000 0.609 0.215311 0.624 0.204815 1.000 0.000000 -rs5751592 22 21827674 1.000 0.000000 0.426 0.370998 0.470 0.328272 1.000 0.000000 -rs5759608 22 21832708 1.000 0.000000 1.000 -0.000000 1.000 -0.000000 1.000 0.000000 -rs5759612 22 21833170 1.000 0.000000 1.000 -0.000000 1.000 -0.000000 1.000 0.000000 -rs2267009 22 21860168 1.000 0.000000 1.000 -0.000000 1.000 -0.000000 1.000 0.000000 -rs2267010 22 21864366 1.000 0.000000 0.729 0.137332 0.734 0.134304 1.000 0.000000 -rs5759636 22 21868698 1.000 0.000000 0.215 0.667360 0.228 0.642256 1.000 0.000000 -rs2071436 22 21871488 1.000 0.000000 1.000 -0.000000 1.000 -0.000000 1.000 0.000000 -rs2267013 22 21875879 1.000 0.000000 0.512 0.290815 0.540 0.267606 1.000 0.000000 -rs6003566 22 21889806 1.000 0.000000 0.361 0.442132 0.389 0.409604 1.000 0.000000 -rs2256725 22 21892891 1.000 0.000000 0.512 0.290815 0.540 0.267606 1.000 0.000000 -rs12160770 22 21892925 1.000 0.000000 0.594 0.225921 0.597 0.224098 1.000 0.000000 -rs5751611 22 21896019 1.000 0.000000 0.893 0.049246 0.894 0.048565 1.000 0.000000 -rs762601 22 21898858 1.000 0.000000 0.897 0.047111 0.893 0.049051 1.000 0.000000 -rs2156921 22 21899063 1.000 0.000000 0.897 0.047111 0.893 0.049051 1.000 0.000000 -rs4822375 22 21905642 1.000 0.000000 0.897 0.047111 0.893 0.049051 1.000 0.000000 +rs2283802 22 21784722 NA 0.000000 1 -0.000000 1 -0.000000 NA 0.000000 +rs2267000 22 21785366 NA 0.000000 0.8929 0.049197 0.8965 0.047450 NA 0.000000 +rs16997606 22 21794754 NA 0.000000 0.5119 0.290815 0.54 0.267606 NA 0.000000 +rs4820537 22 21794810 NA 0.000000 0.2655 0.575935 0.238 0.623423 NA 0.000000 +rs3788347 22 21797804 NA 0.000000 0.5285 0.276955 0.5185 0.285251 NA 0.000000 +rs756632 22 21799918 NA 0.000000 0.8472 0.072014 0.8381 0.076704 NA 0.000000 +rs4820539 22 21807970 NA 0.000000 0.6628 0.178618 0.6688 0.174704 NA 0.000000 +rs2283804 22 21820335 NA 0.000000 0.8879 0.051636 0.8914 0.049927 NA 0.000000 +rs2267006 22 21820990 NA 0.000000 0.8879 0.051636 0.8914 0.049927 NA 0.000000 +rs4822363 22 21821000 NA 0.000000 0.6091 0.215311 0.624 0.204815 NA 0.000000 +rs5751592 22 21827674 NA 0.000000 0.4256 0.370998 0.4696 0.328272 NA 0.000000 +rs5759608 22 21832708 NA 0.000000 1 -0.000000 1 -0.000000 NA 0.000000 +rs5759612 22 21833170 NA 0.000000 1 -0.000000 1 -0.000000 NA 0.000000 +rs2267009 22 21860168 NA 0.000000 1 -0.000000 1 -0.000000 NA 0.000000 +rs2267010 22 21864366 NA 0.000000 0.7289 0.137332 0.734 0.134304 NA 0.000000 +rs5759636 22 21868698 NA 0.000000 0.2151 0.667360 0.2279 0.642256 NA 0.000000 +rs2071436 22 21871488 NA 0.000000 1 -0.000000 1 -0.000000 NA 0.000000 +rs2267013 22 21875879 NA 0.000000 0.5119 0.290815 0.54 0.267606 NA 0.000000 +rs6003566 22 21889806 NA 0.000000 0.3613 0.442132 0.3894 0.409604 NA 0.000000 +rs2256725 22 21892891 NA 0.000000 0.5119 0.290815 0.54 0.267606 NA 0.000000 +rs12160770 22 21892925 NA 0.000000 0.5944 0.225921 0.5969 0.224098 NA 0.000000 +rs5751611 22 21896019 NA 0.000000 0.8928 0.049246 0.8942 0.048565 NA 0.000000 +rs762601 22 21898858 NA 0.000000 0.8972 0.047111 0.8932 0.049051 NA 0.000000 +rs2156921 22 21899063 NA 0.000000 0.8972 0.047111 0.8932 0.049051 NA 0.000000 +rs4822375 22 21905642 NA 0.000000 0.8972 0.047111 0.8932 0.049051 NA 0.000000 diff -r bda77e05c7c0 -r b1165a0614ff test-data/rgtestouts/rgManQQ/Allelep_qqplot.png Binary file test-data/rgtestouts/rgManQQ/Allelep_qqplot.png has changed diff -r bda77e05c7c0 -r b1165a0614ff test-data/rgtestouts/rgManQQ/Armitagep_qqplot.png Binary file test-data/rgtestouts/rgManQQ/Armitagep_qqplot.png has changed

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[hg] galaxy 3574: Two small tweaks to WGA/SNP tests - for rgQC a...
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/bda77e05c7c0 changeset: 3574:bda77e05c7c0 user: fubar: ross Lazarus at gmail period com date: Sat Mar 27 11:42:45 2010 -0400 description: Two small tweaks to WGA/SNP tests - for rgQC and for rgManQQ diffstat: tools/rgenetics/rgManQQ.py | 5 ++--- tools/rgenetics/rgManQQ.xml | 1 + tools/rgenetics/rgQC.xml | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diffs (39 lines): diff -r b5757fb7ab13 -r bda77e05c7c0 tools/rgenetics/rgManQQ.py --- a/tools/rgenetics/rgManQQ.py Fri Mar 26 22:40:46 2010 -0400 +++ b/tools/rgenetics/rgManQQ.py Sat Mar 27 11:42:45 2010 -0400 @@ -189,10 +189,9 @@ if chrom_col == 1 or offset_col == 1: # was passed as zero - do not do manhattan plots chrom_col = 0 offset_col = 0 - if sys.argv[8].lower() in ['1','true']: + grey = 0 + if (sys.argv[8].lower() in ['1','true']): grey = 1 - else: - grey = 0 rcmd = '%s%s' % (rcode,rcode2 % (input_fname,chrom_col,offset_col,pval_cols,title,grey)) rlog,flist = RRun(rcmd=rcmd,title=ctitle,outdir=outdir) flist.sort() diff -r b5757fb7ab13 -r bda77e05c7c0 tools/rgenetics/rgManQQ.xml --- a/tools/rgenetics/rgManQQ.xml Fri Mar 26 22:40:46 2010 -0400 +++ b/tools/rgenetics/rgManQQ.xml Sat Mar 27 11:42:45 2010 -0400 @@ -41,6 +41,7 @@ <param name='pval_col' value='5,7' /> <param name='chrom_col' value='1' /> <param name='offset_col' value='2' /> + <param name='grey' value='0' /> <output name='out_html' file='rgtestouts/rgManQQ/rgManQQtest1.html' ftype='html' lines_diff='17'> <extra_files type="file" name='Allelep_manhattan.png' value='rgtestouts/rgManQQ/Allelep_manhattan.png' compare="sim_size" delta = "100" /> diff -r b5757fb7ab13 -r bda77e05c7c0 tools/rgenetics/rgQC.xml --- a/tools/rgenetics/rgQC.xml Fri Mar 26 22:40:46 2010 -0400 +++ b/tools/rgenetics/rgQC.xml Sat Mar 27 11:42:45 2010 -0400 @@ -37,7 +37,7 @@ <extra_files type="file" name='tinywga.imiss' value="rgtestouts/rgQC/tinywga.imiss" compare="diff" /> <extra_files type="file" name='tinywga.lmendel' value="rgtestouts/rgQC/tinywga.lmendel" compare="diff" /> <extra_files type="file" name='tinywga.lmiss' value="rgtestouts/rgQC/tinywga.lmiss" compare="diff" /> - <extra_files type="file" name='tinywga_All_3x3.pdf' value="rgtestouts/rgQC/tinywga_All_3x3.pdf" compare="diff" lines_diff="1112"/> + <extra_files type="file" name='tinywga_All_3x3.pdf' value="rgtestouts/rgQC/tinywga_All_3x3.pdf" compare="diff" lines_diff="2660"/> <extra_files type="file" name='ldp_tinywga.bed' value="rgtestouts/rgQC/ldp_tinywga.bed" compare="diff" /> <extra_files type="file" name='ldp_tinywga.bim' value="rgtestouts/rgQC/ldp_tinywga.bim" compare="diff" /> <extra_files type="file" name='ldp_tinywga.fam' value="rgtestouts/rgQC/ldp_tinywga.fam" compare="diff" />

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[hg] galaxy 3573: added a grey option for manhattan plot chromos...
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/b5757fb7ab13 changeset: 3573:b5757fb7ab13 user: fubar: ross Lazarus at gmail period com date: Fri Mar 26 22:40:46 2010 -0400 description: added a grey option for manhattan plot chromosome colours diffstat: tools/rgenetics/rgCaCo.py | 15 +++++++-------- tools/rgenetics/rgManQQ.py | 16 ++++++++++------ tools/rgenetics/rgManQQ.xml | 4 +++- tools/rgenetics/rgQC.xml | 4 ++-- 4 files changed, 22 insertions(+), 17 deletions(-) diffs (138 lines): diff -r b8689cf28fa7 -r b5757fb7ab13 tools/rgenetics/rgCaCo.py --- a/tools/rgenetics/rgCaCo.py Fri Mar 26 16:46:44 2010 -0400 +++ b/tools/rgenetics/rgCaCo.py Fri Mar 26 22:40:46 2010 -0400 @@ -112,14 +112,13 @@ if p <> 'NA': # eesh logp = '%9.9f' % -math.log10(p) else: - logp = '1' + logp = 'NA' try: orat = ll[8] - if orat == 'NA': - orat = '1' except: - orat = '1' + orat = 'NA' orat2 = orat + # invert large negative odds ratios if float(orat) < 1 and float(orat) > 0.0: orat2 = '%9.9f' % (1.0/float(orat)) outl = [ll[1],logp, orat2, orat] @@ -207,16 +206,16 @@ flog.write('### offending line #%d in %s = %s' % (lnum,l)) except: pass - width = max(3,1+int(abs(lp))) # get desired precision for output - w = '%d' % width - fps = '%%%s.%sf' % (w,w) # eg '%9.9f' if snp <> lastsnp: if len(outl.keys()) > 3: sl = [outl.get(x,'?') for x in ('snp','chrom','offset','GENO','TREND','ALLELIC','DOM')] res.append('\t'.join(sl)) # last snp line outl = {'snp':snp,'chrom':chrom,'offset':offset} # first 3 cols for gg line lastsnp = snp # reset for next marker - outl[test] = '\t'.join([(fps % fp).strip(),('%6.6f' % lp).strip()]) + #if p == 'NA': + # p = 1.0 + # let's pass downstream for handling R is fine? + outl[test] = '%s\t%f' % (p,lp) if len(outl.keys()) > 3: l = [outl.get(x,'?') for x in ('snp','chrom','offset','GENO','TREND','ALLELIC','DOM')] res.append('\t'.join(l)) # last snp line diff -r b8689cf28fa7 -r b5757fb7ab13 tools/rgenetics/rgManQQ.py --- a/tools/rgenetics/rgManQQ.py Fri Mar 26 16:46:44 2010 -0400 +++ b/tools/rgenetics/rgManQQ.py Fri Mar 26 22:40:46 2010 -0400 @@ -31,7 +31,7 @@ manhattan = function(chrom=NULL,offset=NULL,pvals=NULL, title=NULL, max.y="max", - suggestiveline=0, genomewide=T, size.x.labels=9, size.y.labels=10, annotate=F, SNPlist=NULL,grey=F) { + suggestiveline=0, genomewide=T, size.x.labels=9, size.y.labels=10, annotate=F, SNPlist=NULL,grey=0) { if (annotate & is.null(SNPlist)) stop("You requested annotation but provided no SNPlist!") genomewideline=NULL # was genomewideline=-log10(5e-8) @@ -120,7 +120,7 @@ # instantiate rcode2 string with infile,chromcol,offsetcol,pvalscols,title before saving and running rcode2 = """rgqqMan = function(infile="%s",chromcolumn=%d, offsetcolumn=%d, pvalscolumns=%s, - title="%s") { + title="%s",grey=%d) { d = read.table(infile,head=T,sep='\t') print(paste('###',length(d[,1]),'values read from',infile,'read - now running plots',sep=' ')) for (pvalscolumn in pvalscolumns) { @@ -133,7 +133,7 @@ print(paste('## qqplot on',cname,'done')) if ((chromcolumn > 0) & (offsetcolumn > 0)) { print(paste('## manhattan on',cname,'starting',chromcolumn,offsetcolumn,pvalscolumn)) - mymanplot= manhattan(chrom=d[,chromcolumn],offset=d[,offsetcolumn],pvals=d[,pvalscolumn],title=mytitle) + mymanplot= manhattan(chrom=d[,chromcolumn],offset=d[,offsetcolumn],pvals=d[,pvalscolumn],title=mytitle,grey=grey) print(paste('## manhattan plot on',cname,'done')) ggsave(file=paste(myfname,"manhattan.png",sep='_'),mymanplot,width=11,height=8,dpi=100) } @@ -141,7 +141,7 @@ print(paste('chrom column =',chromcolumn,'offset column = ',offsetcolumn, 'so no Manhattan plot - supply both chromosome and offset as numerics for Manhattan plots if required')) } - ggsave(file=paste(myfname,"qqplot.png",sep='_'),myqqplot,w=5,h=5,dpi=100) + ggsave(file=paste(myfname,"qqplot.png",sep='_'),myqqplot,width=8,height=11,dpi=100) } else { print(paste('pvalue column =',pvalscolumn,'Cannot parse it so no plots possible')) @@ -160,7 +160,7 @@ </command> """ print >> sys.stdout,'## rgManQQ.py. cl=',sys.argv - npar = 7 + npar = 8 if len(sys.argv) < npar: print >> sys.stdout, '## error - too few command line parameters - wanting %d' % npar print >> sys.stdout, u @@ -189,7 +189,11 @@ if chrom_col == 1 or offset_col == 1: # was passed as zero - do not do manhattan plots chrom_col = 0 offset_col = 0 - rcmd = '%s%s' % (rcode,rcode2 % (input_fname,chrom_col,offset_col,pval_cols,title)) + if sys.argv[8].lower() in ['1','true']: + grey = 1 + else: + grey = 0 + rcmd = '%s%s' % (rcode,rcode2 % (input_fname,chrom_col,offset_col,pval_cols,title,grey)) rlog,flist = RRun(rcmd=rcmd,title=ctitle,outdir=outdir) flist.sort() html = [galhtmlprefix % progname,] diff -r b8689cf28fa7 -r b5757fb7ab13 tools/rgenetics/rgManQQ.xml --- a/tools/rgenetics/rgManQQ.xml Fri Mar 26 16:46:44 2010 -0400 +++ b/tools/rgenetics/rgManQQ.xml Fri Mar 26 22:40:46 2010 -0400 @@ -4,7 +4,7 @@ <description>Plots for WGA P values</description> <command interpreter="python"> - rgManQQ.py '$i' "$name" '$out_html' '$out_html.files_path' '$chrom_col' '$offset_col' '$pval_col' + rgManQQ.py '$i' "$name" '$out_html' '$out_html.files_path' '$chrom_col' '$offset_col' '$pval_col' '$grey' </command> <inputs> @@ -23,6 +23,8 @@ <param name="offset_col" type='select' label = 'Base pair offset column in input file' help='Select "None" if offset not available or no Manhattan plot required' dynamic_options="get_phecols(i,True,'offs')" /> + <param name="grey" type="boolean" checked="false" truevalue="true" falsevalue="false" + label="Grey scale for Manhatten plot (default is colour"/> </page> </inputs> diff -r b8689cf28fa7 -r b5757fb7ab13 tools/rgenetics/rgQC.xml --- a/tools/rgenetics/rgQC.xml Fri Mar 26 16:46:44 2010 -0400 +++ b/tools/rgenetics/rgQC.xml Fri Mar 26 22:40:46 2010 -0400 @@ -27,8 +27,8 @@ <composite_data value='tinywga.fam' /> </param> <param name='out_prefix' value='rgQCtest1' /> - <output name='html_file' file='rgtestouts/rgQC/rgQCtest1.html' ftype='html' lines_diff='437'> - <extra_files type="file" name='tinywga_All_Paged.pdf' value="rgtestouts/rgQC/tinywga_All_Paged.pdf" compare="diff" lines_diff="1190"/> + <output name='html_file' file='rgtestouts/rgQC/rgQCtest1.html' ftype='html' lines_diff='250'> + <extra_files type="file" name='tinywga_All_Paged.pdf' value="rgtestouts/rgQC/tinywga_All_Paged.pdf" compare="diff" lines_diff="2600"/> <extra_files type="file" name='tinywga.log' value="rgtestouts/rgQC/tinywga.log" compare="diff" lines_diff="10"/> <extra_files type="file" name='tinywga.frq' value="rgtestouts/rgQC/tinywga.frq" compare="diff" /> <extra_files type="file" name='tinywga.het' value="rgtestouts/rgQC/tinywga.het" compare="diff" />

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[hg] galaxy 3572: Fixed a file name in the GLM test outputs
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/b8689cf28fa7 changeset: 3572:b8689cf28fa7 user: fubar: ross Lazarus at gmail period com date: Fri Mar 26 16:46:44 2010 -0400 description: Fixed a file name in the GLM test outputs Fixed a stoopid typo in the QC marker report call (how did that get there?) Raised the lines_diff count for rgManQQ tests so they pass diffstat: test-data/rgGLM_GLM_topTable.gff | 26 -------------------------- test-data/rgGLMtest1_GLM_topTable.gff | 26 ++++++++++++++++++++++++++ tools/rgenetics/rgManQQ.xml | 2 +- tools/rgenetics/rgQC.py | 21 ++++++++++++--------- tools/rgenetics/rgQC.xml | 2 +- 5 files changed, 40 insertions(+), 37 deletions(-) diffs (148 lines): diff -r d8e1a56b3415 -r b8689cf28fa7 test-data/rgGLM_GLM_topTable.gff --- a/test-data/rgGLM_GLM_topTable.gff Fri Mar 26 14:43:27 2010 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ -track name=rgGLM_TopTable description="rgGLMtest1" visibility=2 useScore=1 color=0,60,120 -chr22 rgGLM variation 21784622 21784822 455 . . rs2283802 logp=0.75 -chr22 rgGLM variation 21785266 21785466 152 . . rs2267000 logp=0.25 -chr22 rgGLM variation 21794654 21794854 230 . . rs16997606 logp=0.38 -chr22 rgGLM variation 21794710 21794910 107 . . rs4820537 logp=0.18 -chr22 rgGLM variation 21797704 21797904 28 . . rs3788347 logp=0.05 -chr22 rgGLM variation 21799818 21800018 45 . . rs756632 logp=0.08 -chr22 rgGLM variation 21807870 21808070 151 . . rs4820539 logp=0.25 -chr22 rgGLM variation 21820235 21820435 723 . . rs2283804 logp=1.19 -chr22 rgGLM variation 21820890 21821090 723 . . rs2267006 logp=1.19 -chr22 rgGLM variation 21820900 21821100 340 . . rs4822363 logp=0.56 -chr22 rgGLM variation 21827574 21827774 337 . . rs5751592 logp=0.55 -chr22 rgGLM variation 21832608 21832808 563 . . rs5759608 logp=0.92 -chr22 rgGLM variation 21833070 21833270 563 . . rs5759612 logp=0.92 -chr22 rgGLM variation 21860068 21860268 455 . . rs2267009 logp=0.75 -chr22 rgGLM variation 21864266 21864466 391 . . rs2267010 logp=0.64 -chr22 rgGLM variation 21868598 21868798 95 . . rs5759636 logp=0.16 -chr22 rgGLM variation 21871388 21871588 455 . . rs2071436 logp=0.75 -chr22 rgGLM variation 21875779 21875979 32 . . rs2267013 logp=0.05 -chr22 rgGLM variation 21889706 21889906 125 . . rs6003566 logp=0.21 -chr22 rgGLM variation 21892791 21892991 32 . . rs2256725 logp=0.05 -chr22 rgGLM variation 21892825 21893025 127 . . rs12160770 logp=0.21 -chr22 rgGLM variation 21895919 21896119 126 . . rs5751611 logp=0.21 -chr22 rgGLM variation 21898758 21898958 446 . . rs762601 logp=0.73 -chr22 rgGLM variation 21898963 21899163 446 . . rs2156921 logp=0.73 -chr22 rgGLM variation 21905542 21905742 446 . . rs4822375 logp=0.73 diff -r d8e1a56b3415 -r b8689cf28fa7 test-data/rgGLMtest1_GLM_topTable.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgGLMtest1_GLM_topTable.gff Fri Mar 26 16:46:44 2010 -0400 @@ -0,0 +1,26 @@ +track name=rgGLM_TopTable description="rgGLMtest1" visibility=2 useScore=1 color=0,60,120 +chr22 rgGLM variation 21784622 21784822 455 . . rs2283802 logp=0.75 +chr22 rgGLM variation 21785266 21785466 152 . . rs2267000 logp=0.25 +chr22 rgGLM variation 21794654 21794854 230 . . rs16997606 logp=0.38 +chr22 rgGLM variation 21794710 21794910 107 . . rs4820537 logp=0.18 +chr22 rgGLM variation 21797704 21797904 28 . . rs3788347 logp=0.05 +chr22 rgGLM variation 21799818 21800018 45 . . rs756632 logp=0.08 +chr22 rgGLM variation 21807870 21808070 151 . . rs4820539 logp=0.25 +chr22 rgGLM variation 21820235 21820435 723 . . rs2283804 logp=1.19 +chr22 rgGLM variation 21820890 21821090 723 . . rs2267006 logp=1.19 +chr22 rgGLM variation 21820900 21821100 340 . . rs4822363 logp=0.56 +chr22 rgGLM variation 21827574 21827774 337 . . rs5751592 logp=0.55 +chr22 rgGLM variation 21832608 21832808 563 . . rs5759608 logp=0.92 +chr22 rgGLM variation 21833070 21833270 563 . . rs5759612 logp=0.92 +chr22 rgGLM variation 21860068 21860268 455 . . rs2267009 logp=0.75 +chr22 rgGLM variation 21864266 21864466 391 . . rs2267010 logp=0.64 +chr22 rgGLM variation 21868598 21868798 95 . . rs5759636 logp=0.16 +chr22 rgGLM variation 21871388 21871588 455 . . rs2071436 logp=0.75 +chr22 rgGLM variation 21875779 21875979 32 . . rs2267013 logp=0.05 +chr22 rgGLM variation 21889706 21889906 125 . . rs6003566 logp=0.21 +chr22 rgGLM variation 21892791 21892991 32 . . rs2256725 logp=0.05 +chr22 rgGLM variation 21892825 21893025 127 . . rs12160770 logp=0.21 +chr22 rgGLM variation 21895919 21896119 126 . . rs5751611 logp=0.21 +chr22 rgGLM variation 21898758 21898958 446 . . rs762601 logp=0.73 +chr22 rgGLM variation 21898963 21899163 446 . . rs2156921 logp=0.73 +chr22 rgGLM variation 21905542 21905742 446 . . rs4822375 logp=0.73 diff -r d8e1a56b3415 -r b8689cf28fa7 tools/rgenetics/rgManQQ.xml --- a/tools/rgenetics/rgManQQ.xml Fri Mar 26 14:43:27 2010 -0400 +++ b/tools/rgenetics/rgManQQ.xml Fri Mar 26 16:46:44 2010 -0400 @@ -39,7 +39,7 @@ <param name='pval_col' value='5,7' /> <param name='chrom_col' value='1' /> <param name='offset_col' value='2' /> - <output name='out_html' file='rgtestouts/rgManQQ/rgManQQtest1.html' ftype='html' lines_diff='10'> + <output name='out_html' file='rgtestouts/rgManQQ/rgManQQtest1.html' ftype='html' lines_diff='17'> <extra_files type="file" name='Allelep_manhattan.png' value='rgtestouts/rgManQQ/Allelep_manhattan.png' compare="sim_size" delta = "100" /> <extra_files type="file" name='Allelep_qqplot.png' value='rgtestouts/rgManQQ/Allelep_qqplot.png' compare="sim_size" diff -r d8e1a56b3415 -r b8689cf28fa7 tools/rgenetics/rgQC.py --- a/tools/rgenetics/rgQC.py Fri Mar 26 14:43:27 2010 -0400 +++ b/tools/rgenetics/rgQC.py Fri Mar 26 16:46:44 2010 -0400 @@ -294,8 +294,7 @@ outfnames = [os.path.join(newfpath,ploturls[x]) for x in range(nplots)] ordoutfnames = [os.path.join(newfpath,ordploturls[x]) for x in range(nplots)] datasources = [markers,markers,markers,markers,subjects,subjects,subjects] # use this table - titles = ["Marker HWE","Marker Missing Genotype", - "Marker MAF","Marker Mendel", + titles = ["Marker HWE","Marker Missing Genotype", "Marker MAF","Marker Mendel", "Subject Missing Genotype","Subject Mendel",'Subject F Statistic'] html = [] pdflist = [] @@ -630,8 +629,7 @@ outfnames = [os.path.join(newfpath,ploturls[x]) for x in range(nplots)] ordoutfnames = [os.path.join(newfpath,ordploturls[x]) for x in range(nplots)] datasources = [markers,markers,markers,markers,subjects,subjects,subjects] # use this table - titles = ["Marker HWE","Marker Missing Genotype", - "Marker MAF","Marker Mendel", + titles = ["Marker HWE","Marker Missing Genotype", "Marker MAF","Marker Mendel", "Subject Missing Genotype","Subject Mendel",'Subject F Statistic'] html = [] pdflist = [] @@ -1148,7 +1146,7 @@ except: inmend = 'NA' try: - fhweall = '%f' % float(hwe_unaff[1]) # the log value + fhweall = '%f' % float(hwe_all[1]) # the log value except: fhweall = 'NA' try: @@ -1263,7 +1261,7 @@ repout = os.path.join(newfpath,basename) subjects,subjectTops = subjectRep(froot=repout,outfname=asubjf,newfpath=newfpath, logf=alogf) # writes the subject_froot.xls file - markers,markerTops = markerRep(froot=newfpath,outfname=amarkf,newfpath=newfpath, + markers,markerTops = markerRep(froot=repout,outfname=amarkf,newfpath=newfpath, logf=alogf) # marker_froot.xls nbreaks = 100 s = '## starting plotpage, newfpath=%s,m=%s,s=%s/n' % (newfpath,markers[:2],subjects[:2]) @@ -1283,9 +1281,14 @@ html.append('<tr><td colspan="3"><a href="%s" type="application/vnd.ms-excel">%s</a>%s tab delimited</td></tr>' % \ (asubjf,'Click here to download the Subject QC Detail report file',size)) for (title,url,ofname) in plotpage: - dat = subjectTops.get(title,None) + ttitle = 'Ranked %s' % title + dat = subjectTops.get(ttitle,None) if not dat: - dat = markerTops.get(title,None) + dat = markerTops.get(ttitle,None) + if not dat: + print '## iterating plotpage - cannot find title=%s/ttitle=%s' % (title,ttitle) + else: + print '## iterating plotpage - found title=%s/ttitle=%s' % (title,ttitle) imghref = '%s.jpg' % os.path.splitext(url)[0] # removes .pdf thumbnail = os.path.join(newfpath,imghref) if not os.path.exists(thumbnail): # for multipage pdfs, mogrify makes multiple jpgs - fugly hack @@ -1297,7 +1300,7 @@ html.append('<tr><td><a href="%s"><img src="%s" alt="%s" hspace="10" align="middle">' \ % (url,imghref,title)) if dat: # one or the other - write as an extra file and make a link here - t = '%s.xls' % (title.replace(' ','_')) + t = '%s.xls' % (ttitle.replace(' ','_')) fname = os.path.join(newfpath,t) f = file(fname,'w') f.write('\n'.join(['\t'.join(x) for x in dat])) # the report diff -r d8e1a56b3415 -r b8689cf28fa7 tools/rgenetics/rgQC.xml --- a/tools/rgenetics/rgQC.xml Fri Mar 26 14:43:27 2010 -0400 +++ b/tools/rgenetics/rgQC.xml Fri Mar 26 16:46:44 2010 -0400 @@ -1,4 +1,4 @@ -<tool id="rgqc1" name="QC reports:"> +<tool id="rgQC1" name="QC reports:"> <code file="rgQC_code.py"/> <description>Marker and Subject measures</description>

1 0

[hg] galaxy 3571: Adding images for manhattan plot tool help
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/d8e1a56b3415 changeset: 3571:d8e1a56b3415 user: fubar: ross Lazarus at gmail period com date: Fri Mar 26 14:43:27 2010 -0400 description: Adding images for manhattan plot tool help diffstat: static/images/Armitagep_manhattan.png | 0 static/images/Armitagep_qqplot.png | 0 2 files changed, 0 insertions(+), 0 deletions(-) diffs (4 lines): diff -r cc8a30a0669f -r d8e1a56b3415 static/images/Armitagep_manhattan.png Binary file static/images/Armitagep_manhattan.png has changed diff -r cc8a30a0669f -r d8e1a56b3415 static/images/Armitagep_qqplot.png Binary file static/images/Armitagep_qqplot.png has changed

1 0

[hg] galaxy 3570: Adding rg test outputs and updated tools
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/cc8a30a0669f changeset: 3570:cc8a30a0669f user: fubar: ross Lazarus at gmail period com date: Fri Mar 26 14:42:15 2010 -0400 description: Adding rg test outputs and updated tools diffstat: .hgignore | 4 + test-data/rgCaCotest1_CaCo.xls | 26 + test-data/rgCaCotest1_CaCo_log.txt | 46 + test-data/rgCaCotest1_CaCo_topTable.gff | 26 + test-data/rgGLM_GLM_topTable.gff | 26 + test-data/rgGLMtest1_GLM.xls | 26 + test-data/rgGLMtest1_GLM_log.txt | 58 + test-data/rgQQtest1.pdf | 384 ++ test-data/rgTDTtest1_TDT.xls | 25 + test-data/rgTDTtest1_TDT_log.txt | 53 + test-data/rgTDTtest1_TDT_topTable.gff | 25 + test-data/rgtestouts/rgClean/rgCleantest1.bed | 1 + test-data/rgtestouts/rgClean/rgCleantest1.bim | 25 + test-data/rgtestouts/rgClean/rgCleantest1.fam | 40 + test-data/rgtestouts/rgClean/rgCleantest1.log | 66 + test-data/rgtestouts/rgClean/rgCleantest1.pbed | 19 + test-data/rgtestouts/rgEigPCA/Rplots.pdf | 59 + test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R | 19 + test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html | 160 + test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.txt | 40 + test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf | 454 +++ test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf.png | 0 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.pdf | 0 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.ps | 502 +++ test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.xtxt | 7 + test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eval.xls | 39 + test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt | 128 + test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls | 45 + test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.evec | 40 + test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.par | 11 + test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt | 23 + test-data/rgtestouts/rgGRR/rgGRRtest1.html | 65 + test-data/rgtestouts/rgGRR/rgGRRtest1.svg | 770 +++++ test-data/rgtestouts/rgGRR/rgGRRtest1_table.xls | 781 +++++ test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.pdf | 0 test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.png | 0 test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.pdf | 0 test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.png | 0 test-data/rgtestouts/rgHaploView/Chromosome22YRI.LD.PNG | 0 test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt | 50 + test-data/rgtestouts/rgHaploView/alljoin.pdf | 0 test-data/rgtestouts/rgHaploView/allnup.pdf | 0 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html | 124 + test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.LD.PNG | 0 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TAGS | 25 + test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS | 9 + test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed | 1 + test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim | 3 + test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam | 40 + test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log | 169 + test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map | 3 + test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.pbed | 22 + test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped | 40 + test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in | 3 + test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out | 22 + test-data/rgtestouts/rgManQQ/Allelep_manhattan.png | 0 test-data/rgtestouts/rgManQQ/Allelep_qqplot.png | 0 test-data/rgtestouts/rgManQQ/Armitagep_manhattan.png | 0 test-data/rgtestouts/rgManQQ/Armitagep_qqplot.png | 0 test-data/rgtestouts/rgManQQ/rgManQQtest1.R | 150 + test-data/rgtestouts/rgManQQ/rgManQQtest1.html | 61 + test-data/rgtestouts/rgPedSub/rgPedSubtest1.log | 12 + test-data/rgtestouts/rgPedSub/rgPedSubtest1.lped | 17 + test-data/rgtestouts/rgPedSub/tinywga.map | 10 + test-data/rgtestouts/rgPedSub/tinywga.ped | 40 + test-data/rgtestouts/rgQC/FQNormtinywga_s_het_cum.jpg | 0 test-data/rgtestouts/rgQC/FQNormtinywga_s_het_cum.pdf | 373 ++ test-data/rgtestouts/rgQC/MarkerDetails_rgQCtest1.xls | 1 + test-data/rgtestouts/rgQC/Ranked_Subject_Missing_Genotype.xls | 21 + test-data/rgtestouts/rgQC/SubjectDetails_rgQCtest1.xls | 41 + test-data/rgtestouts/rgQC/ldp_tinywga.bed | 1 + test-data/rgtestouts/rgQC/ldp_tinywga.bim | 14 + test-data/rgtestouts/rgQC/ldp_tinywga.fam | 40 + test-data/rgtestouts/rgQC/ldp_tinywga.log | 48 + test-data/rgtestouts/rgQC/rgQCtest1.html | 576 ++++ test-data/rgtestouts/rgQC/tinywga.fmendel | 14 + test-data/rgtestouts/rgQC/tinywga.frq | 26 + test-data/rgtestouts/rgQC/tinywga.het | 41 + test-data/rgtestouts/rgQC/tinywga.hwe | 76 + test-data/rgtestouts/rgQC/tinywga.imendel | 40 + test-data/rgtestouts/rgQC/tinywga.imiss | 41 + test-data/rgtestouts/rgQC/tinywga.lmendel | 26 + test-data/rgtestouts/rgQC/tinywga.lmiss | 26 + test-data/rgtestouts/rgQC/tinywga.log | 48 + test-data/rgtestouts/rgQC/tinywga.mendel | 1 + test-data/rgtestouts/rgQC/tinywga.prune.in | 14 + test-data/rgtestouts/rgQC/tinywga.prune.out | 11 + test-data/rgtestouts/rgQC/tinywga.sexcheck | 41 + test-data/rgtestouts/rgQC/tinywga_All_3x3.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_3x3.pdf | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-0.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-1.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-2.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-3.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-4.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged.pdf | 0 test-data/rgtestouts/rgQC/tinywga_fracmiss.jpg | 0 test-data/rgtestouts/rgQC/tinywga_fracmiss.pdf | 333 ++ test-data/rgtestouts/rgQC/tinywga_fracmiss_cum.jpg | 0 test-data/rgtestouts/rgQC/tinywga_fracmiss_cum.pdf | 369 ++ test-data/rgtestouts/rgQC/tinywga_s_het.jpg | 0 test-data/rgtestouts/rgQC/tinywga_s_het.pdf | 344 ++ test-data/rgtestouts/rgQC/tinywga_s_het_cum.jpg | 0 test-data/rgtestouts/rgQC/tinywga_s_het_cum.pdf | 379 ++ test-data/rgtestouts/rgfakePed/rgfakePedtest1.lped | 16 + test-data/rgtestouts/rgfakePed/rgfakePedtest1.map | 10 + test-data/rgtestouts/rgfakePed/rgfakePedtest1.ped | 40 + test-data/rgtestouts/rgfakePhe/rgfakePhetest1.pphe | 41 + test-data/rgtestouts/rgfakePhe/script_file | 7 + tools/rgenetics/listFiles.py | 227 + tools/rgenetics/plinkbinJZ.py | 868 ++++++ tools/rgenetics/rgCaCo.py | 282 ++ tools/rgenetics/rgCaCo.xml | 101 + tools/rgenetics/rgCaCo_code.py | 45 + tools/rgenetics/rgClean.py | 160 + tools/rgenetics/rgClean.xml | 155 + tools/rgenetics/rgClean_code.py | 28 + tools/rgenetics/rgEigPCA.py | 385 ++ tools/rgenetics/rgEigPCA.xml | 142 + tools/rgenetics/rgEigPCA_code.py | 27 + tools/rgenetics/rgGLM.py | 286 ++ tools/rgenetics/rgGLM.xml | 139 + tools/rgenetics/rgGLM_code.py | 59 + tools/rgenetics/rgGRR.py | 1092 ++++++++ tools/rgenetics/rgGRR.xml | 94 + tools/rgenetics/rgGRR_code.py | 23 + tools/rgenetics/rgGTOOL.py | 58 + tools/rgenetics/rgGTOOL.xml | 54 + tools/rgenetics/rgGTOOL_code.py | 19 + tools/rgenetics/rgHaploView.py | 521 +++ tools/rgenetics/rgHaploView.xml | 153 + tools/rgenetics/rgHaploView_code.py | 84 + tools/rgenetics/rgLDIndep.py | 182 + tools/rgenetics/rgLDIndep.xml | 157 + tools/rgenetics/rgLDIndep_code.py | 25 + tools/rgenetics/rgManQQ.py | 223 + tools/rgenetics/rgManQQ.xml | 117 + tools/rgenetics/rgManQQ_code.py | 50 + tools/rgenetics/rgPedSub.py | 305 ++ tools/rgenetics/rgPedSub.xml | 143 + tools/rgenetics/rgPedSub_code.py | 78 + tools/rgenetics/rgQC.py | 1334 ++++++++++ tools/rgenetics/rgQC.xml | 109 + tools/rgenetics/rgQC_code.py | 38 + tools/rgenetics/rgQQ.py | 365 ++ tools/rgenetics/rgQQ.xml | 99 + tools/rgenetics/rgQQ_code.py | 72 + tools/rgenetics/rgRegion.py | 80 + tools/rgenetics/rgRegion.xml | 60 + tools/rgenetics/rgRegion_code.py | 47 + tools/rgenetics/rgTDT.py | 263 + tools/rgenetics/rgTDT.xml | 84 + tools/rgenetics/rgTDT_code.py | 43 + tools/rgenetics/rgfakePed.py | 535 ++++ tools/rgenetics/rgfakePed.xml | 111 + tools/rgenetics/rgfakePed_code.py | 53 + tools/rgenetics/rgfakePhe.py | 469 +++ tools/rgenetics/rgfakePhe.xml | 132 + tools/rgenetics/rgfakePhe_code.py | 46 + tools/rgenetics/rgutils.py | 281 ++ 160 files changed, 18356 insertions(+), 0 deletions(-) diffs (truncated from 18957 to 3000 lines): diff -r 4906f2302c85 -r cc8a30a0669f .hgignore --- a/.hgignore Fri Mar 26 14:14:40 2010 -0400 +++ b/.hgignore Fri Mar 26 14:42:15 2010 -0400 @@ -1,3 +1,7 @@ +syntax: regexp + +\.svn$ + syntax: glob .hg* diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgCaCotest1_CaCo.xls --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgCaCotest1_CaCo.xls Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,26 @@ +rs Chr Offset Genop log10Genop Armitagep log10Armitagep Allelep log10Allelep Domp log10Domp +rs2283802 22 21784722 1.000 0.000000 1.000 -0.000000 1.000 -0.000000 1.000 0.000000 +rs2267000 22 21785366 1.000 0.000000 0.893 0.049197 0.896 0.047450 1.000 0.000000 +rs16997606 22 21794754 1.000 0.000000 0.512 0.290815 0.540 0.267606 1.000 0.000000 +rs4820537 22 21794810 1.000 0.000000 0.266 0.575935 0.238 0.623423 1.000 0.000000 +rs3788347 22 21797804 1.000 0.000000 0.528 0.276955 0.518 0.285251 1.000 0.000000 +rs756632 22 21799918 1.000 0.000000 0.847 0.072014 0.838 0.076704 1.000 0.000000 +rs4820539 22 21807970 1.000 0.000000 0.663 0.178618 0.669 0.174704 1.000 0.000000 +rs2283804 22 21820335 1.000 0.000000 0.888 0.051636 0.891 0.049927 1.000 0.000000 +rs2267006 22 21820990 1.000 0.000000 0.888 0.051636 0.891 0.049927 1.000 0.000000 +rs4822363 22 21821000 1.000 0.000000 0.609 0.215311 0.624 0.204815 1.000 0.000000 +rs5751592 22 21827674 1.000 0.000000 0.426 0.370998 0.470 0.328272 1.000 0.000000 +rs5759608 22 21832708 1.000 0.000000 1.000 -0.000000 1.000 -0.000000 1.000 0.000000 +rs5759612 22 21833170 1.000 0.000000 1.000 -0.000000 1.000 -0.000000 1.000 0.000000 +rs2267009 22 21860168 1.000 0.000000 1.000 -0.000000 1.000 -0.000000 1.000 0.000000 +rs2267010 22 21864366 1.000 0.000000 0.729 0.137332 0.734 0.134304 1.000 0.000000 +rs5759636 22 21868698 1.000 0.000000 0.215 0.667360 0.228 0.642256 1.000 0.000000 +rs2071436 22 21871488 1.000 0.000000 1.000 -0.000000 1.000 -0.000000 1.000 0.000000 +rs2267013 22 21875879 1.000 0.000000 0.512 0.290815 0.540 0.267606 1.000 0.000000 +rs6003566 22 21889806 1.000 0.000000 0.361 0.442132 0.389 0.409604 1.000 0.000000 +rs2256725 22 21892891 1.000 0.000000 0.512 0.290815 0.540 0.267606 1.000 0.000000 +rs12160770 22 21892925 1.000 0.000000 0.594 0.225921 0.597 0.224098 1.000 0.000000 +rs5751611 22 21896019 1.000 0.000000 0.893 0.049246 0.894 0.048565 1.000 0.000000 +rs762601 22 21898858 1.000 0.000000 0.897 0.047111 0.893 0.049051 1.000 0.000000 +rs2156921 22 21899063 1.000 0.000000 0.897 0.047111 0.893 0.049051 1.000 0.000000 +rs4822375 22 21905642 1.000 0.000000 0.897 0.047111 0.893 0.049051 1.000 0.000000 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgCaCotest1_CaCo_log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgCaCotest1_CaCo_log.txt Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,46 @@ + +@----------------------------------------------------------@ +| PLINK! | v1.06 | 24/Apr/2009 | +|----------------------------------------------------------| +| (C) 2009 Shaun Purcell, GNU General Public License, v2 | +|----------------------------------------------------------| +| For documentation, citation & bug-report instructions: | +| http://pngu.mgh.harvard.edu/purcell/plink/ | +@----------------------------------------------------------@ + +Skipping web check... [ --noweb ] +Writing this text to log file [ rgCaCotest1.log ] +Analysis started: Thu Mar 25 21:01:31 2010 + +Options in effect: + --noweb + --bfile /opt/galaxy/test-data/tinywga + --out rgCaCotest1 + --model + +Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] +25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] +Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] +40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] +40 individuals with nonmissing phenotypes +Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) +Missing phenotype value is also -9 +10 cases, 30 controls and 0 missing +21 males, 19 females, and 0 of unspecified sex +Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] +Detected that binary PED file is v1.00 SNP-major mode +Before frequency and genotyping pruning, there are 25 SNPs +27 founders and 13 non-founders found +Total genotyping rate in remaining individuals is 0.995 +0 SNPs failed missingness test ( GENO > 1 ) +0 SNPs failed frequency test ( MAF < 0 ) +After frequency and genotyping pruning, there are 25 SNPs +After filtering, 10 cases, 30 controls and 0 missing +After filtering, 21 males, 19 females, and 0 of unspecified sex +Full-model association tests, minimum genotype count: --cell 5 +Writing full model association results to [ rgCaCotest1.model ] + +Analysis finished: Thu Mar 25 21:01:31 2010 + +###maxp=0.667360,minp=-0.000000,prange=1.167360,scalefact=856.633772 +Rgenetics V000.1 April 2007 http://rgenetics.org Galaxy Tools, rgCaCo.py started 25/03/2010 21:01:31 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgCaCotest1_CaCo_topTable.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgCaCotest1_CaCo_topTable.gff Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,26 @@ +track name=rgGLM_TopTable description="rgCaCotest1" visibility=2 useScore=1 color=0,60,120 +chr22 rgGLM variation 21784622 21784822 0 . . rs2283802 logp=-0.00 +chr22 rgGLM variation 21785266 21785466 42 . . rs2267000 logp=0.05 +chr22 rgGLM variation 21794654 21794854 249 . . rs16997606 logp=0.29 +chr22 rgGLM variation 21794710 21794910 493 . . rs4820537 logp=0.58 +chr22 rgGLM variation 21797704 21797904 237 . . rs3788347 logp=0.28 +chr22 rgGLM variation 21799818 21800018 61 . . rs756632 logp=0.07 +chr22 rgGLM variation 21807870 21808070 153 . . rs4820539 logp=0.18 +chr22 rgGLM variation 21820235 21820435 44 . . rs2283804 logp=0.05 +chr22 rgGLM variation 21820890 21821090 44 . . rs2267006 logp=0.05 +chr22 rgGLM variation 21820900 21821100 184 . . rs4822363 logp=0.22 +chr22 rgGLM variation 21827574 21827774 317 . . rs5751592 logp=0.37 +chr22 rgGLM variation 21832608 21832808 0 . . rs5759608 logp=-0.00 +chr22 rgGLM variation 21833070 21833270 0 . . rs5759612 logp=-0.00 +chr22 rgGLM variation 21860068 21860268 0 . . rs2267009 logp=-0.00 +chr22 rgGLM variation 21864266 21864466 117 . . rs2267010 logp=0.14 +chr22 rgGLM variation 21868598 21868798 571 . . rs5759636 logp=0.67 +chr22 rgGLM variation 21871388 21871588 0 . . rs2071436 logp=-0.00 +chr22 rgGLM variation 21875779 21875979 249 . . rs2267013 logp=0.29 +chr22 rgGLM variation 21889706 21889906 378 . . rs6003566 logp=0.44 +chr22 rgGLM variation 21892791 21892991 249 . . rs2256725 logp=0.29 +chr22 rgGLM variation 21892825 21893025 193 . . rs12160770 logp=0.23 +chr22 rgGLM variation 21895919 21896119 42 . . rs5751611 logp=0.05 +chr22 rgGLM variation 21898758 21898958 40 . . rs762601 logp=0.05 +chr22 rgGLM variation 21898963 21899163 40 . . rs2156921 logp=0.05 +chr22 rgGLM variation 21905542 21905742 40 . . rs4822375 logp=0.05 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgGLM_GLM_topTable.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgGLM_GLM_topTable.gff Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,26 @@ +track name=rgGLM_TopTable description="rgGLMtest1" visibility=2 useScore=1 color=0,60,120 +chr22 rgGLM variation 21784622 21784822 455 . . rs2283802 logp=0.75 +chr22 rgGLM variation 21785266 21785466 152 . . rs2267000 logp=0.25 +chr22 rgGLM variation 21794654 21794854 230 . . rs16997606 logp=0.38 +chr22 rgGLM variation 21794710 21794910 107 . . rs4820537 logp=0.18 +chr22 rgGLM variation 21797704 21797904 28 . . rs3788347 logp=0.05 +chr22 rgGLM variation 21799818 21800018 45 . . rs756632 logp=0.08 +chr22 rgGLM variation 21807870 21808070 151 . . rs4820539 logp=0.25 +chr22 rgGLM variation 21820235 21820435 723 . . rs2283804 logp=1.19 +chr22 rgGLM variation 21820890 21821090 723 . . rs2267006 logp=1.19 +chr22 rgGLM variation 21820900 21821100 340 . . rs4822363 logp=0.56 +chr22 rgGLM variation 21827574 21827774 337 . . rs5751592 logp=0.55 +chr22 rgGLM variation 21832608 21832808 563 . . rs5759608 logp=0.92 +chr22 rgGLM variation 21833070 21833270 563 . . rs5759612 logp=0.92 +chr22 rgGLM variation 21860068 21860268 455 . . rs2267009 logp=0.75 +chr22 rgGLM variation 21864266 21864466 391 . . rs2267010 logp=0.64 +chr22 rgGLM variation 21868598 21868798 95 . . rs5759636 logp=0.16 +chr22 rgGLM variation 21871388 21871588 455 . . rs2071436 logp=0.75 +chr22 rgGLM variation 21875779 21875979 32 . . rs2267013 logp=0.05 +chr22 rgGLM variation 21889706 21889906 125 . . rs6003566 logp=0.21 +chr22 rgGLM variation 21892791 21892991 32 . . rs2256725 logp=0.05 +chr22 rgGLM variation 21892825 21893025 127 . . rs12160770 logp=0.21 +chr22 rgGLM variation 21895919 21896119 126 . . rs5751611 logp=0.21 +chr22 rgGLM variation 21898758 21898958 446 . . rs762601 logp=0.73 +chr22 rgGLM variation 21898963 21899163 446 . . rs2156921 logp=0.73 +chr22 rgGLM variation 21905542 21905742 446 . . rs4822375 logp=0.73 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgGLMtest1_GLM.xls --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgGLMtest1_GLM.xls Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,26 @@ +rs chrom offset ADD_stat ADD_p ADD_log10p +rs2283802 22 21784722 1.369 0.1789 0.747390 +rs2267000 22 21785366 0.5866 0.5609 0.251115 +rs16997606 22 21794754 -0.8178 0.4185 0.378305 +rs4820537 22 21794810 0.4346 0.6663 0.176330 +rs3788347 22 21797804 -0.1292 0.8979 0.046772 +rs756632 22 21799918 0.202 0.841 0.075204 +rs4820539 22 21807970 0.5836 0.563 0.249492 +rs2283804 22 21820335 -1.902 0.0648 1.188425 +rs2267006 22 21820990 -1.902 0.0648 1.188425 +rs4822363 22 21821000 1.105 0.2761 0.558934 +rs5751592 22 21827674 1.099 0.2788 0.554707 +rs5759608 22 21832708 -1.596 0.1189 0.924818 +rs5759612 22 21833170 -1.596 0.1189 0.924818 +rs2267009 22 21860168 1.369 0.1789 0.747390 +rs2267010 22 21864366 -1.227 0.2276 0.642828 +rs5759636 22 21868698 0.3942 0.6957 0.157578 +rs2071436 22 21871488 1.369 0.1789 0.747390 +rs2267013 22 21875879 -0.1449 0.8855 0.052811 +rs6003566 22 21889806 -0.4952 0.6233 0.205303 +rs2256725 22 21892891 -0.1449 0.8855 0.052811 +rs12160770 22 21892925 0.5031 0.618 0.209012 +rs5751611 22 21896019 0.5008 0.6195 0.207959 +rs762601 22 21898858 1.35 0.1849 0.733063 +rs2156921 22 21899063 1.35 0.1849 0.733063 +rs4822375 22 21905642 1.35 0.1849 0.733063 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgGLMtest1_GLM_log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgGLMtest1_GLM_log.txt Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,58 @@ +rgGLM.py called with ['/opt/galaxy/tools/rgenetics/rgGLM.py', '/opt/galaxy/test-data/tinywga', '/opt/galaxy/test-data/tinywga', 'rgGLMtest1', 'c1', '', '/opt/galaxy/test-data/rgGLMtest1_GLM.xls', '/opt/galaxy/test-data/rgGLMtest1_GLM_log.txt', 'tinywga', '', '', '', '1', '1', '0', '0', '/opt/galaxy/test-data/rgGLM_GLM_topTable.gff'] +vcl=['plink', '--noweb', '--bfile', '/opt/galaxy/test-data/tinywga', '--pheno-name', '"c1"', '--pheno', '/opt/galaxy/test-data/tinywga.pphe', '--out', 'tinywga', '--mind 1', '--geno 1', '--maf 0', '--linear'] +xformQassoc got resf=/tmp/tmpCB6CwWrgGLM/tinywga.assoc.linear, outfname=/opt/galaxy/test-data/rgGLMtest1_GLM.xls +###maxp=1.188425,minp=0.046772,prange=1.641653,scalefact=609.142127 + + +@----------------------------------------------------------@ +| PLINK! | v1.06 | 24/Apr/2009 | +|----------------------------------------------------------| +| (C) 2009 Shaun Purcell, GNU General Public License, v2 | +|----------------------------------------------------------| +| For documentation, citation & bug-report instructions: | +| http://pngu.mgh.harvard.edu/purcell/plink/ | +@----------------------------------------------------------@ + +Skipping web check... [ --noweb ] +Writing this text to log file [ tinywga.log ] +Analysis started: Thu Mar 25 21:01:31 2010 + +Options in effect: + --noweb + --bfile /opt/galaxy/test-data/tinywga + --pheno-name c1 + --pheno /opt/galaxy/test-data/tinywga.pphe + --out tinywga + --mind 1 + --geno 1 + --maf 0 + --linear + +Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] +25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] +Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] +40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] +40 individuals with nonmissing phenotypes +Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) +Missing phenotype value is also -9 +10 cases, 30 controls and 0 missing +21 males, 19 females, and 0 of unspecified sex +Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] +Detected that binary PED file is v1.00 SNP-major mode +Reading alternate phenotype from [ /opt/galaxy/test-data/tinywga.pphe ] +40 individuals with non-missing alternate phenotype +Assuming a quantitative trait +Missing phenotype value is -9 +Before frequency and genotyping pruning, there are 25 SNPs +27 founders and 13 non-founders found +Total genotyping rate in remaining individuals is 0.995 +0 SNPs failed missingness test ( GENO > 1 ) +0 SNPs failed frequency test ( MAF < 0 ) +After frequency and genotyping pruning, there are 25 SNPs +After filtering, 40 individuals with non-missing status +After filtering, 21 males, 19 females, and 0 of unspecified sex +Converting data to Individual-major format +Writing linear model association results to [ tinywga.assoc.linear ] + +Analysis finished: Thu Mar 25 21:01:31 2010 + diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgQQtest1.pdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgQQtest1.pdf Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,384 @@ +%PDF-1.4 +%âãÏÓ\r +1 0 obj +<< +/CreationDate (D:20100325210132) +/ModDate (D:20100325210132) +/Title (R Graphics 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+/dieresis /.notdef /ring /cedilla /.notdef /hungarumlaut /ogonek /caron /space] +>> +endobj +9 0 obj +<< +/Type /Font +/Subtype /Type1 +/Name /F1 +/BaseFont /ZapfDingbats +>> +endobj +10 0 obj << +/Type /Font +/Subtype /Type1 +/Name /F2 +/BaseFont /Helvetica +/Encoding 8 0 R +>> endobj +11 0 obj << +/Type /Font +/Subtype /Type1 +/Name /F3 +/BaseFont /Helvetica-Bold +/Encoding 8 0 R +>> endobj +xref +0 12 +0000000000 65535 f +0000000021 00000 n +0000000164 00000 n +0000006425 00000 n +0000006508 00000 n +0000000213 00000 n +0000000293 00000 n +0000006405 00000 n +0000006612 00000 n +0000006869 00000 n +0000006952 00000 n +0000007049 00000 n +trailer +<< +/Size 12 +/Info 1 0 R +/Root 2 0 R +>> +startxref +7151 +%%EOF diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgTDTtest1_TDT.xls --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgTDTtest1_TDT.xls Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,25 @@ +rs chrom offset a1 a2 transmitted untransmitted TDTChiSq TDTp -log10TDTp AbsTDTOR TDTOR +rs2283802 22 21784722 4 2 4 4 0 1 -0.000000 1 1 +rs2267000 22 21785366 4 2 4 5 0.1111 0.7389 0.131414 1.250000 0.8 +rs16997606 22 21794754 1 3 3 3 0 1 -0.000000 1 1 +rs4820537 22 21794810 1 3 3 6 1 0.3173 0.498530 2.000000 0.5 +rs3788347 22 21797804 3 1 5 4 0.1111 0.7389 0.131414 1.25 1.25 +rs756632 22 21799918 4 2 2 1 0.3333 0.5637 0.248952 2 2 +rs4820539 22 21807970 1 3 4 5 0.1111 0.7389 0.131414 1.250000 0.8 +rs2283804 22 21820335 1 2 5 3 0.5 0.4795 0.319211 1.667 1.667 +rs2267006 22 21820990 3 1 5 3 0.5 0.4795 0.319211 1.667 1.667 +rs4822363 22 21821000 4 2 1 1 0 1 -0.000000 1 1 +rs5751592 22 21827674 4 2 2 5 1.286 0.2568 0.590405 2.500000 0.4 +rs5759608 22 21832708 2 4 7 4 0.8182 0.3657 0.436875 1.75 1.75 +rs5759612 22 21833170 3 1 7 4 0.8182 0.3657 0.436875 1.75 1.75 +rs2267009 22 21860168 3 4 4 4 0 1 -0.000000 1 1 +rs2267010 22 21864366 3 1 1 1 0 1 -0.000000 1 1 +rs5759636 22 21868698 4 2 0 1 1 0.3173 0.498530 0 0 +rs2071436 22 21871488 4 2 4 4 0 1 -0.000000 1 1 +rs2267013 22 21875879 3 1 3 1 1 0.3173 0.498530 3 3 +rs6003566 22 21889806 3 1 3 2 0.2 0.6547 0.183958 1.5 1.5 +rs2256725 22 21892891 2 1 3 1 1 0.3173 0.498530 3 3 +rs5751611 22 21896019 2 4 8 5 0.6923 0.4054 0.392116 1.6 1.6 +rs762601 22 21898858 1 3 7 4 0.8182 0.3657 0.436875 1.75 1.75 +rs2156921 22 21899063 3 1 7 4 0.8182 0.3657 0.436875 1.75 1.75 +rs4822375 22 21905642 1 3 7 4 0.8182 0.3657 0.436875 1.75 1.75 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgTDTtest1_TDT_log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgTDTtest1_TDT_log.txt Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,53 @@ + +@----------------------------------------------------------@ +| PLINK! | v1.06 | 24/Apr/2009 | +|----------------------------------------------------------| +| (C) 2009 Shaun Purcell, GNU General Public License, v2 | +|----------------------------------------------------------| +| For documentation, citation & bug-report instructions: | +| http://pngu.mgh.harvard.edu/purcell/plink/ | +@----------------------------------------------------------@ + +Skipping web check... [ --noweb ] +Writing this text to log file [ rgTDTtest1.log ] +Analysis started: Thu Mar 25 21:01:31 2010 + +Options in effect: + --noweb + --bfile /opt/galaxy/test-data/tinywga + --out rgTDTtest1 + --mind 0.5 + --tdt + +Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] +25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] +Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] +40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] +40 individuals with nonmissing phenotypes +Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) +Missing phenotype value is also -9 +10 cases, 30 controls and 0 missing +21 males, 19 females, and 0 of unspecified sex +Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] +Detected that binary PED file is v1.00 SNP-major mode +Before frequency and genotyping pruning, there are 25 SNPs +27 founders and 13 non-founders found +0 of 40 individuals removed for low genotyping ( MIND > 0.5 ) +Total genotyping rate in remaining individuals is 0.995 +0 SNPs failed missingness test ( GENO > 1 ) +0 SNPs failed frequency test ( MAF < 0 ) +After frequency and genotyping pruning, there are 25 SNPs +After filtering, 10 cases, 30 controls and 0 missing +After filtering, 21 males, 19 females, and 0 of unspecified sex +14 nuclear families, 1 founder singletons found +13 non-founders with 2 parents in 13 nuclear families +0 non-founders without 2 parents in 0 nuclear families +10 affected offspring trios +0 phenotypically discordant parent pairs found +Converting data to Individual-major format +0 Mendel errors detected in total +Writing TDT results (asymptotic) to [ rgTDTtest1.tdt ] + +Analysis finished: Thu Mar 25 21:01:31 2010 + +###maxp=0.590405,minp=-0.000000,prange=1.090405,scalefact=917.090439 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgTDTtest1_TDT_topTable.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgTDTtest1_TDT_topTable.gff Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,25 @@ +track name=rgTDT_Top_Table description="rgTDTtest1" visibility=2 useScore=1 color=0,60,120 +chr22 rgGLM variation 21784622 21784822 0 . . rs2283802 logp=-0.00 +chr22 rgGLM variation 21785266 21785466 120 . . rs2267000 logp=0.13 +chr22 rgGLM variation 21794654 21794854 0 . . rs16997606 logp=-0.00 +chr22 rgGLM variation 21794710 21794910 457 . . rs4820537 logp=0.50 +chr22 rgGLM variation 21797704 21797904 120 . . rs3788347 logp=0.13 +chr22 rgGLM variation 21799818 21800018 228 . . rs756632 logp=0.25 +chr22 rgGLM variation 21807870 21808070 120 . . rs4820539 logp=0.13 +chr22 rgGLM variation 21820235 21820435 292 . . rs2283804 logp=0.32 +chr22 rgGLM variation 21820890 21821090 292 . . rs2267006 logp=0.32 +chr22 rgGLM variation 21820900 21821100 0 . . rs4822363 logp=-0.00 +chr22 rgGLM variation 21827574 21827774 541 . . rs5751592 logp=0.59 +chr22 rgGLM variation 21832608 21832808 400 . . rs5759608 logp=0.44 +chr22 rgGLM variation 21833070 21833270 400 . . rs5759612 logp=0.44 +chr22 rgGLM variation 21860068 21860268 0 . . rs2267009 logp=-0.00 +chr22 rgGLM variation 21864266 21864466 0 . . rs2267010 logp=-0.00 +chr22 rgGLM variation 21868598 21868798 457 . . rs5759636 logp=0.50 +chr22 rgGLM variation 21871388 21871588 0 . . rs2071436 logp=-0.00 +chr22 rgGLM variation 21875779 21875979 457 . . rs2267013 logp=0.50 +chr22 rgGLM variation 21889706 21889906 168 . . rs6003566 logp=0.18 +chr22 rgGLM variation 21892791 21892991 457 . . rs2256725 logp=0.50 +chr22 rgGLM variation 21895919 21896119 359 . . rs5751611 logp=0.39 +chr22 rgGLM variation 21898758 21898958 400 . . rs762601 logp=0.44 +chr22 rgGLM variation 21898963 21899163 400 . . rs2156921 logp=0.44 +chr22 rgGLM variation 21905542 21905742 400 . . rs4822375 logp=0.44 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgClean/rgCleantest1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgClean/rgCleantest1.bed Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,1 @@ +lÿëþ¿¾+êóª¿ü £ïªîþ¨êÿïªûÿÿÿÿÿÿþï®¨ª"ëú £ïªîþ¨ÿÿ»ÿÿïïþÿèÿþ"ÿ«ïªîþ¨:*ÿïêüº.«ë:*ÿïêüº.«ëÿÿÿÿ¯ÿ¿ïþ¿ÿþªÿ¯û¿ïþ¿:*»ïêìª,«À:*»ïêìª,«Àÿëþ¿¾+êóª¿ÿÿÿÿûÿúÿÿÿÿÿÿÿÿÿ¿þ¿ÿëþ¿¾+êóª¿ºûÿÿ¿»ÿÿþ¿êÿÿªûÿÿÿÿÿºûÿÿ¿»ÿÿþ¿mÿÿÿýÿÿÿÿÿ ú¢ª±«¯ü(:ú¢ÿ¿«¯ü(:ú¢ÿ¿«¯ü(:ú¢ÿ¿«¯ü( \ No newline at end of file diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgClean/rgCleantest1.bim --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgClean/rgCleantest1.bim Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,25 @@ +22 rs2283802 0 21784722 4 2 +22 rs2267000 0 21785366 4 2 +22 rs16997606 0 21794754 1 3 +22 rs4820537 0 21794810 1 3 +22 rs3788347 0 21797804 3 1 +22 rs756632 0 21799918 4 2 +22 rs4820539 0 21807970 1 3 +22 rs2283804 0 21820335 1 2 +22 rs2267006 0 21820990 3 1 +22 rs4822363 0 21821000 4 2 +22 rs5751592 0 21827674 4 2 +22 rs5759608 0 21832708 2 4 +22 rs5759612 0 21833170 3 1 +22 rs2267009 0 21860168 3 4 +22 rs2267010 0 21864366 3 1 +22 rs5759636 0 21868698 4 2 +22 rs2071436 0 21871488 4 2 +22 rs2267013 0 21875879 3 1 +22 rs6003566 0 21889806 3 1 +22 rs2256725 0 21892891 2 1 +22 rs12160770 0 21892925 1 3 +22 rs5751611 0 21896019 2 4 +22 rs762601 0 21898858 1 3 +22 rs2156921 0 21899063 3 1 +22 rs4822375 0 21905642 1 3 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgClean/rgCleantest1.fam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgClean/rgCleantest1.fam Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,40 @@ +101 1 3 2 2 2 +101 2 0 0 2 1 +101 3 0 0 1 1 +105 1 3 2 2 2 +105 2 0 0 2 1 +105 3 0 0 1 1 +112 1 3 2 1 2 +112 2 0 0 2 1 +112 3 0 0 1 1 +117 1 3 2 2 2 +117 2 0 0 2 1 +117 3 0 0 1 1 +12 1 3 2 1 2 +12 2 0 0 2 1 +12 3 0 0 1 1 +13 1 3 2 1 2 +13 2 0 0 2 1 +13 3 0 0 1 1 +1334 1 10 11 1 2 +1334 10 0 0 1 1 +1334 11 0 0 2 1 +1334 12 0 0 1 1 +1334 13 0 0 2 1 +1334 2 12 13 2 2 +1340 1 9 10 1 2 +1340 10 0 0 2 1 +1340 11 0 0 1 1 +1340 12 0 0 2 1 +1340 2 11 12 2 2 +1340 9 0 0 1 1 +1341 1 11 12 1 1 +1341 11 0 0 1 1 +1341 12 0 0 2 1 +1341 13 0 0 1 1 +1341 14 0 0 2 1 +1341 2 13 14 2 1 +1344 1 12 13 1 1 +1344 12 0 0 1 1 +1344 13 0 0 2 1 +1345 12 0 0 1 1 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgClean/rgCleantest1.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgClean/rgCleantest1.log Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,66 @@ +rgClean.py started, called as /opt/galaxy/tools/rgenetics/rgClean.py /opt/galaxy/test-data tinywga rgCleantest1 1 1 0 0 1 1 /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.pbed /opt/galaxy/test-data/rgtestouts/rgClean 0 0 0 0 + +@----------------------------------------------------------@ +| PLINK! | v1.06 | 24/Apr/2009 | +|----------------------------------------------------------| +| (C) 2009 Shaun Purcell, GNU General Public License, v2 | +|----------------------------------------------------------| +| For documentation, citation & bug-report instructions: | +| http://pngu.mgh.harvard.edu/purcell/plink/ | +@----------------------------------------------------------@ + +Skipping web check... [ --noweb ] +Writing this text to log file [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.log ] +Analysis started: Thu Mar 25 21:01:24 2010 + +Options in effect: +--noweb +--bfile /opt/galaxy/test-data/tinywga +--make-bed +--out /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1 +--set-hh-missing +--mind 1 +--geno 1 +--maf 0 +--hwe 0 +--me 1 1 + +Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] +25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] +Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] +40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] +40 individuals with nonmissing phenotypes +Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) +Missing phenotype value is also -9 +10 cases, 30 controls and 0 missing +21 males, 19 females, and 0 of unspecified sex +Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] +Detected that binary PED file is v1.00 SNP-major mode +Before frequency and genotyping pruning, there are 25 SNPs +27 founders and 13 non-founders found +0 markers to be excluded based on HWE test ( p <= 0 ) +0 markers failed HWE test in cases +0 markers failed HWE test in controls +Total genotyping rate in remaining individuals is 0.995 +0 SNPs failed missingness test ( GENO > 1 ) +0 SNPs failed frequency test ( MAF < 0 ) +After frequency and genotyping pruning, there are 25 SNPs +After filtering, 10 cases, 30 controls and 0 missing +After filtering, 21 males, 19 females, and 0 of unspecified sex +14 nuclear families, 1 founder singletons found +13 non-founders with 2 parents in 13 nuclear families +0 non-founders without 2 parents in 0 nuclear families +10 affected offspring trios +0 phenotypically discordant parent pairs found +Converting data to Individual-major format +Filtering SNPs/families for Mendel Error rates above 1, 1 +0 Mendel errors detected in total +0 families ( 0 individuals ) removed due to Mendel errors +0 markers removed due to Mendel errors, 25 remaining +Writing pedigree information to [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.fam ] +Writing map (extended format) information to [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.bim ] +Writing genotype bitfile to [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.bed ] +Using (default) SNP-major mode +Converting data to SNP-major format + +Analysis finished: Thu Mar 25 21:01:24 2010 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgClean/rgCleantest1.pbed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgClean/rgCleantest1.pbed Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="utf-8" ?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> +<meta name="generator" content="Galaxy rgClean.py tool output - see http://g2.trac.bx.psu.edu/" /> +<title></title> +<link rel="stylesheet" href="/static/style/base.css" type="text/css" /> +</head> +<body> +<div class="document"> +<ul> +<li><a href="rgCleantest1.bed">rgCleantest1.bed</a></li> +<li><a href="rgCleantest1.bim">rgCleantest1.bim</a></li> +<li><a href="rgCleantest1.fam">rgCleantest1.fam</a></li> +<li><a href="rgCleantest1.log">rgCleantest1.log</a></li> +<li><a href="rgCleantest1.pbed">rgCleantest1.pbed</a></li> +</ul> +</ul></br></div></body></html> \ No newline at end of file diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/Rplots.pdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgEigPCA/Rplots.pdf Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,59 @@ +%PDF-1.4 +%âãÏÓ\r +1 0 obj +<< +/CreationDate (D:20100325210125) +/ModDate (D:20100325210125) +/Title (R Graphics Output) +/Producer (R 2.10.1) +/Creator (R) +>> +endobj +2 0 obj +<< +/Type /Catalog +/Pages 3 0 R +>> +endobj +3 0 obj +<< +/Type /Pages +/Kids [ +] +/Count 0 +/MediaBox [0 0 504 504] +>> +endobj +4 0 obj +<< +/ProcSet [/PDF /Text] +/Font <<>> +/ExtGState << >> +>> +endobj +5 0 obj +<< +/Type /Encoding +/BaseEncoding /WinAnsiEncoding +/Differences [ 45/minus 96/quoteleft +144/dotlessi /grave /acute /circumflex /tilde /macron /breve /dotaccent +/dieresis /.notdef /ring /cedilla /.notdef /hungarumlaut /ogonek /caron /space] +>> +endobj +xref +0 6 +0000000000 65535 f +0000000021 00000 n +0000000164 00000 n +0000000213 00000 n +0000000290 00000 n +0000000361 00000 n +trailer +<< +/Size 6 +/Info 1 0 R +/Root 2 0 R +>> +startxref +618 +%%EOF diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,19 @@ +llist=c("Control","Case") +glist=c(2,3) +par(lab=c(10,10,10)) +par(mai=c(1,1,1,0.5)) +pdf("rgEigPCAtest1_PCAPlot.pdf",h=8,w=10) +par(lab=c(10,10,10)) +pca1 = c(0.127600,0.027200,0.145200,0.088700,-0.002600,-0.245300,-0.241200,0.035800,0.290500,0.160700,0.167500,0.027200,0.027200,-0.087000,-0.063000,-0.188600,0.026800,-0.064300,0.092700,-0.241200,0.005600,0.026100,-0.160800,-0.160800,0.026100,0.074200,0.030200,-0.249300,0.183300,-0.102700,0.231200,-0.245300,-0.245300,-0.245300,0.301500,0.030200,0.030200,0.259300) +pca2 = c(0.006000,-0.179400,0.266600,0.076500,-0.036700,-0.016500,0.253700,-0.176600,0.081100,-0.124700,0.041800,-0.179400,-0.179400,0.015400,-0.265600,-0.025100,-0.000800,0.041800,-0.221000,0.253700,-0.205100,-0.035400,-0.034900,-0.034900,-0.035400,0.081900,0.234800,-0.286700,0.120600,0.293900,-0.180800,-0.016500,-0.016500,-0.016500,0.215900,0.234800,0.234800,-0.191600) +pgvec = c(2,2,3,2,2,3,2,2,3,2,2,3,2,2,3,2,2,3,2,2,2,2,3,2,2,2,3,2,2,2,2,2,2,2,2,2,2,2) +plot(pca1,pca2,type='p',main='rgEigPCAtest1', ylab='Second ancestry eigenvector',xlab='First ancestry eigenvector',col=pgvec,cex=0.8,pch=pgvec) +legend("top",legend=llist,pch=glist,col=glist,title="Sample") +grid(nx = 10, ny = 10, col = "lightgray", lty = "dotted") +dev.off() +png("rgEigPCAtest1_PCAPlot.pdf.png",h=8,w=10,units="in",res=72) +plot(pca1,pca2,type='p',main='rgEigPCAtest1', ylab='Second ancestry eigenvector',xlab='First ancestry eigenvector',col=pgvec,cex=0.8,pch=pgvec) +legend("top",legend=llist,pch=glist,col=glist,title="Sample") +grid(nx = 10, ny = 10, col = "lightgray", lty = "dotted") +dev.off() +#R script autogenerated by rgenetics/rgutils.py on 25/03/2010 21:01:25 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,160 @@ +<?xml version="1.0" encoding="utf-8" ?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> +<meta name="generator" content="Galaxy rgEigPCA.py tool output - see http://g2.trac.bx.psu.edu/" /> +<title></title> +<link rel="stylesheet" href="/static/style/base.css" type="text/css" /> +</head> +<body> +<div class="document"> +<h4>Output from rgEigPCA.py run at 25/03/2010 21:01:25<br/> +</h4> +newfilepath=/opt/galaxy/test-data/rgtestouts/rgEigPCA, rexe=R(click on the image below to see a much higher quality PDF version)<table border="0" cellpadding="10" cellspacing="10"><tr><td> +<a href="rgEigPCAtest1_PCAPlot.pdf"><img src="rgEigPCAtest1_PCAPlot.pdf.png" alt="Samples plotted in first 2 eigenvector space" hspace="10" align="left" /></a></td></tr></table><br/> +<div class="document">All Files:<ol><li><a href="rgEigPCAtest1_eval.xls">rgEigPCAtest1_eval.xls (507 B)</a></li> +<li><a href="rgEigPCAtest1_pca.xls.par">rgEigPCAtest1_pca.xls.par (311 B)</a></li> +<li><a href="rgEigPCAtest1_PCAPlot.pdf.png">rgEigPCAtest1_PCAPlot.pdf.png (27.1 KB)</a></li> +<li><a href="rgEigPCAtest1_log.txt">rgEigPCAtest1_log.txt (6.0 KB)</a></li> +<li><a href="rgEigPCAtest1.html">rgEigPCAtest1.html </a></li> +<li><a href="rgEigPCAtest1_eigensoftplot.pdf.xtxt">rgEigPCAtest1_eigensoftplot.pdf.xtxt (257 B)</a></li> +<li><a href="rgEigPCAtest1_eigensoftplot.pdf.ps">rgEigPCAtest1_eigensoftplot.pdf.ps (13.6 KB)</a></li> +<li><a href="rgEigPCAtest1_pca.xls.evec">rgEigPCAtest1_pca.xls.evec (3.3 KB)</a></li> +<li><a href="rgEigPCAtest1_pca.xls">rgEigPCAtest1_pca.xls (1.3 KB)</a></li> +<li><a href="rgEigPCAtest1_PCAPlot.pdf">rgEigPCAtest1_PCAPlot.pdf (7.9 KB)</a></li> +<li><a href="rgEigPCAtest1.txt">rgEigPCAtest1.txt (3.3 KB)</a></li> +<li><a href="rgEigPCAtest1_eigensoftplot.pdf.pdf">rgEigPCAtest1_eigensoftplot.pdf.pdf (2.1 KB)</a></li> +<li><a href="rgEigPCAtest1.R">rgEigPCAtest1.R (1.6 KB)</a></li> +<li><a href="Rplots.pdf">Rplots.pdf (813 B)</a></li> +</ol></div><div class="document">Log rgEigPCAtest1_log.txt contents follow below<p/><pre>parameter file: rgEigPCAtest1_pca.xls.par +### THE INPUT PARAMETERS +##PARAMETER NAME: VALUE +genotypename: /opt/galaxy/test-data/tinywga.ped +snpname: /opt/galaxy/test-data/tinywga.map +indivname: /opt/galaxy/test-data/tinywga.ped +evecoutname: rgEigPCAtest1_pca.xls.evec +evaloutname: rgEigPCAtest1_eval.xls +altnormstyle: NO +numoutevec: 4 +numoutlieriter: 2 +numoutlierevec: 2 +outliersigmathresh: 2 +qtmode: 0 +## smartpca version: 8000 +norm used + +genetic distance set from physical distance +genotype file processed +number of samples used: 40 number of snps used: 25 +REMOVED outlier 1334:2 iter 1 evec 1 sigmage -2.329 +number of samples after outlier removal: 39 + +## Tracy-Widom statistics: rows: 39 cols: 24 + #N eigenvalue difference twstat p-value effect. n + 1 11.481974 NA -0.712 0.332198 8.854 + 2 7.739771 -3.742203 -1.302 0.510496 8.388 + 3 7.254586 -0.485185 -0.171 0.201072 7.095 + 4 4.270950 -2.983636 -0.191 0.205302 8.005 + 5 2.538320 -1.732630 -0.341 0.238117 9.118 + 6 1.667964 -0.870356 -0.231 0.21376 9.910 + 7 1.043403 -0.624560 -0.269 0.222042 11.590 + 8 0.653401 -0.390003 NA NA NA + 9 0.391044 -0.262357 NA NA NA + 10 0.338164 -0.052880 NA NA NA + 11 0.263384 -0.074780 NA NA NA + 12 0.150750 -0.112634 NA NA NA + 13 0.085580 -0.065170 NA NA NA + 14 0.065301 -0.020279 NA NA NA + 15 0.048797 -0.016504 NA NA NA + 16 0.006611 -0.042186 NA NA NA + kurtosis snps indivs + eigenvector 1 1.926 2.122 + eigenvector 2 2.599 2.148 + eigenvector 3 2.593 2.873 + eigenvector 4 3.165 2.831 +population: 0 Case 9 +population: 1 Control 30 + +## Average divergence between populations: + Case Control popsize + Case 1.028 0.954 9 + Control 0.954 0.972 30 + + +number of blocks for moving block jackknife: 1 +fst *1000: + C C + C 0 0 + C 0 0 + +s.dev * 1000000: + C C + C 0 0 + C 0 0 + +## Anova statistics for population differences along each eigenvector: + p-value + eigenvector_1_Case_Control_ 0.841067 + eigenvector_2_Case_Control_ 0.758376 + eigenvector_3_Case_Control_ 0.238793 + eigenvector_4_Case_Control_ 0.678458 + +## Statistical significance of differences beween populations: + pop1 pop2 chisq p-value |pop1| |pop2| +popdifference: Case Control 1.810 0.77061 9 30 + +eigbestsnp 1 rs762601 22 21898858 1.674 +eigbestsnp 1 rs2156921 22 21899063 1.674 +eigbestsnp 1 rs4822375 22 21905642 1.674 +eigbestsnp 1 rs5751611 22 21896019 1.635 +eigbestsnp 1 rs4820537 22 21794810 1.542 +eigbestsnp 1 rs3788347 22 21797804 1.413 +eigbestsnp 1 rs2267000 22 21785366 1.151 +eigbestsnp 1 rs4820539 22 21807970 1.141 +eigbestsnp 1 rs5751592 22 21827674 0.890 +eigbestsnp 1 rs2283804 22 21820335 0.815 +eigbestsnp 1 rs2267006 22 21820990 0.815 +eigbestsnp 2 rs5759608 22 21832708 2.197 +eigbestsnp 2 rs5759612 22 21833170 2.197 +eigbestsnp 2 rs2283804 22 21820335 1.643 +eigbestsnp 2 rs2267006 22 21820990 1.643 +eigbestsnp 2 rs2283802 22 21784722 1.283 +eigbestsnp 2 rs2267009 22 21860168 1.283 +eigbestsnp 2 rs2071436 22 21871488 1.283 +eigbestsnp 2 rs756632 22 21799918 0.942 +eigbestsnp 2 rs16997606 22 21794754 0.715 +eigbestsnp 2 rs6003566 22 21889806 0.645 +eigbestsnp 2 rs762601 22 21898858 0.545 +eigbestsnp 3 rs16997606 22 21794754 1.770 +eigbestsnp 3 rs6003566 22 21889806 1.725 +eigbestsnp 3 rs3788347 22 21797804 1.452 +eigbestsnp 3 rs2267000 22 21785366 1.386 +eigbestsnp 3 rs2283802 22 21784722 1.247 +eigbestsnp 3 rs2267009 22 21860168 1.247 +eigbestsnp 3 rs2071436 22 21871488 1.247 +eigbestsnp 3 rs4820537 22 21794810 1.168 +eigbestsnp 3 rs762601 22 21898858 1.153 +eigbestsnp 3 rs2156921 22 21899063 1.153 +eigbestsnp 3 rs4822375 22 21905642 1.153 +eigbestsnp 4 rs756632 22 21799918 2.146 +eigbestsnp 4 rs4820539 22 21807970 1.938 +eigbestsnp 4 rs2267013 22 21875879 1.917 +eigbestsnp 4 rs2256725 22 21892891 1.917 +eigbestsnp 4 rs2283804 22 21820335 1.336 +eigbestsnp 4 rs2267006 22 21820990 1.336 +eigbestsnp 4 rs6003566 22 21889806 1.000 +eigbestsnp 4 rs16997606 22 21794754 0.875 +eigbestsnp 4 rs5751611 22 21896019 0.823 +eigbestsnp 4 rs5759636 22 21868698 0.799 +eigbestsnp 4 rs2267000 22 21785366 0.584 +packedancestrymap output +##end of smartpca run + +Correlation between eigenvector 1 (of 4) and Case/Control status is 0.033 +Correlation between eigenvector 2 (of 4) and Case/Control status is 0.051 +Correlation between eigenvector 3 (of 4) and Case/Control status is 0.193 +Correlation between eigenvector 4 (of 4) and Case/Control status is -0.069 +</pre></div>If you need to rerun this analysis, the command line used was +smartpca.perl -i /opt/galaxy/test-data/tinywga.ped -a /opt/galaxy/test-data/tinywga.map -b /opt/galaxy/test-data/tinywga.ped -o rgEigPCAtest1_pca.xls -p rgEigPCAtest1_eigensoftplot.pdf -e rgEigPCAtest1_eval.xls -l rgEigPCAtest1_log.txt -k 4 -m 2 -t 2 -s 2 +<p/></div></body></html> diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.txt Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,40 @@ + #eigvals: 11.482 7.740 7.255 4.271 + 101:1 0.1276 0.0060 0.1550 -0.3329 Case + 101:2 0.1276 0.0060 0.1550 -0.3329 Control + 101:3 0.0272 -0.1794 0.3241 -0.0243 Control + 105:1 0.1452 0.2666 -0.0845 -0.3446 Case + 105:2 0.0887 0.0765 0.0527 0.0326 Control + 105:3 -0.0026 -0.0367 -0.1333 -0.2045 Control + 112:1 -0.2453 -0.0165 -0.0856 0.0221 Case + 112:2 -0.2412 0.2537 0.0100 -0.0961 Control + 112:3 0.0358 -0.1766 -0.1010 0.1423 Control + 117:1 0.2905 0.0811 -0.0332 0.2245 Case + 117:2 0.1607 -0.1247 0.1495 0.0759 Control + 117:3 0.1675 0.0418 0.0449 0.2637 Control + 12:1 0.0272 -0.1794 0.3241 -0.0243 Case + 12:2 0.0272 -0.1794 0.3241 -0.0243 Control + 12:3 -0.0870 0.0154 0.2295 -0.1150 Control + 13:1 -0.0630 -0.2656 0.1607 -0.0055 Case + 13:2 -0.1886 -0.0251 -0.0558 -0.0102 Control + 13:3 0.0268 -0.0008 0.3404 -0.0369 Control + 1334:1 -0.0643 0.0418 0.0358 0.0343 Case + 1334:10 0.0927 -0.2210 -0.1938 -0.0651 Control + 1334:11 -0.2412 0.2537 0.0100 -0.0961 Control + 1334:12 0.0056 -0.2051 -0.2132 -0.1240 Control + 1334:13 0.0261 -0.0354 -0.0819 0.2399 Control + 1340:1 -0.1608 -0.0349 0.0222 0.1244 Case + 1340:10 -0.1608 -0.0349 0.0222 0.1244 Control + 1340:11 0.0261 -0.0354 -0.0819 0.2399 Control + 1340:12 0.0742 0.0819 -0.0833 -0.0528 Control + 1340:2 0.0302 0.2348 0.0136 0.1216 Case + 1340:9 -0.2493 -0.2867 -0.1811 0.1404 Control + 1341:1 0.1833 0.1206 -0.1248 -0.0491 Control + 1341:11 -0.1027 0.2939 -0.1091 -0.1832 Control + 1341:12 0.2312 -0.1808 -0.3129 -0.1522 Control + 1341:13 -0.2453 -0.0165 -0.0856 0.0221 Control + 1341:14 -0.2453 -0.0165 -0.0856 0.0221 Control + 1341:2 -0.2453 -0.0165 -0.0856 0.0221 Control + 1344:1 0.3015 0.2159 0.0173 0.3393 Control + 1344:12 0.0302 0.2348 0.0136 0.1216 Control + 1344:13 0.0302 0.2348 0.0136 0.1216 Control + 1345:12 0.2593 -0.1916 -0.2862 -0.1609 Control diff -r 4906f2302c85 -r cc8a30a0669f 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+3625 2383 Crs +4054 3254 Crs +1167 519 Crs +5028 3541 Crs +2475 4827 Crs +5455 1304 Crs +1202 2524 Crs +1202 2524 Crs +1202 2524 Crs +6083 4248 Crs +3661 4388 Crs +3661 4388 Crs +5706 1224 Crs +6594 4599 Crs +1.000 UL +LTb +714 420 M +6248 0 V +0 4452 V +-6248 0 V +714 420 L +1.000 UP +stroke +grestore +end +showpage +%%Trailer +%%DocumentFonts: Helvetica +%%Pages: 1 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.xtxt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eigensoftplot.pdf.xtxt Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,7 @@ +set terminal postscript color +set title "" +set xlabel "eigenvector 1" +set ylabel "eigenvector 2" +plot "rgEigPCAtest1_pca.xls.evec.1:2:Case" using 2:3 title "Case" , \ + "rgEigPCAtest1_pca.xls.evec.1:2:Control" using 2:3 title "Control" +## pause 9999 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eval.xls --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_eval.xls Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,39 @@ + 11.481974 + 7.739771 + 7.254586 + 4.270950 + 2.538320 + 1.667964 + 1.043403 + 0.653401 + 0.391044 + 0.338164 + 0.263384 + 0.150750 + 0.085580 + 0.065301 + 0.048797 + 0.006611 + 0.000000 + 0.000000 + 0.000000 + 0.000000 + 0.000000 + 0.000000 + 0.000000 + 0.000000 + 0.000000 + 0.000000 + -0.000000 + -0.000000 + -0.000000 + -0.000000 + -0.000000 + -0.000000 + -0.000000 + -0.000000 + -0.000000 + -0.000000 + -0.000000 + -0.000000 + -0.000000 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,128 @@ +parameter file: rgEigPCAtest1_pca.xls.par +### THE INPUT PARAMETERS +##PARAMETER NAME: VALUE +genotypename: /opt/galaxy/test-data/tinywga.ped +snpname: /opt/galaxy/test-data/tinywga.map +indivname: /opt/galaxy/test-data/tinywga.ped +evecoutname: rgEigPCAtest1_pca.xls.evec +evaloutname: rgEigPCAtest1_eval.xls +altnormstyle: NO +numoutevec: 4 +numoutlieriter: 2 +numoutlierevec: 2 +outliersigmathresh: 2 +qtmode: 0 +## smartpca version: 8000 +norm used + +genetic distance set from physical distance +genotype file processed +number of samples used: 40 number of snps used: 25 +REMOVED outlier 1334:2 iter 1 evec 1 sigmage -2.329 +number of samples after outlier removal: 39 + +## Tracy-Widom statistics: rows: 39 cols: 24 + #N eigenvalue difference twstat p-value effect. n + 1 11.481974 NA -0.712 0.332198 8.854 + 2 7.739771 -3.742203 -1.302 0.510496 8.388 + 3 7.254586 -0.485185 -0.171 0.201072 7.095 + 4 4.270950 -2.983636 -0.191 0.205302 8.005 + 5 2.538320 -1.732630 -0.341 0.238117 9.118 + 6 1.667964 -0.870356 -0.231 0.21376 9.910 + 7 1.043403 -0.624560 -0.269 0.222042 11.590 + 8 0.653401 -0.390003 NA NA NA + 9 0.391044 -0.262357 NA NA NA + 10 0.338164 -0.052880 NA NA NA + 11 0.263384 -0.074780 NA NA NA + 12 0.150750 -0.112634 NA NA NA + 13 0.085580 -0.065170 NA NA NA + 14 0.065301 -0.020279 NA NA NA + 15 0.048797 -0.016504 NA NA NA + 16 0.006611 -0.042186 NA NA NA + kurtosis snps indivs + eigenvector 1 1.926 2.122 + eigenvector 2 2.599 2.148 + eigenvector 3 2.593 2.873 + eigenvector 4 3.165 2.831 +population: 0 Case 9 +population: 1 Control 30 + +## Average divergence between populations: + Case Control popsize + Case 1.028 0.954 9 + Control 0.954 0.972 30 + + +number of blocks for moving block jackknife: 1 +fst *1000: + C C + C 0 0 + C 0 0 + +s.dev * 1000000: + C C + C 0 0 + C 0 0 + +## Anova statistics for population differences along each eigenvector: + p-value + eigenvector_1_Case_Control_ 0.841067 + eigenvector_2_Case_Control_ 0.758376 + eigenvector_3_Case_Control_ 0.238793 + eigenvector_4_Case_Control_ 0.678458 + +## Statistical significance of differences beween populations: + pop1 pop2 chisq p-value |pop1| |pop2| +popdifference: Case Control 1.810 0.77061 9 30 + +eigbestsnp 1 rs762601 22 21898858 1.674 +eigbestsnp 1 rs2156921 22 21899063 1.674 +eigbestsnp 1 rs4822375 22 21905642 1.674 +eigbestsnp 1 rs5751611 22 21896019 1.635 +eigbestsnp 1 rs4820537 22 21794810 1.542 +eigbestsnp 1 rs3788347 22 21797804 1.413 +eigbestsnp 1 rs2267000 22 21785366 1.151 +eigbestsnp 1 rs4820539 22 21807970 1.141 +eigbestsnp 1 rs5751592 22 21827674 0.890 +eigbestsnp 1 rs2283804 22 21820335 0.815 +eigbestsnp 1 rs2267006 22 21820990 0.815 +eigbestsnp 2 rs5759608 22 21832708 2.197 +eigbestsnp 2 rs5759612 22 21833170 2.197 +eigbestsnp 2 rs2283804 22 21820335 1.643 +eigbestsnp 2 rs2267006 22 21820990 1.643 +eigbestsnp 2 rs2283802 22 21784722 1.283 +eigbestsnp 2 rs2267009 22 21860168 1.283 +eigbestsnp 2 rs2071436 22 21871488 1.283 +eigbestsnp 2 rs756632 22 21799918 0.942 +eigbestsnp 2 rs16997606 22 21794754 0.715 +eigbestsnp 2 rs6003566 22 21889806 0.645 +eigbestsnp 2 rs762601 22 21898858 0.545 +eigbestsnp 3 rs16997606 22 21794754 1.770 +eigbestsnp 3 rs6003566 22 21889806 1.725 +eigbestsnp 3 rs3788347 22 21797804 1.452 +eigbestsnp 3 rs2267000 22 21785366 1.386 +eigbestsnp 3 rs2283802 22 21784722 1.247 +eigbestsnp 3 rs2267009 22 21860168 1.247 +eigbestsnp 3 rs2071436 22 21871488 1.247 +eigbestsnp 3 rs4820537 22 21794810 1.168 +eigbestsnp 3 rs762601 22 21898858 1.153 +eigbestsnp 3 rs2156921 22 21899063 1.153 +eigbestsnp 3 rs4822375 22 21905642 1.153 +eigbestsnp 4 rs756632 22 21799918 2.146 +eigbestsnp 4 rs4820539 22 21807970 1.938 +eigbestsnp 4 rs2267013 22 21875879 1.917 +eigbestsnp 4 rs2256725 22 21892891 1.917 +eigbestsnp 4 rs2283804 22 21820335 1.336 +eigbestsnp 4 rs2267006 22 21820990 1.336 +eigbestsnp 4 rs6003566 22 21889806 1.000 +eigbestsnp 4 rs16997606 22 21794754 0.875 +eigbestsnp 4 rs5751611 22 21896019 0.823 +eigbestsnp 4 rs5759636 22 21868698 0.799 +eigbestsnp 4 rs2267000 22 21785366 0.584 +packedancestrymap output +##end of smartpca run + +Correlation between eigenvector 1 (of 4) and Case/Control status is 0.033 +Correlation between eigenvector 2 (of 4) and Case/Control status is 0.051 +Correlation between eigenvector 3 (of 4) and Case/Control status is 0.193 +Correlation between eigenvector 4 (of 4) and Case/Control status is -0.069 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,45 @@ +4 +11.4820 +7.7400 +7.2550 +4.2710 + 0.3015 0.2159 0.0173 0.3393 + -0.2453 -0.0165 -0.0856 0.0221 + 0.0268 -0.0008 0.3404 -0.0369 + 0.3015 0.2159 0.0173 0.3393 + -0.2453 -0.0165 -0.0856 0.0221 + 0.0268 -0.0008 0.3404 -0.0369 + 0.3015 0.2159 0.0173 0.3393 + -0.2453 -0.0165 -0.0856 0.0221 + 0.0268 -0.0008 0.3404 -0.0369 + 0.3015 0.2159 0.0173 0.3393 + -0.2453 -0.0165 -0.0856 0.0221 + 0.0268 -0.0008 0.3404 -0.0369 + 0.3015 0.2159 0.0173 0.3393 + -0.2453 -0.0165 -0.0856 0.0221 + 0.0268 -0.0008 0.3404 -0.0369 + 0.3015 0.2159 0.0173 0.3393 + -0.2453 -0.0165 -0.0856 0.0221 + 0.0268 -0.0008 0.3404 -0.0369 + 0.3015 0.2159 0.0173 0.3393 + -0.1608 -0.0349 0.0222 0.1244 + -0.1027 0.2939 -0.1091 -0.1832 + 0.2593 -0.1916 -0.2862 -0.1609 + 0.0302 0.2348 0.0136 0.1216 + -0.2453 -0.0165 -0.0856 0.0221 + 0.3015 0.2159 0.0173 0.3393 + -0.1608 -0.0349 0.0222 0.1244 + -0.1027 0.2939 -0.1091 -0.1832 + 0.2593 -0.1916 -0.2862 -0.1609 + -0.2453 -0.0165 -0.0856 0.0221 + -0.2493 -0.2867 -0.1811 0.1404 + 0.3015 0.2159 0.0173 0.3393 + -0.1027 0.2939 -0.1091 -0.1832 + 0.2593 -0.1916 -0.2862 -0.1609 + 0.0302 0.2348 0.0136 0.1216 + -0.2453 -0.0165 -0.0856 0.0221 + -0.2453 -0.0165 -0.0856 0.0221 + 0.3015 0.2159 0.0173 0.3393 + 0.2593 -0.1916 -0.2862 -0.1609 + 0.0302 0.2348 0.0136 0.1216 + 0.2593 -0.1916 -0.2862 -0.1609 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.evec --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.evec Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,40 @@ + #eigvals: 11.482 7.740 7.255 4.271 + 101:1 0.1276 0.0060 0.1550 -0.3329 Case + 101:2 0.1276 0.0060 0.1550 -0.3329 Control + 101:3 0.0272 -0.1794 0.3241 -0.0243 Control + 105:1 0.1452 0.2666 -0.0845 -0.3446 Case + 105:2 0.0887 0.0765 0.0527 0.0326 Control + 105:3 -0.0026 -0.0367 -0.1333 -0.2045 Control + 112:1 -0.2453 -0.0165 -0.0856 0.0221 Case + 112:2 -0.2412 0.2537 0.0100 -0.0961 Control + 112:3 0.0358 -0.1766 -0.1010 0.1423 Control + 117:1 0.2905 0.0811 -0.0332 0.2245 Case + 117:2 0.1607 -0.1247 0.1495 0.0759 Control + 117:3 0.1675 0.0418 0.0449 0.2637 Control + 12:1 0.0272 -0.1794 0.3241 -0.0243 Case + 12:2 0.0272 -0.1794 0.3241 -0.0243 Control + 12:3 -0.0870 0.0154 0.2295 -0.1150 Control + 13:1 -0.0630 -0.2656 0.1607 -0.0055 Case + 13:2 -0.1886 -0.0251 -0.0558 -0.0102 Control + 13:3 0.0268 -0.0008 0.3404 -0.0369 Control + 1334:1 -0.0643 0.0418 0.0358 0.0343 Case + 1334:10 0.0927 -0.2210 -0.1938 -0.0651 Control + 1334:11 -0.2412 0.2537 0.0100 -0.0961 Control + 1334:12 0.0056 -0.2051 -0.2132 -0.1240 Control + 1334:13 0.0261 -0.0354 -0.0819 0.2399 Control + 1340:1 -0.1608 -0.0349 0.0222 0.1244 Case + 1340:10 -0.1608 -0.0349 0.0222 0.1244 Control + 1340:11 0.0261 -0.0354 -0.0819 0.2399 Control + 1340:12 0.0742 0.0819 -0.0833 -0.0528 Control + 1340:2 0.0302 0.2348 0.0136 0.1216 Case + 1340:9 -0.2493 -0.2867 -0.1811 0.1404 Control + 1341:1 0.1833 0.1206 -0.1248 -0.0491 Control + 1341:11 -0.1027 0.2939 -0.1091 -0.1832 Control + 1341:12 0.2312 -0.1808 -0.3129 -0.1522 Control + 1341:13 -0.2453 -0.0165 -0.0856 0.0221 Control + 1341:14 -0.2453 -0.0165 -0.0856 0.0221 Control + 1341:2 -0.2453 -0.0165 -0.0856 0.0221 Control + 1344:1 0.3015 0.2159 0.0173 0.3393 Control + 1344:12 0.0302 0.2348 0.0136 0.1216 Control + 1344:13 0.0302 0.2348 0.0136 0.1216 Control + 1345:12 0.2593 -0.1916 -0.2862 -0.1609 Control diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.par --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.par Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,11 @@ +genotypename: /opt/galaxy/test-data/tinywga.ped +snpname: /opt/galaxy/test-data/tinywga.map +indivname: /opt/galaxy/test-data/tinywga.ped +evecoutname: rgEigPCAtest1_pca.xls.evec +evaloutname: rgEigPCAtest1_eval.xls +altnormstyle: NO +numoutevec: 4 +numoutlieriter: 2 +numoutlierevec: 2 +outliersigmathresh: 2 +qtmode: 0 diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,23 @@ +Reading genotypes for 40 subjects and 25 markers +Calculating 780 pairs, updating every 78 pairs... +Estimated time is 0.00 to 0.00 seconds ... +0.003503 sec at pair 78 of 780 (10.00%): 556652.337848 marker*pairs/sec +0.005636 sec at pair 156 of 780 (20.00%): 691982.977283 marker*pairs/sec +0.007769 sec at pair 234 of 780 (30.00%): 752982.213220 marker*pairs/sec +0.009869 sec at pair 312 of 780 (40.00%): 790345.731265 marker*pairs/sec +0.011900 sec at pair 390 of 780 (50.00%): 819314.887905 marker*pairs/sec +0.013981 sec at pair 468 of 780 (60.00%): 836843.791886 marker*pairs/sec +0.015971 sec at pair 546 of 780 (70.00%): 854664.262256 marker*pairs/sec +0.017976 sec at pair 624 of 780 (80.00%): 867821.563192 marker*pairs/sec +0.020017 sec at pair 702 of 780 (90.00%): 876748.317016 marker*pairs/sec +T1: 0.00267601013184 T2: 0.0181350708008 T3: 0.000470638275146 TOT: 0.0224170684814 0 pairs with no (or not enough) comparable genotypes (0.0%) +Relstate dupe: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 +Relstate parentchild: mean(mean)=1.68 sdev(mean)=0.19, mean(sdev)=0.39 sdev(sdev)=0.19 +Relstate sibpairs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 +Relstate halfsibs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 +Relstate parents: mean(mean)=1.46 sdev(mean)=0.25, mean(sdev)=0.55 sdev(sdev)=0.17 +Relstate unrelated: mean(mean)=1.44 sdev(mean)=0.21, mean(sdev)=0.58 sdev(sdev)=0.15 +Relstate unknown: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 +780 pairs are available of 780 +Outliers: 0 +Plotting ... \ No newline at end of file diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgGRR/rgGRRtest1.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgGRR/rgGRRtest1.html Fri Mar 26 14:42:15 2010 -0400 @@ -0,0 +1,65 @@ +<?xml version="1.0" encoding="utf-8" ?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> +<meta name="generator" content="Galaxy rgGRR.py tool output - see http://g2.trac.bx.psu.edu/" /> +<title></title> +<link rel="stylesheet" href="/static/style/base.css" type="text/css" /> +</head> +<body> +<div class="document"> +<h4><div>Output from rgGRR.py run at 25/03/2010 21:01:24<br> +</h4> +If you need to rerun this analysis, the command line was +<pre>'/opt/galaxy/tools/rgenetics/rgGRR.py' '/opt/galaxy/test-data/tinywga' 'tinywga' '/opt/galaxy/test-data/rgtestouts/rgGRR/rgGRRtest1.html' '/opt/galaxy/test-data/rgtestouts/rgGRR' 'rgGRRtest1' '100' '6'</pre> +</div> <embed src="rgGRRtest1.svg" type="image/svg+xml" width="1150" height="600" /><div><h4>Click the links below to save output files and plots</h4><br><ol> +<li><a href="rgGRRtest1.svg" type="image/svg+xml" >rgGRR Plot (requires SVG)</a></li> +<li><a href="rgGRRtest1_table.xls">Mean by SD alleles shared - 780 rows</a></li> +<li><a href="rgGRRtest1.html">rgGRRtest1.html</a></li> +<li><a href="Log_rgGRRtest1.txt">Log_rgGRRtest1.txt</a></li> +</ol></div><div><h2>Outliers in tab delimited files linked above are also listed below</h2></div><div><hr><h3>Log from this job (also stored in Log_rgGRRtest1.txt)</h3><pre>Reading genotypes for 40 subjects and 25 markers + +Calculating 780 pairs, updating every 78 pairs... + +Estimated time is 0.00 to 0.00 seconds ... + +0.003503 sec at pair 78 of 780 (10.00%): 556652.337848 marker*pairs/sec + +0.005636 sec at pair 156 of 780 (20.00%): 691982.977283 marker*pairs/sec + +0.007769 sec at pair 234 of 780 (30.00%): 752982.213220 marker*pairs/sec + +0.009869 sec at pair 312 of 780 (40.00%): 790345.731265 marker*pairs/sec + +0.011900 sec at pair 390 of 780 (50.00%): 819314.887905 marker*pairs/sec + +0.013981 sec at pair 468 of 780 (60.00%): 836843.791886 marker*pairs/sec + +0.015971 sec at pair 546 of 780 (70.00%): 854664.262256 marker*pairs/sec + +0.017976 sec at pair 624 of 780 (80.00%): 867821.563192 marker*pairs/sec + +0.020017 sec at pair 702 of 780 (90.00%): 876748.317016 marker*pairs/sec + +T1: 0.00267601013184 T2: 0.0181350708008 T3: 0.000470638275146 TOT: 0.0224170684814 0 pairs with no (or not enough) comparable genotypes (0.0%) + +Relstate dupe: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 + +Relstate parentchild: mean(mean)=1.68 sdev(mean)=0.19, mean(sdev)=0.39 sdev(sdev)=0.19 + +Relstate sibpairs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 + +Relstate halfsibs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 + +Relstate parents: mean(mean)=1.46 sdev(mean)=0.25, mean(sdev)=0.55 sdev(sdev)=0.17 + +Relstate unrelated: mean(mean)=1.44 sdev(mean)=0.21, mean(sdev)=0.58 sdev(sdev)=0.15 + +Relstate unknown: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 + +780 pairs are available of 780 + +Outliers: 0 + +Plotting ...</pre><hr></div></body></html> diff -r 4906f2302c85 -r cc8a30a0669f test-data/rgtestouts/rgGRR/rgGRRtest1.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgtestouts/rgGRR/rgGRRtest1.svg Fri Mar 26 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[hg] galaxy 3569: require numpy before bx-python where numpy is ...
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/4906f2302c85 changeset: 3569:4906f2302c85 user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Mar 26 14:14:40 2010 -0400 description: require numpy before bx-python where numpy is dependant diffstat: lib/galaxy/visualization/tracks/data/array_tree.py | 4 +++- 1 files changed, 3 insertions(+), 1 deletions(-) diffs (14 lines): diff -r 5bbd895570d4 -r 4906f2302c85 lib/galaxy/visualization/tracks/data/array_tree.py --- a/lib/galaxy/visualization/tracks/data/array_tree.py Fri Mar 26 12:37:20 2010 -0400 +++ b/lib/galaxy/visualization/tracks/data/array_tree.py Fri Mar 26 14:14:40 2010 -0400 @@ -2,7 +2,9 @@ Array tree data provider for the Galaxy track browser. """ -import pkg_resources; pkg_resources.require( "bx-python" ) +import pkg_resources +pkg_resources.require( "numpy" ) +pkg_resources.require( "bx-python" ) from bx.arrays.array_tree import FileArrayTreeDict from math import floor, ceil, log, pow

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[hg] galaxy 3568: Missed the actual tool files for new join in l...
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/5bbd895570d4 changeset: 3568:5bbd895570d4 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Fri Mar 26 12:37:20 2010 -0400 description: Missed the actual tool files for new join in last commit... diffstat: tools/new_operations/column_join.py | 175 +++++++++++++++++++++++++++++++++++ tools/new_operations/column_join.xml | 150 ++++++++++++++++++++++++++++++ 2 files changed, 325 insertions(+), 0 deletions(-) diffs (333 lines): diff -r a9e25e05ae8d -r 5bbd895570d4 tools/new_operations/column_join.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/new_operations/column_join.py Fri Mar 26 12:37:20 2010 -0400 @@ -0,0 +1,175 @@ +#!/usr/bin/env python + +""" +This tool takes a tab-delimited text file as input and creates filters on columns based on certain properties. The tool will skip over invalid lines within the file, informing the user about the number of lines skipped. + +usage: %prog output input1 input2 column1[,column2[,column3[,...]]] hinge1[,hinge2[,hinge3[,...]]] [other_input1 [other_input2 [other_input3 ...]]] + output: the output pileup + input1: the pileup file to start with + input2: the second pileup file to join + hinge: the columns to be used for matching + columns: the columns that should appear in the output + other_inputs: the other input files to join + +""" + +import os, re, sys, tempfile + +def stop_err( msg ): + sys.stderr.write( msg ) + sys.exit() + +def ref_compare( ref1, ref2 ): + """ + Compares items like 'chr10' and 'chrM' or 'scaffold2' and scaffold10' so that + first part handled as text but last part as number + """ + pat = re.compile( '(?P<text>\D*)(?P<number>\d+)?' ) + r1 = pat.match( ref1 ) + r2 = pat.match( ref2 ) + if not r2: + return 1 + elif not r1: + return -1 + text1, num1 = r1.groupdict()[ 'text' ].strip(), r1.groupdict()[ 'number' ] + text2, num2 = r2.groupdict()[ 'text' ].strip(), r2.groupdict()[ 'number' ] + if text2 == '' and ( num2 == '' or num2 is None ): + return 1 + elif text1 == '' and ( num1 == '' or num1 is None ): + return -1 + if text1 > text2: + return 1 + elif text1 == text2: + if not ( num1 is None or num2 is None ): + num1 = int( num1 ) + num2 = int( num2 ) + if num1 > num2: + return 1 + elif num1 == num2: + return 0 + elif num1 < num2: + return -1 + elif text1 < text2: + return -1 + +def ref_pos_sort( infile, outfile ): + """Given input file name, sorts logically (text vs. numeric) into provided output file name.""" + ref_locs = {} + bad_lines = [] + fin = open( infile, 'rb' ) + line = fin.readline() + while line.strip(): + if True: + try: + ref_seq, ref_loc = line.split( '\t' )[:2] + try: + ref_locs[ ref_seq ][ long( ref_loc ) ] = fin.tell() - len( line.strip() ) - 1 + except KeyError: + ref_locs[ ref_seq ] = { long( ref_loc ): fin.tell() - len( line.strip() ) - 1 } + except ValueError: + bad_lines.append( line ) + except ValueError: + bad_line.append( line ) + line = fin.readline() + fin.close() + refs = ref_locs.keys() + refs.sort( ref_compare ) + fin = open( infile, 'rb' ) + fout = open( outfile, 'wb' ) + for ref in refs: + locs = ref_locs[ ref ].keys() + locs.sort() + for loc in locs: + fin.seek( ref_locs[ ref ][ loc ] ) + fout.write( fin.readline() ) + fout.close() + fin.close() + +def min_chr_pos( chr_pos ): + """Given line and hinge, identifies the 'smallest' one, from left to right""" + if len( chr_pos ) == 0 and ''.join( chr_pos ): + return '' + min_loc = len( chr_pos ) + min_ref_pos = [] + loc = 0 + for c_pos in chr_pos: + if c_pos.strip(): + ref, pos = c_pos.split( '\t' )[:2] + pos = int( pos ) + if not min_ref_pos: + min_ref_pos = [ ref, pos ] + min_loc = loc + else: + ref_comp = ref_compare( ref, min_ref_pos[0] ) + if ref_comp < 0: + min_ref_pos = [ ref, pos ] + min_loc = loc + elif ref_comp == 0 and pos < min_ref_pos[1]: + min_ref_pos[1] = pos + min_loc = loc + loc += 1 + return '%s\t%s' % tuple( min_ref_pos ), min_loc + +def __main__(): + output = sys.argv[1] + input1 = sys.argv[2] + input2 = sys.argv[3] + hinge = int( sys.argv[4] ) + cols = [ int( c ) for c in sys.argv[5].split( ',' ) ] + inputs = sys.argv[6:] + assert len( cols ) > 2, 'You need to select at least one column in addition to the first two' + # make sure all files are sorted in same way, ascending + tmp_input_files = [] + input_files = [ input1, input2 ] + input_files.extend( inputs ) + for in_file in input_files: + tmp_file = tempfile.NamedTemporaryFile() + tmp_file_name = tmp_file.name + tmp_file.close() + ref_pos_sort( in_file, tmp_file_name ) + tmp_file = open( tmp_file_name, 'rb' ) + tmp_input_files.append( tmp_file ) + # cycle through files, getting smallest line of all files one at a time + # also have to keep track of vertical position of extra columns + fout = file( output, 'w' ) + old_current_chr_pos = '' + first_line = True + current_lines = [ f.readline() for f in tmp_input_files ] + last_lines = ''.join( current_lines ).strip() + last_loc = -1 + while last_lines: + # get the "minimum" hinge, which should come first, and the file location in list + current_chr_pos, loc = min_chr_pos( [ '\t'.join( line.split( '\t' )[ :hinge ] ) for line in current_lines ] ) + # first output empty columns for vertical alignment (account for "missing" files) + if current_chr_pos != old_current_chr_pos: + last_loc = -1 + if loc - last_loc > 1: + current_data = [ '' for col in range( ( loc - last_loc - 1 ) * len( cols[ hinge: ] ) ) ] + else: + current_data = [] + # now output actual data + split_line = current_lines[ loc ].strip().split( '\t' ) + if ''.join( split_line ): + for col in cols: + if col > hinge: + current_data.append( split_line[ col - 1 ] ) + current_lines[ loc ] = tmp_input_files[ loc ].readline() + if current_chr_pos == old_current_chr_pos: + fout.write( '\t%s' % '\t'.join( current_data ) ) + else: + if not first_line: + fout.write( '\n' ) + fout.write( '%s\t%s' % ( current_chr_pos, '\t'.join( current_data ) ) ) + first_line = False + old_current_chr_pos = current_chr_pos + if last_lines == ''.join( current_lines ).strip(): + break + last_lines = ''.join( current_lines ).strip() + last_loc = loc + fout.write( '\n' ) + for f in tmp_input_files: + os.unlink( f.name ) + fout.close() +# sys.stderr.write('******************\n'+file(fout.name, 'r').read()+'\n******************\n') + +if __name__ == "__main__" : __main__() diff -r a9e25e05ae8d -r 5bbd895570d4 tools/new_operations/column_join.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/new_operations/column_join.xml Fri Mar 26 12:37:20 2010 -0400 @@ -0,0 +1,150 @@ +<tool id="column_join" name="Column Join" version="1.0.0"> + <description></description> + <command interpreter="python"> + column_join.py + $output + $input1 + $input2 + $hinge + $columns + #for $f in $file_chooser: + ${f.input} + #end for + </command> + <inputs> + <param name="input1" type="data" format="tabular" label="Choose the first file for the join" /> + <param name="columns" type="data_column" data_ref="input1" multiple="true" numerical="false" label="Include these column" help="Multi-select list - hold the appropriate key while clicking to select multiple columns" /> + <param name="hinge" type="data_column" data_ref="input1" multiple="false" numerical="false" label="Use this column and columns to left the 'hinge' (matching data for each join)" help="All columns to left of selected column (plus selected column) will be used. Select 2 for pileup" /> + <param name="input2" type="data" format="tabular" label="Choose the second file for the join" /> + <repeat name="file_chooser" title="Additional Input"> + <param name="input" label="Additional input file" type="data" format="tabular" /> + </repeat> + </inputs> + <outputs> + <data name="output" format="pileup" /> + </outputs> + <tests> + <test> + <param name="input1" value="column_join_in1.pileup" ftype="pileup" /> + <param name="columns" value="1,2,3,4,5,7" /> + <param name="hinge" value="1,2" /> + <param name="input2" value="column_join_in2.pileup" ftype="pileup" /> + <param name="input" value="column_join_in3.pileup" ftype="pileup" /> + <output name="output" file="column_join_out1.pileup" ftype="pileup" /> + </test> + <test> + <param name="input1" value="column_join_in4.pileup" ftype="pileup" /> + <param name="columns" value="1,2,3,4" /> + <param name="hinge" value="1,2" /> + <param name="input2" value="column_join_in5.pileup" ftype="pileup" /> + <param name="input" value="column_join_in6.pileup" ftype="pileup" /> + <output name="output" file="column_join_out2.pileup" ftype="pileup" /> + </test> + <test> + <param name="input1" value="column_join_in7.pileup" ftype="pileup" /> + <param name="columns" value="1,2,3,4,5" /> + <param name="hinge" value="1,2" /> + <param name="input2" value="column_join_in8.pileup" ftype="pileup" /> + <param name="input" value="column_join_in9.pileup" ftype="pileup" /> + <output name="output" file="column_join_out3.pileup" ftype="pileup" /> + </test> + </tests> + <help> +**What it does** + +This tool allows you to join several files with the same column structure into one file, removing certain columns if necessary. The user needs to select a 'hinge', which is the number of left-most columns to match on. They also need to select the columns to include in the join, which should include the hinge columns, too. + +----- + +**Example** + +Given the following files:: + + FILE 1 + chr2 1 T 6 .C..., I$$III + chr2 2 G 6 ..N.., III@II + chr2 3 C 7 ..C..., I$IIIII + chr2 4 G 7 .G...., I#IIIII + chr2 5 G 7 ...N.., IIII#BI + chr2 6 A 7 ..T..., I$IDIII + chr1 1 C 1 ^:. I + chr1 2 G 2 .^:. $I + chr1 3 A 2 .. I% + chr1 4 C 2 .. I$ + chr1 5 T 3 ..^:. I#I + chr1 6 G 3 ..^:, I#I + + FILE 2 + chr1 3 T 1 ^:. I + chr1 4 G 2 .^:. $I + chr1 5 T 2 .. I% + chr1 6 C 3 ..^:. III + chr1 7 G 3 ..^:. I#I + chr1 8 T 4 ...^:, I#II + chr2 77 C 6 .G..., I$$III + chr2 78 G 6 ..N.., III@II + chr2 79 T 7 ..N..., I$IIIII + chr2 80 C 7 .G...., I#IIIII + chr2 81 G 7 ...A.., IIII#BI + chr2 82 A 8 ...G..., I$IDIIII + chr2 83 T 8 .A.....N IIIIIIII + chr2 84 A 9 ......T. I$IIIIIII + + FILE 3 + chr1 1 A 1 . I + chr1 2 T 2 G. I$ + chr1 3 C 2 ., I@ + chr1 4 C 3 ..N III + chr1 42 C 5 ...N^:. III@I + chr1 43 C 5 .N..^:. IIIII + chr1 44 T 5 .A.., IA@II + chr1 45 A 6 .N...^:. IIIII$ + chr1 46 G 6 .GN..^:. I@IIII + chr1 47 A 7 ....^:.., IIIII$I + chr2 73 T 5 .N.., II$II + chr2 74 A 5 ...., IIIII + chr2 75 T 5 ...., IIIII + chr2 76 T 5 ...., IIIII + chr2 77 C 5 ...., IIIBI + chr2 78 T 5 ...., IDIII + +To join on columns 3 and 4 combining on columns 1 and 2, columns 1-4 should be selected for the 'Include these columns' option, and column 2 selected for the 'hinge'. With these settings, the following would be output:: + + chr1 1 C 1 A 1 + chr1 2 G 2 T 2 + chr1 3 A 2 T 1 C 2 + chr1 4 C 2 G 2 C 3 + chr1 5 T 3 T 2 + chr1 6 G 3 C 3 + chr1 7 G 3 + chr1 8 T 4 + chr1 42 C 5 + chr1 43 C 5 + chr1 44 T 5 + chr1 45 A 6 + chr1 46 G 6 + chr1 47 A 7 + chr2 1 T 6 + chr2 2 G 6 + chr2 3 C 7 + chr2 4 G 7 + chr2 5 G 7 + chr2 6 A 7 + chr2 73 T 5 + chr2 74 A 5 + chr2 75 T 5 + chr2 76 T 5 + chr2 77 C 6 C 5 + chr2 78 G 6 T 5 + chr2 79 T 7 + chr2 80 C 7 + chr2 81 G 7 + chr2 82 A 8 + chr2 83 T 8 + chr2 84 A 9 + + + </help> +</tool> + +

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[hg] galaxy 3567: merge to 3566:3ac95cd927d7
by Greg Von Kuster 15 Apr '10

15 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/a9e25e05ae8d changeset: 3567:a9e25e05ae8d user: fubar: ross Lazarus at gmail period com date: Fri Mar 26 12:11:01 2010 -0400 description: merge to 3566:3ac95cd927d7 diffstat: datatypes_conf.xml.sample | 2 + lib/galaxy/datatypes/registry.py | 3 + lib/galaxy/datatypes/tabular.py | 93 ++ lib/galaxy/datatypes/test/10col.pileup | 30 + lib/galaxy/datatypes/test/6col.pileup | 30 + test-data/1.pileup | 1000 ++++++++++++++++++++++++++++++++ test-data/column_join_in1.pileup | 30 + test-data/column_join_in2.pileup | 30 + test-data/column_join_in3.pileup | 30 + test-data/column_join_in4.pileup | 25 + test-data/column_join_in5.pileup | 25 + test-data/column_join_in6.pileup | 25 + test-data/column_join_in7.pileup | 32 + test-data/column_join_in8.pileup | 23 + test-data/column_join_in9.pileup | 25 + test-data/column_join_out1.pileup | 60 + test-data/column_join_out2.pileup | 65 ++ test-data/column_join_out3.pileup | 70 ++ test/functional/test_get_data.py | 17 + tool_conf.xml.sample | 1 + 20 files changed, 1616 insertions(+), 0 deletions(-) diffs (1743 lines): diff -r 5cc5e94345b8 -r a9e25e05ae8d datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample Fri Mar 26 12:02:22 2010 -0400 +++ b/datatypes_conf.xml.sample Fri Mar 26 12:11:01 2010 -0400 @@ -61,6 +61,7 @@ <converter file="maf_to_interval_converter.xml" target_datatype="interval"/> </datatype> <datatype extension="pdf" type="galaxy.datatypes.images:Image" mimetype="application/pdf"/> + <datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true" /> <datatype extension="png" type="galaxy.datatypes.images:Image" mimetype="image/png"/> <datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" /> <datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/> @@ -239,6 +240,7 @@ <sniffer type="galaxy.datatypes.interval:CustomTrack"/> <sniffer type="galaxy.datatypes.interval:Gff"/> <sniffer type="galaxy.datatypes.interval:Gff3"/> + <sniffer type="galaxy.datatypes.tabular:Pileup"/> <sniffer type="galaxy.datatypes.interval:Interval"/> <sniffer type="galaxy.datatypes.tabular:Sam"/> </sniffers> diff -r 5cc5e94345b8 -r a9e25e05ae8d lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py Fri Mar 26 12:02:22 2010 -0400 +++ b/lib/galaxy/datatypes/registry.py Fri Mar 26 12:11:01 2010 -0400 @@ -155,6 +155,7 @@ 'laj' : images.Laj(), 'lav' : sequence.Lav(), 'maf' : sequence.Maf(), + 'pileup' : tabular.Pileup(), 'qualsolid' : qualityscore.QualityScoreSOLiD(), 'qualsolexa' : qualityscore.QualityScoreSolexa(), 'qual454' : qualityscore.QualityScore454(), @@ -185,6 +186,7 @@ 'laj' : 'text/plain', 'lav' : 'text/plain', 'maf' : 'text/plain', + 'pileup' : 'text/plain', 'qualsolid' : 'text/plain', 'qualsolexa' : 'text/plain', 'qual454' : 'text/plain', @@ -218,6 +220,7 @@ interval.CustomTrack(), interval.Gff(), interval.Gff3(), + tabular.Pileup(), interval.Interval(), tabular.Sam() ] diff -r 5cc5e94345b8 -r a9e25e05ae8d lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py Fri Mar 26 12:02:22 2010 -0400 +++ b/lib/galaxy/datatypes/tabular.py Fri Mar 26 12:11:01 2010 -0400 @@ -327,3 +327,96 @@ except: pass return False + +class Pileup( Tabular ): + """Tab delimited data in pileup (6- or 10-column) format""" + file_ext = "pileup" + + """Add metadata elements""" + MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter ) + MetadataElement( name="startCol", default=2, desc="Start column", param=metadata.ColumnParameter ) + MetadataElement( name="baseCol", default=3, desc="Reference base column", param=metadata.ColumnParameter ) + + def init_meta( self, dataset, copy_from=None ): + Tabular.init_meta( self, dataset, copy_from=copy_from ) + + def set_peek( self, dataset, line_count=None, is_multi_byte=False ): + """Set the peek and blurb text""" + if not dataset.dataset.purged: + dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) + if line_count is None: + # See if line_count is stored in the metadata + if dataset.metadata.data_lines: + dataset.blurb = "%s genomic coordinates" % util.commaify( str( dataset.metadata.data_lines ) ) + else: + # Number of lines is not known ( this should not happen ), and auto-detect is + # needed to set metadata + dataset.blurb = "? genomic coordinates" + else: + dataset.blurb = "%s genomic coordinates" % util.commaify( str( line_count ) ) + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + + def make_html_table( self, dataset, skipchars=[] ): + """Create HTML table, used for displaying peek""" + out = ['<table cellspacing="0" cellpadding="3">'] + comments = [] + try: + # Generate column header + out.append('<tr>') + for i in range( 1, dataset.metadata.columns+1 ): + if i == dataset.metadata.chromCol: + out.append( '<th>%s.Chrom</th>' % i ) + elif i == dataset.metadata.startCol: + out.append( '<th>%s.Start</th>' % i ) + elif i == dataset.metadata.baseCol: + out.append( '<th>%s.Base</th>' % i ) + else: + out.append( '<th>%s</th>' % i ) + out.append('</tr>') + out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) ) + out.append( '</table>' ) + out = "".join( out ) + except Exception, exc: + out = "Can't create peek %s" % str( exc ) + return out + + def repair_methods( self, dataset ): + """Return options for removing errors along with a description""" + return [ ("lines", "Remove erroneous lines") ] + + def sniff( self, filename ): + """ + Checks for 'pileup-ness' + + There are two main types of pileup: 6-column and 10-column. For both, + the first three and last two columns are the same. We only check the + first three to allow for some personalization of the format. + + >>> fname = get_test_fname( 'interval.interval' ) + >>> Pileup().sniff( fname ) + False + >>> fname = get_test_fname( '6col.pileup' ) + >>> Pileup().sniff( fname ) + True + >>> fname = get_test_fname( '10col.pileup' ) + >>> Pileup().sniff( fname ) + True + """ + headers = get_headers( filename, '\t' ) + try: + for hdr in headers: + if hdr and not hdr[0].startswith( '#' ): + if len( hdr ) < 3: + return False + try: + # chrom start in column 1 (with 0-based columns) + # and reference base is in column 2 + check = int( hdr[1] ) + assert hdr[2] in [ 'A', 'C', 'G', 'T', 'N', 'a', 'c', 'g', 't', 'n' ] + except: + return False + return True + except: + return False diff -r 5cc5e94345b8 -r a9e25e05ae8d lib/galaxy/datatypes/test/10col.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/test/10col.pileup Fri Mar 26 12:11:01 2010 -0400 @@ -0,0 +1,30 @@ +chrM 1 G G 25 0 25 1 ^:. I +chrM 2 T T 25 0 25 1 . I +chrM 3 T T 25 0 25 1 . I +chrM 4 A A 36 0 25 3 .^:.^:. II+ +chrM 5 A A 36 0 25 3 ... III +chrM 6 T T 36 0 25 3 ... III +chrM 7 G G 42 0 25 5 ...^:.^:. IIIII +chrM 8 T T 45 0 25 6 .....^:. IIIIII +chrM 9 A A 51 0 25 8 ......^:.^:. IIIIIIII +chrM 10 G G 54 0 25 9 ........^:. IIIIIIIII +chrM 11 C C 57 0 25 10 .........^:. IIIIIIIIII +chrM 12 T T 60 0 25 11 ..........^:. IIIIIIIIIII +chrM 13 T T 78 0 25 17 ...........^:.^:.^:.^:.^:.^:. IIIIIIIIIIIIIIIII +chrM 14 A A 56 0 25 18 .......G.........^:. BIIIIIII+IIIIIIIII +chrM 15 A A 87 0 25 20 ..................^:.^:. DIIIIIII(IIIIIIIIIII +chrM 16 T T 87 0 25 20 .................... IIIIIIIIIIIIIIIIIIII +chrM 17 A A 87 0 25 20 .................... 9IIIIIIIIIIIIIIIIIII +chrM 18 A A 87 0 25 20 .................... @IIIIIIIIIIIIIIIIIII +chrM 19 T T 55 0 25 20 ..................GG IIIIIIIIIIIIIIIIII'A +chrM 20 A A 54 0 25 20 ..................C. IIIIIIIIIIIIIII2II#$ +chrM 21 T T 87 0 25 20 .................... IIIIIIIIIIIIIIIIIIII +chrM 22 A A 87 0 25 20 .................... IIIIIIIIIIIIIIAIIIII +chrM 23 A A 87 0 25 20 .................... 9IIIIIIIIII0IIIIIIII +chrM 24 A A 87 0 25 20 ........N........... IIIIIIII"IIIIICIIIII +chrM 25 G G 57 0 25 21 ...A................^:. A@.$IIIIIIIFIIIIIIIII +chrM 26 C C 57 0 25 21 .......A............. IIHIDII&IIIIIIIIIIIII +chrM 27 A A 99 0 25 24 .....................^:.^:.^:. IE8IFIII9IIIIIIIIIIIIIII +chrM 28 A A 99 0 25 24 ........................ 1FIIIIIIIIIIIIIIIIDEIIII +chrM 29 G G 55 0 25 24 ..................NN.... ;IIIIII+HII=IIIIII""IIII +chrM 30 G G 68 0 25 25 ...C....................^:. ;I?&IAI0IIIIIIIIIIIIIIIII diff -r 5cc5e94345b8 -r a9e25e05ae8d lib/galaxy/datatypes/test/6col.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/test/6col.pileup Fri Mar 26 12:11:01 2010 -0400 @@ -0,0 +1,30 @@ +chrM 42 C 1 ^:. I +chrM 43 C 2 .^:. II +chrM 44 T 2 .. II +chrM 45 A 3 ..^:. III +chrM 46 G 4 ...^:. IIII +chrM 47 A 5 ....^:, IIIII +chrM 48 T 5 ...., IIIII +chrM 49 G 5 ...., IIIII +chrM 50 A 5 ...., IIIII +chrM 51 G 5 ...., IIIII +chrM 52 T 5 ...., IIIII +chrM 53 A 5 ...., IIIII +chrM 54 T 5 ...., IIIII +chrM 55 T 5 ...., IIIII +chrM 56 C 5 ...., IIIII +chrM 57 T 5 ...., IIIII +chrM 58 T 5 ...., IIIII +chrM 59 A 5 ...., IIIII +chrM 60 C 5 ...., IIIII +chrM 61 T 5 ...., IIIII +chrM 62 C 5 ...., IIIII +chrM 63 C 5 ...., IIIII +chrM 64 A 5 ...., IIIII +chrM 65 T 5 ...., IIIII +chrM 66 A 5 ...., IIIII +chrM 67 A 5 ...., IIIII +chrM 68 A 5 ...., IIICI +chrM 69 C 5 ...., IIIII +chrM 70 A 5 ...., IIIII +chrM 71 C 5 ...., IIIII diff -r 5cc5e94345b8 -r a9e25e05ae8d test-data/1.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.pileup Fri Mar 26 12:11:01 2010 -0400 @@ -0,0 +1,1000 @@ +chrM 42 C 1 ^:. I +chrM 43 C 2 .^:. II +chrM 44 T 2 .. II +chrM 45 A 3 ..^:. III +chrM 46 G 4 ...^:. IIII +chrM 47 A 5 ....^:, IIIII +chrM 48 T 5 ...., IIIII +chrM 49 G 5 ...., IIIII +chrM 50 A 5 ...., IIIII +chrM 51 G 5 ...., IIIII +chrM 52 T 5 ...., IIIII +chrM 53 A 5 ...., IIIII +chrM 54 T 5 ...., IIIII +chrM 55 T 5 ...., IIIII +chrM 56 C 5 ...., IIIII +chrM 57 T 5 ...., IIIII +chrM 58 T 5 ...., IIIII +chrM 59 A 5 ...., IIIII +chrM 60 C 5 ...., IIIII +chrM 61 T 5 ...., IIIII +chrM 62 C 5 ...., IIIII +chrM 63 C 5 ...., IIIII +chrM 64 A 5 ...., IIIII +chrM 65 T 5 ...., IIIII +chrM 66 A 5 ...., IIIII +chrM 67 A 5 ...., IIIII +chrM 68 A 5 ...., IIICI +chrM 69 C 5 ...., IIIII +chrM 70 A 5 ...., IIIII +chrM 71 C 5 ...., IIIII +chrM 72 A 5 ...., IAIII +chrM 73 T 5 ...., IIIII +chrM 74 A 5 ...., IIIII +chrM 75 G 5 ...., %IIII +chrM 76 G 5 T..., *IIII +chrM 77 C 5 .$..., GIIII +chrM 78 T 4 .$.., IIII +chrM 79 T 3 .., III +chrM 80 G 3 .$., I1I +chrM 81 G 2 .$, II +chrM 82 T 1 ,$ I +chrM 83 C 2 ^:.^:. II +chrM 84 C 2 .. II +chrM 85 T 2 .. II +chrM 86 A 2 .. II +chrM 87 G 2 .. II +chrM 88 C 2 .. II +chrM 89 C 2 .. II +chrM 90 T 2 .. II +chrM 91 T 2 .. II +chrM 92 T 2 .. II +chrM 93 T 2 .. II +chrM 94 T 2 .. II +chrM 95 A 2 .. II +chrM 96 T 2 .. II +chrM 97 T 2 .. II +chrM 98 A 2 .. II +chrM 99 G 2 .. II +chrM 100 T 2 .. II +chrM 101 T 2 .. II +chrM 102 A 2 .. II +chrM 103 T 2 .. II +chrM 104 T 2 .. II +chrM 105 A 2 .. IE +chrM 106 A 2 .. II +chrM 107 T 2 .. II +chrM 108 A 2 .. II +chrM 109 G 2 .. II +chrM 110 A 2 .. II +chrM 111 A 2 .. I2 +chrM 112 T 2 .. II +chrM 113 T 2 .. II +chrM 114 A 2 .. H7 +chrM 115 C 2 .. II +chrM 116 A 2 .. II +chrM 117 C 2 .. II +chrM 118 A 2 .$.$ F8 +chrM 156 T 1 ^:, & +chrM 157 C 1 , I +chrM 158 A 2 g^:g I> +chrM 159 C 2 ,, /F +chrM 160 G 2 ,, II +chrM 161 T 2 ,, I> +chrM 162 C 2 ,, .- +chrM 163 T 2 ,, I8 +chrM 164 C 2 ,, 4F +chrM 165 T 2 ,, II +chrM 166 A 2 ,, II +chrM 167 C 2 ,, ;6 +chrM 168 G 2 ,, II +chrM 169 A 2 ,, II +chrM 170 T 2 ,, II +chrM 171 T 2 ,, IB +chrM 172 A 2 ,, II +chrM 173 A 2 ,, II +chrM 174 A 2 ,, II +chrM 175 A 2 ,, II +chrM 176 G 2 ,, II +chrM 177 G 2 ,, II +chrM 178 A 2 ,, II +chrM 179 G 2 ,, II +chrM 180 C 2 ,, II +chrM 181 A 3 ,,^:, III +chrM 182 G 3 ,,, III +chrM 183 G 3 ,,, III +chrM 184 T 3 ,,, III +chrM 185 A 3 ,,, III +chrM 186 T 3 ,,, III +chrM 187 C 3 ,,, III +chrM 188 A 3 ,,, III +chrM 189 A 3 ,,, III +chrM 190 G 3 ,,, III +chrM 191 C 3 ,$,, III +chrM 192 A 2 ,, II +chrM 193 C 2 ,$, II +chrM 194 A 1 , I +chrM 195 C 1 , I +chrM 196 T 1 , F +chrM 197 A 1 , I +chrM 198 G 1 , I +chrM 199 A 1 , I +chrM 200 A 1 , I +chrM 201 A 2 ,^:. I- +chrM 202 G 2 ,. II +chrM 203 T 2 ,. II +chrM 204 A 2 ,. II +chrM 205 G 2 ,. I6 +chrM 206 C 2 ,. II +chrM 207 T 2 ,. I, +chrM 208 C 2 ,. II +chrM 209 A 2 ,. II +chrM 210 T 2 ,. II +chrM 211 A 2 ,. II +chrM 212 A 2 ,. IE +chrM 213 C 2 ,. IC +chrM 214 A 2 ,. I; +chrM 215 C 2 ,. II +chrM 216 C 2 ,$. II +chrM 217 T 1 . I +chrM 218 T 1 . I +chrM 219 G 1 T I +chrM 220 C 1 . I +chrM 221 T 1 . I +chrM 222 C 1 . E +chrM 223 A 1 . 4 +chrM 224 G 1 T 9 +chrM 225 C 1 . : +chrM 226 C 1 . ? +chrM 227 A 1 . . +chrM 228 C 1 . C +chrM 229 A 3 .^:,^:, %II +chrM 230 C 3 .,, 8II +chrM 231 C 3 .,, 9II +chrM 232 C 3 .,, III +chrM 233 C 3 .,, AI' +chrM 234 C 3 .,, DI+ +chrM 235 A 3 .,, &I@ +chrM 236 C 3 .$,a +I$ +chrM 237 G 2 ,, II +chrM 238 G 2 ,, II +chrM 239 G 2 ,, II +chrM 240 A 2 ,, II +chrM 241 C 2 ,, I+ +chrM 242 A 2 ,, II +chrM 243 C 2 ,, II +chrM 244 A 3 ,,^:, II; +chrM 245 G 3 ,,, II* +chrM 246 C 3 ,,n II" +chrM 247 A 3 ,,, III +chrM 248 G 4 ,,,^:. IIII +chrM 249 T 4 ,,,. II)I +chrM 250 G 4 ,,,. II2I +chrM 251 A 4 ,,,. II(I +chrM 252 T 4 ,,,. II*I +chrM 253 A 4 ,,,. II7I +chrM 254 A 4 ,,,. II1I +chrM 255 A 4 ,,,. II?I +chrM 256 A 4 ,,,. II9I +chrM 257 A 4 ,,,. II?I +chrM 258 T 4 ,,,. II$I +chrM 259 T 5 ,,,.^:. II&II +chrM 260 A 5 ,,,.. II,II +chrM 261 A 5 ,,,.. II/II +chrM 262 G 5 ,,,.. II5II +chrM 263 C 5 ,,a.. II%II +chrM 264 T 5 ,$,$,.. II%II +chrM 265 A 3 ,.. )II +chrM 266 T 3 ,.. +II +chrM 267 G 4 ,..^:. *III +chrM 268 A 4 ,... EIII +chrM 269 A 4 ,... =III +chrM 270 C 4 a... ;III +chrM 271 G 4 ,... ;III +chrM 272 A 4 ,... 8@II +chrM 273 A 4 ,... 1III +chrM 274 A 4 ,... ICII +chrM 275 G 4 ,... IIII +chrM 276 T 4 ,... IIII +chrM 277 T 4 ,... IIII +chrM 278 C 4 ,... IIII +chrM 279 G 4 ,$... IIII +chrM 280 A 3 ... III +chrM 281 C 3 ... GII +chrM 282 T 3 ... III +chrM 283 A 3 .$.. IFI +chrM 284 A 3 ..^:, IAI +chrM 285 G 3 .., ;II +chrM 286 T 4 ..,^:. IIII +chrM 287 C 4 ..,. II4I +chrM 288 A 4 ..,. @III +chrM 289 T 4 ..,. IIII +chrM 290 A 4 ..,. @:II +chrM 291 T 4 ..,. IIAI +chrM 292 T 4 ..,. IIII +chrM 293 A 4 ..,. 8;II +chrM 294 A 4 .$.,. I<II +chrM 295 A 3 .,. 4II +chrM 296 T 3 .,. III +chrM 297 A 3 .,. BII +chrM 298 A 3 .,. CII +chrM 299 G 3 .,. III +chrM 300 G 3 .,. ;II +chrM 301 G 3 .,. III +chrM 302 T 3 .$,. III +chrM 303 T 2 ,. II +chrM 304 G 2 ,. II +chrM 305 G 2 ,. II +chrM 306 T 2 ,. II +chrM 307 A 2 ,. II +chrM 308 A 2 ,. II +chrM 309 A 2 ,. II +chrM 310 T 2 ,. II +chrM 311 T 2 ,. II +chrM 312 T 3 ,.^:. III +chrM 313 C 3 ,.. III +chrM 314 G 3 ,.. III +chrM 315 T 3 ,.. III +chrM 316 G 3 ,.. III +chrM 317 C 3 ,.. III +chrM 318 C 3 ,.. III +chrM 319 A 3 ,$.. III +chrM 320 G 2 .. II +chrM 321 C 2 .$. II +chrM 322 C 1 . I +chrM 323 A 1 . I +chrM 324 C 1 . I +chrM 325 C 1 . I +chrM 326 G 1 . I +chrM 327 C 1 . I +chrM 328 G 1 . I +chrM 329 G 1 . I +chrM 330 T 1 . I +chrM 331 C 1 . I +chrM 332 A 1 . I +chrM 333 T 1 . I +chrM 334 A 1 . I +chrM 335 C 1 . I +chrM 336 G 1 . I +chrM 337 A 1 . I +chrM 338 T 1 . I +chrM 339 T 1 . I +chrM 340 A 1 . I +chrM 341 A 1 . D +chrM 342 C 1 . I +chrM 343 C 1 . I +chrM 344 C 1 . I +chrM 345 A 1 . I +chrM 346 A 1 . ; +chrM 347 A 1 .$ 7 +chrM 360 C 1 ^:. I +chrM 361 G 1 . I +chrM 362 G 1 . I +chrM 363 C 1 . I +chrM 364 G 1 . I +chrM 365 T 1 . I +chrM 366 A 1 . I +chrM 367 A 1 . I +chrM 368 A 1 . I +chrM 369 G 1 . I +chrM 370 C 1 . I +chrM 371 G 1 . I +chrM 372 T 1 . I +chrM 373 G 1 . I +chrM 374 T 1 . I +chrM 375 C 1 . I +chrM 376 A 1 . I +chrM 377 A 1 . I +chrM 378 A 1 . I +chrM 379 G 1 . I +chrM 380 A 1 . I +chrM 381 C 1 T I +chrM 382 T 1 . I +chrM 383 A 1 . I +chrM 384 A 1 . I +chrM 385 T 1 . I +chrM 386 A 1 G I +chrM 387 C 1 . I +chrM 388 C 1 . I +chrM 389 A 2 .^:. II +chrM 390 A 3 ..^:. III +chrM 391 A 3 ... >II +chrM 392 A 3 ... III +chrM 393 T 3 ... III +chrM 394 A 3 ... III +chrM 395 A 3 .$.. III +chrM 396 A 2 .. II +chrM 397 G 2 .. II +chrM 398 T 2 .. EI +chrM 399 T 2 .. II +chrM 400 A 3 ..^:. III +chrM 401 A 3 ... III +chrM 402 A 3 ... III +chrM 403 A 3 ... III +chrM 404 C 3 ... III +chrM 405 C 3 ... III +chrM 406 C 3 ... EII +chrM 407 A 3 ... III +chrM 408 G 3 ... III +chrM 409 T 3 ... 0II +chrM 410 T 3 ... III +chrM 411 A 4 ...^:, IIII +chrM 412 A 4 ..., FIII +chrM 413 G 4 ..., IIIH +chrM 414 C 4 ...a III2 +chrM 415 C 4 TTTt III7 +chrM 416 G 5 ...,^:, II?7: +chrM 417 T 5 ...,, ;IIE@ +chrM 418 A 5 ...,, IIIII +chrM 419 A 5 ...,, IIIII +chrM 420 A 5 ...,, FIIII +chrM 421 A 5 ...,, IIIII +chrM 422 A 5 ...,, >IIII +chrM 423 G 6 ...,,^:, HII/I, +chrM 424 C 6 .$..a,, ;II-I: +chrM 425 T 5 .$.,,, IIIIF +chrM 426 A 5 .,,,^:, III@I +chrM 427 C 5 .,,,, III$I +chrM 428 A 5 .,,,, IIIII +chrM 429 A 5 .,,,, IIII. +chrM 430 C 5 .,,,a I%I5' +chrM 431 C 5 .,,,, I(I5< +chrM 432 A 5 .,,,, IIIII +chrM 433 A 5 .,,,, 0IIII +chrM 434 A 5 .,,,, =IIII +chrM 435 G 5 .$,,,, EIIII +chrM 436 T 4 ,,,, III5 +chrM 437 A 4 ,,,, IIII +chrM 438 A 4 ,,,, IIII +chrM 439 A 4 ,,,, IIII +chrM 440 A 4 ,,,, IIIF +chrM 441 T 6 ,,,,^:.^:. III;II +chrM 442 A 6 ,,,,.. IIIIII +chrM 443 G 6 ,,,,.. IIIIII +chrM 444 A 6 ,,,,.. IIIIII +chrM 445 C 6 ,,,,.. IIIIII +chrM 446 T 6 ,$,,,.. IIIIII +chrM 447 A 5 ,,,.. IIIII +chrM 448 C 5 ,,,.. IIIII +chrM 449 G 6 ,,,..^:, IIIII6 +chrM 450 A 6 ,,,.., IIIIII +chrM 451 A 6 ,$,,.., IIIIII +chrM 452 A 5 ,,.., IIIII +chrM 453 G 5 ,,.., IIIII +chrM 454 T 6 ,,..,^:, IIIIII +chrM 455 G 6 ,,..,, IIIIII +chrM 456 A 6 ,,..,, IIIIII +chrM 457 C 6 ,,..,, IIIII= +chrM 458 T 6 ,$,..,, IIIIII +chrM 459 T 5 ,..,, IIIII +chrM 460 T 5 ,..,, IIIII +chrM 461 A 5 ,$..,, IIIII +chrM 462 A 4 ..,, IIII +chrM 463 T 4 ..,, IIIC +chrM 464 A 4 ..,, IIII +chrM 465 C 4 ..,, IIII +chrM 466 C 4 ..,, IIII +chrM 467 T 4 ..,, II>? +chrM 468 C 4 ..,, IIII +chrM 469 T 4 ..,, IIIG +chrM 470 G 4 ..,, %III +chrM 471 A 4 ..,, 4;II +chrM 472 C 4 ..,, II3I +chrM 473 T 4 ..,, IIII +chrM 474 A 4 ..,, ;III +chrM 475 C 4 ..,, IIII +chrM 476 A 4 .$.$,, 32II +chrM 477 C 2 ,, II +chrM 478 G 2 ,, II +chrM 479 A 2 ,, II +chrM 480 T 3 ,,^:. III +chrM 481 A 3 ,,. III +chrM 482 G 3 ,,. III +chrM 483 C 4 ,,.^:, IIIE +chrM 484 T 4 ,$,., III9 +chrM 485 A 3 ,., III +chrM 486 A 3 ,., III +chrM 487 G 3 ,., III +chrM 488 A 3 ,., III +chrM 489 C 3 ,$., III +chrM 490 C 2 ., II +chrM 491 C 2 ., II +chrM 492 A 2 ., II +chrM 493 A 2 ., II +chrM 494 A 2 ., II +chrM 495 C 2 ., II +chrM 496 T 2 ., I2 +chrM 497 G 2 ., II +chrM 498 G 2 ., II +chrM 499 G 2 ., II +chrM 500 A 2 ., II +chrM 501 T 2 ., II +chrM 502 T 2 ., II +chrM 503 A 2 ., II +chrM 504 G 2 ., II +chrM 505 A 2 ., GI +chrM 506 T 2 ., II +chrM 507 A 2 ., II +chrM 508 C 2 ., II +chrM 509 C 2 ., II +chrM 510 C 3 .,^:. III +chrM 511 C 3 .,. III +chrM 512 A 3 .,. 6II +chrM 513 C 3 .,. III +chrM 514 T 3 .,. III +chrM 515 A 3 .$,. III +chrM 516 T 2 ,. II +chrM 517 G 2 ,. II +chrM 518 C 3 ,$.^:. III +chrM 519 T 2 .. II +chrM 520 T 3 ..^:, III +chrM 521 A 3 .., III +chrM 522 G 3 .., II, +chrM 523 C 3 .., III +chrM 524 C 3 .., II7 +chrM 525 C 3 .., III +chrM 526 T 3 .., II? +chrM 527 A 3 .., III +chrM 528 A 3 .., III +chrM 529 A 3 .., FII +chrM 530 C 3 .., II+ +chrM 531 T 3 .., III +chrM 532 A 3 .., :II +chrM 533 A 3 .., DGI +chrM 534 A 3 .., III +chrM 535 A 3 .., ?CI +chrM 536 T 3 .., III +chrM 537 A 3 .., 9II +chrM 538 G 3 .., III +chrM 539 C 3 .., III +chrM 540 T 3 .., III +chrM 541 T 3 .., III +chrM 542 A 4 ..,^:. IIII +chrM 543 C 4 ..,. IIII +chrM 544 C 4 ..,. IIII +chrM 545 A 4 N$.,. "III +chrM 546 C 3 .,. III +chrM 547 A 3 .,. DII +chrM 548 A 3 .,. EII +chrM 549 C 3 .,. III +chrM 550 A 3 .,. III +chrM 551 A 3 .,. 6II +chrM 552 A 3 .,. GII +chrM 553 G 3 .$,. ?II +chrM 554 C 2 ,. I< +chrM 555 T 2 ,$. II +chrM 556 A 2 .^:. II +chrM 557 T 2 .. II +chrM 558 T 2 .. II +chrM 559 C 2 .. II +chrM 560 G 2 .. II +chrM 561 C 2 .. II +chrM 562 C 2 .. II +chrM 563 A 2 .. CI +chrM 564 G 2 .. II +chrM 565 A 2 .. GI +chrM 566 G 2 .. II +chrM 567 T 2 .. /I +chrM 568 A 2 .. DI +chrM 569 C 2 .. II +chrM 570 T 2 .. II +chrM 571 A 2 .. II +chrM 572 C 2 .. FI +chrM 573 T 2 .. 9I +chrM 574 A 2 .. II +chrM 575 G 2 .. II +chrM 576 C 2 .. II +chrM 577 A 3 .$.^:. III +chrM 578 A 2 .. II +chrM 579 C 2 .. II +chrM 580 A 3 ..^:, III +chrM 581 G 3 .., III +chrM 582 C 3 .., II? +chrM 583 C 3 ..a II- +chrM 584 T 3 .., IIH +chrM 585 A 3 .., III +chrM 586 A 3 .., III +chrM 587 A 4 ..,^:, IIII +chrM 588 A 4 ..,, IIII +chrM 589 C 4 ..,, IIII +chrM 590 T 4 ..,, II.5 +chrM 591 C 4 .$.,, II<I +chrM 592 A 3 .,, III +chrM 593 A 3 .,, III +chrM 594 A 3 .,, III +chrM 595 G 3 .,, III +chrM 596 G 3 .,, III +chrM 597 A 3 .,, :EI +chrM 598 C 3 .,, III +chrM 599 T 4 .,,^:. II@I +chrM 600 T 4 .,,. IIII +chrM 601 G 4 .,,. IIII +chrM 602 G 4 .,,. IIII +chrM 603 C 4 .,,. IIII +chrM 604 G 4 .,,. IIII +chrM 605 G 4 .,,. IIII +chrM 606 T 4 .,,. 5III +chrM 607 G 4 .,,. IIII +chrM 608 C 4 .,,. *III +chrM 609 T 5 .,,.^:, ?IIII +chrM 610 T 5 .,,., IIII8 +chrM 611 T 5 .,,., IIIII +chrM 612 A 5 T$,,., 3IIII +chrM 613 C 4 ,,., III) +chrM 614 A 4 ,,., IIII +chrM 615 T 4 ,$,., IIII +chrM 616 C 3 ,., III +chrM 617 C 3 ,., III +chrM 618 C 3 ,., III +chrM 619 T 3 ,., IF9 +chrM 620 C 3 ,., II7 +chrM 621 T 3 ,., III +chrM 622 A 3 ,$., I7I +chrM 623 G 2 ., II +chrM 624 A 2 ., 9I +chrM 625 G 2 ., II +chrM 626 G 2 ., II +chrM 627 A 2 ., 2I +chrM 628 G 2 ., II +chrM 629 C 2 ., II +chrM 630 C 2 ., II +chrM 631 T 2 ., II +chrM 632 G 2 ., II +chrM 633 T 2 ., II +chrM 634 T 2 .$, II +chrM 635 C 1 , I +chrM 636 C 1 , I +chrM 637 A 1 , I +chrM 638 T 1 , I +chrM 639 A 1 , I +chrM 640 A 1 , I +chrM 641 T 1 , I +chrM 642 C 1 , I +chrM 643 G 1 , I +chrM 644 A 1 ,$ I +chrM 646 A 1 ^:. I +chrM 647 A 1 . I +chrM 648 A 1 . I +chrM 649 C 2 .^:, II +chrM 650 C 2 ., II +chrM 651 C 2 ., II +chrM 652 C 3 .,^:, II) +chrM 653 G 3 .,, II2 +chrM 654 A 3 .,, III +chrM 655 T 4 .,,^:. II*I +chrM 656 A 4 .,,. IIII +chrM 657 A 4 .,,. IIII +chrM 658 A 4 .,,. IIII +chrM 659 C 4 .,,. IIII +chrM 660 C 4 .,,. IIII +chrM 661 C 4 .,,. IIII +chrM 662 C 4 .,,. IIFI +chrM 663 A 4 .,,. =IDI +chrM 664 C 4 .,,. II6I +chrM 665 C 5 .,,.^:, IIIII +chrM 666 A 5 .,,., BIIII +chrM 667 T 5 .,,., II5I+ +chrM 668 C 5 .,,., IIIII +chrM 669 C 5 .,,., IIIII +chrM 670 C 5 .,a., II.II +chrM 671 T 5 .,,., IIIIA +chrM 672 T 6 .,,.,^:. FI9I.I +chrM 673 G 6 .,,.,. IIIIII +chrM 674 C 6 .,,.,. IIIIII +chrM 675 T 6 .,,.,. IIIIII +chrM 676 A 6 .,,.,. ,IIEII +chrM 677 A 7 .,,.,.^:. 3II;III +chrM 678 T 7 .,,.,.. IIIIDII +chrM 679 T 7 .,,.,.. CIIIIII +chrM 680 C 7 .,,.,.. IIIIIII +chrM 681 A 7 .$,,.,.. 9IIIIII +chrM 682 G 6 ,,.,.. II$III +chrM 683 C 6 ,,.,.. IIIIII +chrM 684 C 6 ,$,.,.. IIIIII +chrM 685 T 5 ,.,.. IIIII +chrM 686 A 5 ,.,.. IIIII +chrM 687 T 5 ,$.,.. IIIII +chrM 688 A 4 .,.. IIII +chrM 689 T 4 .,.. IIII +chrM 690 A 4 .$,.. IIII +chrM 691 C 3 ,.. III +chrM 692 C 3 ,.. III +chrM 693 G 4 ,..^:, IIII +chrM 694 C 4 ,.., IIII +chrM 695 C 4 ,.., IIII +chrM 696 A 4 ,.., IIII +chrM 697 T 4 ,.., IIII +chrM 698 C 4 ,.., IIII +chrM 699 T 4 ,.., IIII +chrM 700 T 4 ,$.., IIII +chrM 701 C 3 .., III +chrM 702 A 3 .., III +chrM 703 G 3 .., 2II +chrM 704 C 3 .., III +chrM 705 A 3 N., "II +chrM 706 A 3 .., I5I +chrM 707 A 3 .$., GII +chrM 708 C 2 ., II +chrM 709 C 2 ., II +chrM 710 C 2 ., II +chrM 711 T 2 ., II +chrM 712 A 2 .$, II +chrM 713 A 1 , I +chrM 714 A 1 , I +chrM 715 C 1 , I +chrM 716 A 1 , I +chrM 717 A 1 , I +chrM 718 G 1 , I +chrM 719 G 2 ,^:, I& +chrM 720 T 2 ,g I$ +chrM 721 A 2 ,, I3 +chrM 722 C 2 ,, I$ +chrM 723 C 2 ,t I& +chrM 724 G 2 ,, I) +chrM 725 A 2 ,, II +chrM 726 A 3 ,,^:. III +chrM 727 G 3 ,,. III +chrM 728 T 3 ,$,. III +chrM 729 A 2 ,. II +chrM 730 A 2 n. "I +chrM 731 G 2 ,. II +chrM 732 C 3 a.^:. $II +chrM 733 A 3 ,.. III +chrM 734 C 3 ,.. %II +chrM 735 A 3 ,.. III +chrM 736 A 3 ,.. *II +chrM 737 A 3 ,.. III +chrM 738 T 3 ,.. III +chrM 739 A 3 ,.. III +chrM 740 T 3 ,.. III +chrM 741 C 3 ,.. III +chrM 742 C 3 ,.. III +chrM 743 A 3 ,.. III +chrM 744 A 3 ,.. III +chrM 745 C 3 ,.. III +chrM 746 A 3 ,.. IIE +chrM 747 T 3 ,.. III +chrM 748 A 3 ,.. III +chrM 749 A 3 ,.. III +chrM 750 A 3 ,.. III +chrM 751 A 3 ,.. IAI +chrM 752 A 3 ,.. III +chrM 753 C 3 ,.. III +chrM 754 G 3 ,$.. III +chrM 755 T 2 .. II +chrM 756 T 3 ..^:, III +chrM 757 A 3 .., III +chrM 758 G 3 .., III +chrM 759 G 3 .., III +chrM 760 T 3 .., =II +chrM 761 C 3 .$., IID +chrM 762 A 2 ., =I +chrM 763 A 2 ., EI +chrM 764 G 2 ., II +chrM 765 G 2 ., II +chrM 766 T 2 ., :I +chrM 767 G 3 .$,^:, III +chrM 768 T 2 ,, I> +chrM 769 A 3 ,,^:, III +chrM 770 G 3 ,,, III +chrM 771 C 3 ,,, IHI +chrM 772 C 3 ,a, I)/ +chrM 773 C 3 ,,, I7I +chrM 774 A 4 ,,,^:. II:I +chrM 775 T 4 ,,,. IH.I +chrM 776 G 4 ,,,. IIII +chrM 777 G 4 ,,,. IIII +chrM 778 G 4 ,,,. IIII +chrM 779 A 4 ,,,. IIAI +chrM 780 T 4 ,,,. IIGI +chrM 781 G 4 ,,,. IIII +chrM 782 G 4 ,,,. IIII +chrM 783 A 4 ,,,. IIII +chrM 784 G 4 ,,,. IIII +chrM 785 A 4 ,,,. IIII +chrM 786 G 4 ,,,. IIII +chrM 787 A 4 ,,,. IIII +chrM 788 A 4 ,,,. IIII +chrM 789 A 4 ,,,. IIII +chrM 790 T 5 ,,,.^:. IIIII +chrM 791 G 5 ,$,,.. IIIII +chrM 792 G 4 ,,.. IIII +chrM 793 G 4 ,,.. IIII +chrM 794 C 4 ,,.. IIII +chrM 795 T 4 ,,.. IIII +chrM 796 A 4 ,,.. IIII +chrM 797 C 4 ,,.. IIII +chrM 798 A 4 ,,.. IIII +chrM 799 T 4 ,,.. IIII +chrM 800 T 4 ,,.. IIII +chrM 801 T 4 ,,.. IIII +chrM 802 T 4 ,$,.. IIII +chrM 803 C 3 ,.. III +chrM 804 T 3 ,$.. III +chrM 805 A 2 .. II +chrM 806 C 3 ..^:. III +chrM 807 C 3 ... III +chrM 808 C 3 ... III +chrM 809 T 3 .$.. III +chrM 810 A 3 ..^:, III +chrM 811 A 3 .., III +chrM 812 G 3 .., II7 +chrM 813 A 3 .., III +chrM 814 A 3 .., III +chrM 815 C 3 .., III +chrM 816 A 3 .., III +chrM 817 A 3 .., III +chrM 818 G 3 .., III +chrM 819 A 3 .., III +chrM 820 A 3 .., &II +chrM 821 C 3 .., III +chrM 822 T 3 .., III +chrM 823 T 3 ..n II" +chrM 824 T 3 .., III +chrM 825 A 3 .$., III +chrM 826 A 3 .,^:. III +chrM 827 C 3 .,. III +chrM 828 C 3 .,. III +chrM 829 C 4 .,.^:, IIII +chrM 830 G 4 .,., IIII +chrM 831 G 4 .,., IIII +chrM 832 A 4 .,., IIII +chrM 833 C 4 .,., IIII +chrM 834 G 4 .,., IIII +chrM 835 A 4 .,., IIII +chrM 836 A 4 .,., 8III +chrM 837 A 4 .,., IIII +chrM 838 G 4 .,., IIII +chrM 839 T 5 .,.,^:, 4:IIG +chrM 840 C 5 .,.,, IIIII +chrM 841 T 5 .$,.,, IIIII +chrM 842 C 4 ,.,, IIII +chrM 843 C 4 ,.,, IIII +chrM 844 A 4 ,.,, IIII +chrM 845 T 4 ,$.,, IIII +chrM 846 G 3 .,, @II +chrM 847 A 3 .,, III +chrM 848 A 3 .,, III +chrM 849 A 3 .,, III +chrM 850 C 3 .,, III +chrM 851 T 3 .,, III +chrM 852 G 3 .,, III +chrM 853 G 3 .,, III +chrM 854 A 3 .,, EII +chrM 855 G 3 .,, DII +chrM 856 A 3 .,, III +chrM 857 C 3 .,, III +chrM 858 T 4 .,,^:, IIIA +chrM 859 A 4 .,,, @III +chrM 860 A 4 .,,, IIII +chrM 861 A 4 .$,,, EIII +chrM 862 G 3 ,,, III +chrM 863 G 3 ,,, III +chrM 864 A 3 ,$,, III +chrM 865 G 2 ,, II +chrM 866 G 2 ,, II +chrM 867 A 2 ,, II +chrM 868 T 2 ,, II +chrM 869 T 2 ,, II +chrM 870 T 2 ,, II +chrM 871 A 2 ,, II +chrM 872 G 2 ,, II +chrM 873 C 2 ,, II +chrM 874 A 2 ,$, II +chrM 875 G 1 , I +chrM 876 T 1 , I +chrM 877 A 1 , I +chrM 878 A 1 , I +chrM 879 A 1 , I +chrM 880 T 1 , I +chrM 881 T 1 , I +chrM 882 A 1 , I +chrM 883 A 1 , I +chrM 884 G 1 , I +chrM 885 A 1 , I +chrM 886 A 1 , I +chrM 887 T 1 , ( +chrM 888 A 1 , I +chrM 889 G 1 , I +chrM 890 A 1 , I +chrM 891 G 1 , I +chrM 892 A 1 , I +chrM 893 G 1 ,$ I +chrM 898 A 1 ^:, I +chrM 899 T 2 ,^:. /I +chrM 900 T 2 ,. 7I +chrM 901 G 2 ,. CI +chrM 902 A 2 ,. II +chrM 903 A 2 ,. II +chrM 904 T 2 ,. II +chrM 905 C 3 ,.^:, III +chrM 906 A 3 ,., III +chrM 907 G 3 ,., III +chrM 908 G 3 ,., III +chrM 909 C 3 ,., III +chrM 910 C 3 ,., III +chrM 911 A 4 ,.,^:, IIII +chrM 912 T 4 ,.,, IIEG +chrM 913 G 4 ,.,, III: +chrM 914 A 4 ,.,, IIII +chrM 915 A 4 ,.,, IIII +chrM 916 G 4 ,.,, III5 +chrM 917 C 4 ,.,, III5 +chrM 918 G 4 ,.,, IIII +chrM 919 C 4 ,.,, III< +chrM 920 G 4 ,.,, IIII +chrM 921 C 4 ,.,, IIII +chrM 922 A 4 ,.,, IIII +chrM 923 C 4 ,.,, III8 +chrM 924 A 4 ,.,, IFII +chrM 925 C 4 ,.,, IIII +chrM 926 A 4 ,.,, IIII +chrM 927 C 4 ,.,, IIII +chrM 928 C 5 ,.,,^:, IIII: +chrM 929 G 5 ,.,,, IIIE: +chrM 930 C 5 ,.,,, IIIII +chrM 931 C 5 ,.,,, IIIIF +chrM 932 C 5 ,.,,, IIIIC +chrM 933 G 5 ,$.,,, I?II: +chrM 934 T 4 .$,,, 4II> +chrM 935 C 3 ,,, III +chrM 936 A 3 ,,, III +chrM 937 C 3 ,,, II1 +chrM 938 C 3 ,,, III +chrM 939 C 3 ,,, III +chrM 940 T 3 ,$,, III +chrM 941 C 2 ,, II +chrM 942 C 2 ,, I' +chrM 943 T 2 ,, II +chrM 944 T 2 ,, II +chrM 945 A 2 ,, II +chrM 946 A 2 ,$, II +chrM 947 A 1 , I +chrM 948 T 1 , I +chrM 949 A 1 , I +chrM 950 T 1 , I +chrM 951 C 1 , I +chrM 952 A 1 , I +chrM 953 C 1 , I +chrM 954 A 1 , I +chrM 955 A 2 ,^:. II +chrM 956 A 2 ,. II +chrM 957 T 2 ,. II +chrM 958 C 3 ,.^:. III +chrM 959 A 3 ,.. III +chrM 960 T 3 ,.. III +chrM 961 A 3 ,.. III +chrM 962 A 3 ,.. III +chrM 963 C 4 ,$..^:. IIII +chrM 964 A 3 ... I(; +chrM 965 T 3 ... III +chrM 966 A 4 ...^:. IIII +chrM 967 A 4 .... IIII +chrM 968 C 4 .... IEII +chrM 969 A 4 .... IIII +chrM 970 T 4 .... IIII +chrM 971 A 4 .... IIII +chrM 972 A 4 .... IIII +chrM 973 A 4 .... II0I +chrM 974 A 5 ....^:. IIIII +chrM 975 C 5 ..... IIIII +chrM 976 C 5 ..... IIIII +chrM 977 G 5 ..... IIIII +chrM 978 T 5 ..... IIIII +chrM 979 G 5 ..... I0III +chrM 980 A 5 ..... IIII4 +chrM 981 C 5 ..... IIIII +chrM 982 C 5 ..... IIIII +chrM 983 C 5 ..... IIIII +chrM 984 A 5 ..... -IGII +chrM 985 A 5 ..... 4GIII +chrM 986 A 5 ..... BDGII +chrM 987 C 5 ..... IDIII +chrM 988 A 5 ..... @<III +chrM 989 T 5 ..... IIIII +chrM 990 A 5 .$.... I@III +chrM 991 T 4 .... IICI +chrM 992 G 4 T... )III +chrM 993 A 4 .$... ?ICI +chrM 994 A 3 ... III +chrM 995 A 3 ... III +chrM 996 G 3 ... III +chrM 997 G 3 ... III +chrM 998 A 3 .$.. 4II +chrM 999 G 3 ..^:. III +chrM 1000 A 3 ... III +chrM 1001 C 3 .$.. III +chrM 1002 A 2 .. II +chrM 1003 A 2 .. II +chrM 1004 G 2 .. II +chrM 1005 T 2 .. II +chrM 1006 C 2 .. II +chrM 1007 G 2 .. CI +chrM 1008 T 2 .. II +chrM 1009 A 2 .$. II +chrM 1010 A 1 . I +chrM 1011 C 1 . I +chrM 1012 A 1 . I +chrM 1013 A 1 . I +chrM 1014 G 1 . I +chrM 1015 G 1 . I +chrM 1016 T 1 . I +chrM 1017 A 1 . I +chrM 1018 A 1 . I +chrM 1019 G 1 . I +chrM 1020 T 1 . I +chrM 1021 A 1 . I +chrM 1022 T 1 . I +chrM 1023 A 1 . I +chrM 1024 C 1 . I +chrM 1025 C 1 . I +chrM 1026 G 1 . I +chrM 1027 G 1 . I +chrM 1028 A 1 . I +chrM 1029 A 1 . I +chrM 1030 G 1 . I +chrM 1031 G 2 .^:. II +chrM 1032 T 2 .. EI +chrM 1033 G 2 .. II +chrM 1034 T 2 .$. II +chrM 1035 A 2 .^:. II +chrM 1036 C 2 .. II +chrM 1037 T 2 .. II +chrM 1038 T 2 .. II +chrM 1039 G 2 .. II +chrM 1040 G 2 .. II +chrM 1041 A 2 .. II +chrM 1042 T 2 .. II +chrM 1043 A 3 ..^:, III +chrM 1044 A 3 .., III +chrM 1045 C 3 .., II7 +chrM 1046 C 3 .., II- +chrM 1047 A 3 .., III +chrM 1048 A 3 .., III +chrM 1049 A 3 .., III +chrM 1050 G 3 .., III +chrM 1051 T 3 .., III +chrM 1052 G 3 .., III +chrM 1053 T 3 .., GII +chrM 1054 A 3 .., III +chrM 1055 G 3 .., :II +chrM 1056 C 3 ..a HI% +chrM 1057 T 3 .., III +chrM 1058 T 3 .., III +chrM 1059 A 3 .., BII +chrM 1060 A 3 .., GII +chrM 1061 A 3 .., HII +chrM 1062 C 3 .., III +chrM 1063 A 3 .., DII +chrM 1064 A 3 .., BII +chrM 1065 A 3 .., 1II +chrM 1066 G 3 .$., &II +chrM 1067 C 2 ., II +chrM 1068 A 2 ., II +chrM 1069 T 2 ., II +chrM 1070 C 2 .$, II +chrM 1071 C 1 , I +chrM 1072 A 1 , I +chrM 1073 G 1 , I +chrM 1074 C 1 , I +chrM 1075 T 1 , I +chrM 1076 T 1 , I +chrM 1077 A 1 , I +chrM 1078 C 1 ,$ I +chrM 1090 T 1 ^:, I +chrM 1091 T 1 , I +chrM 1092 C 1 n " +chrM 1093 A 1 , I +chrM 1094 C 1 , I +chrM 1095 T 1 , 7 +chrM 1096 C 1 a B +chrM 1097 A 1 , I +chrM 1098 A 1 , I +chrM 1099 A 1 , I +chrM 1100 A 1 , I +chrM 1101 T 1 , I +chrM 1102 G 2 ,^:, (I +chrM 1103 A 2 ,, II +chrM 1104 A 2 ,, I+ +chrM 1105 C 2 ,, .I +chrM 1106 A 2 ,, 8I diff -r 5cc5e94345b8 -r a9e25e05ae8d test-data/column_join_in1.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/column_join_in1.pileup Fri Mar 26 12:11:01 2010 -0400 @@ -0,0 +1,30 @@ +chrM 1 A G 25 0 25 1 ^:. I +chrM 2 C T 25 0 25 2 .N I$ +chrM 3 T G 27 0 25 2 .. II +chrM 4 G C 36 0 25 3 .^:.^:. II+ +chrM 5 T A 38 0 25 3 ... III +chrM 6 T A 39 0 25 4 .N.. I$II +chrM 7 G C 43 0 25 5 ...^:.^:. IIIII +chrM 8 A C 46 0 25 6 .....^:. IIIIII +chrM 9 T G 53 0 25 8 ..G...^:.^:. IIIII$II +chrM 10 T G 56 0 25 9 ........^:. IIIIIIIII +chrM 11 C G 57 0 25 10 .........^:. IIIIIIIIII +chrM 12 T C 61 0 25 11 ..........^:. IIIIIIIIIII +chrM 13 T G 79 0 25 15 .........^:.^:.^:.^:.^:.^:. IIIIIIIIIIII#II +chrM 14 A C 58 0 25 18 .......G.........^:. BIIIIIII+IIIIIIIII +chrM 15 G A 87 0 25 19 ..N...............^:.^:. DIIIIII$(IIIIIIIIIII +chrM 16 G C 88 0 25 20 .........N.......... IIIIIIIIIIIIIIIIIIII +chrM 17 A C 88 0 25 20 .........G.......... 9IIIIIIIIIIIIIIIIIII +chrM 18 G A 89 0 25 20 ...A................ @IIIIIIIIIIIIIIIIIII +chrM 19 G T 58 0 25 20 ....T.............GG IIIIIIIIIIIIIIIIII'A +chrM 20 T C 55 0 25 20 .........C........C. IIIIIIIIIIIIIII2II#$ +chrM 21 C T 87 0 25 20 ..........G......... IIIIIIIIIIIIIIIIIIII +chrM 22 C A 87 0 25 20 ..........N......... IIIIIIIIIIIIIIAIIIII +chrM 23 A G 87 0 25 20 .....T.............. 9IIIIIIIIII0IIIIIIII +chrM 24 A T 89 0 25 20 .....N..N........... III$IIII"IIIIICII#II +chrM 25 G A 57 0 25 21 ...A................^:. A@.$IIIIIIIFIIIIIIIII +chrM 26 C G 58 0 25 22 ...N....A............. IIHIDII&IIIIII@IIIIII +chrM 27 T A 99 0 25 23 ....................^:.^:.^:. IE8IFIII9IIIIIIIIIIIIII +chrM 28 A C 99 0 25 24 ..G..................... 1FIIIIIIIIIIIIIIIIDEIIII +chrM 29 G C 58 0 25 25 ........C.........NN.... ;IIIIII+HII=III$III""IIII +chrM 30 T T 65 0 25 25 ...C....................^:. ;I?&IAI0IIIIIIIIIIIIIIIII diff -r 5cc5e94345b8 -r a9e25e05ae8d test-data/column_join_in2.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/column_join_in2.pileup Fri Mar 26 12:11:01 2010 -0400 @@ -0,0 +1,30 @@ +chrM 1 T G 25 0 25 1 ^:. I +chrM 2 C A 25 0 25 1 . I +chrM 3 C A 25 0 25 2 .. I+ +chrM 4 G A 36 0 25 3 .^:.^:. II+ +chrM 5 A T 36 0 25 3 ... IDI +chrM 6 A G 36 0 25 4 ..T. IIBI +chrM 7 C G 42 0 25 5 ...^:.^:. ID@II +chrM 8 T T 45 0 25 6 .....^:. III$BI +chrM 9 C A 51 0 25 8 ......^:.^:. $#III+III +chrM 10 G G 54 0 25 9 ........^:. III$III#I +chrM 11 T C 57 0 25 10 .........^:. IIIDBIIIII +chrM 12 A T 60 0 25 11 ..........^:. IIIIIIIII$I +chrM 13 A T 78 0 25 18 ..A.........^:.^:.^:.^:.^:.^:. III#$IIIIII+IIDIIB +chrM 14 G A 56 0 25 19 ........T.........^:. BIIIIIII+IIII$IBIII +chrM 15 G A 87 0 25 20 ..................^:.^:. DIIIIIII(IIIIIIIIIII +chr1 1 T T 87 0 25 20 .............T...... IIIIIIIIIIII$DIIIIII +chr1 2 A T 87 0 25 20 ......G............. 9IIIIIIIIIIIIICBIIII +chr1 3 A G 87 0 25 20 ....A............... @IIIIIIIII#IIII#IIII +chr1 4 A T 55 0 25 20 ..................GG IIIII@II$IIIIIIIII'A +chr1 5 C A 54 0 25 20 .......A..........C. IIIIIIIIIDIIIII2II#$ +chr1 6 G T 87 0 25 20 .............A...... IIIIIIIBIIIIII#IIIII +chr1 7 A C 87 0 25 20 ..........C......... IIIII+IIIIIIIIAIIIII +chr1 8 G A 87 0 25 20 ....G.........T..... 9IIIIIIIIII0IIIIIIII +chr1 9 A T 87 0 25 20 ........N........... IIII$III"IIIIICIIIII +chr1 10 G A 57 0 25 21 ...A................^:. A@.$IIIIIIIFIIIIIIIII +chr1 11 C A 57 0 25 22 ....G...A............. IIHIDII&IIIIII#III$II +chr1 12 T A 99 0 25 24 .....................^:.^:.^:. IE8IFIII9IIIIIIIIIIIIIII +chr1 13 A C 99 0 25 25 ...N..................... 1FIIIIIIIIIIIIIIIIDEII$II +chr1 14 G C 55 0 25 25 ....G..............NN.... ;IIIBIII+HII=IIIIII""IIII +chr1 15 T G 68 0 25 28 ...C.......N............^:. ;I?&IAI0IIIIIII@II#$II@II diff -r 5cc5e94345b8 -r a9e25e05ae8d test-data/column_join_in3.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/column_join_in3.pileup Fri Mar 26 12:11:01 2010 -0400 @@ -0,0 +1,30 @@ +chr1 1 G G 25 0 25 1 ^:. I +chr1 2 T T 25 0 25 1 . I +chr1 3 T T 27 0 25 1 . I +chr1 4 A A 36 0 25 2 .^:. I+ +chr1 5 A A 36 0 25 3 ... III +chr1 6 T T 36 0 25 4 .N.. II#I +chr1 7 G G 42 0 25 5 ...^:.^:. IIIII +chr1 8 T T 45 0 25 6 .....^:. IIIIII +chr1 9 A A 51 0 25 7 .....^:.^:. IBIIIII +chr1 10 G G 54 0 25 9 ........^:. IIIIIIIII +chr1 11 C C 57 0 25 10 .........^:. IIIIIIII"I +chr1 12 T T 60 0 25 11 ..........^:. IIIIIIDIIII +chr1 13 T T 78 0 25 17 ...........^:.^:.^:.^:.^:.^:. IIII"$IIIIIIIIIII +chr1 14 A A 56 0 25 18 .......G.........^:. BIIIIIII+IIIIIIIII +chr1 15 A A 87 0 25 20 ....N.............^:.^:. DIII$III(IIIIIIIIIII +chr4 1 T T 90 0 25 20 ..........N......... IIIIIIIII$IIIIIIIIII +chr4 2 A A 87 0 25 20 .......C............ 9IIIIIIIII"IIIIIIIII +chr4 3 A A 34 0 25 20 ......G............. @IIIIIIIIIIII#IIIIII +chr4 4 T T 55 0 25 21 ...........N.......GG IIIII@IIIIIIIIIIIII'A +chr4 5 A A 54 0 25 21 ...N...............C. IIII"IIIIIIIIIII2II#$ +chr4 6 T T 87 0 25 21 ................N.... IIIIIIII$IIIIIIIIIIII +chr4 7 A A 80 0 25 21 .....G............... III$IIIIIIIIIIIAIIIII +chr4 8 A A 87 0 25 22 ..N................... 9IIIIIIIIII0IIIII"$III +chr4 9 A A 87 0 25 22 .GG.......N........... IIII$IIIII"IIIIICIIIII +chr4 10 G G 57 0 25 23 .....A................^:. A@.$IIIIIIIIIFIIIIIIIII +chr4 11 C C 57 0 25 25 .......A.....GN.......... IIHIDII&III#IIIIIIIIIIIII +chr4 12 A A 99 0 25 26 .......................^:.^:.^:. IE8IFIII9IIIIIII$IIIIIIIII +chr4 13 A A 99 0 25 27 ........N.................. 1FIIIIII$IIIIIIIIIIIIDEIIII +chr4 14 G G 55 0 25 28 ..N...................NN.... ;III$I#IIII+HII=IIIIII""IIII +chr4 15 G G 68 0 25 30 ...C....N..G.................^:. ;I?&IAI0IIIIIII$#I$@IIIIIIIIII diff -r 5cc5e94345b8 -r a9e25e05ae8d test-data/column_join_in4.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/column_join_in4.pileup Fri Mar 26 12:11:01 2010 -0400 @@ -0,0 +1,25 @@ +chr2 1 T 6 .C..., I$$III +chr2 2 G 6 ..N.., III@II +chr2 3 C 7 ..C..., I$IIIII +chr2 4 G 7 .G...., I#IIIII +chr2 5 G 7 ...N.., IIII#BI +chr2 6 A 7 ..T..., I$IDIII +chr2 7 T 8 ...C..., IIIBD$II +chr2 8 A 8 ..A...., IBI#IIII +chr2 9 C 9 .GA..N.., I$IBIII#I +chr2 10 T 9 ........, I$II#IIII +chr2 11 C 10 .>>..T..., IIII@I$I$I +chr2 12 G 10 .N..G...., III$IIIIII +chr2 13 A 11 ....A..T.., IIIIII#I@II +chr1 1 C 1 ^:. I +chr1 2 G 2 .^:. $I +chr1 3 A 2 .. I% +chr1 4 C 2 .. I$ +chr1 5 T 3 ..^:. I#I +chr1 6 G 3 ..^:, I#I +chr1 7 C 4 .N., IIII +chr1 8 A 4 ..., I$II +chr1 9 T 5 ..C., I#IDI +chr1 10 G 5 N..., IBII@ +chr1 11 A 5 .C.., I$II# +chr1 12 C 5 ..N., I$III diff -r 5cc5e94345b8 -r a9e25e05ae8d test-data/column_join_in5.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/column_join_in5.pileup Fri Mar 26 12:11:01 2010 -0400 @@ -0,0 +1,25 @@ +chr1 42 T 1 ^:. I +chr1 43 G 2 .^:. $I +chr1 44 T 2 .. I% +chr1 45 C 3 ..^:. III +chr1 46 G 3 ..^:. I#I +chr1 47 T 4 ...^:, I#II +chr1 48 A 4 .N., IIII +chr1 49 C 5 ...., IIIII +chr1 50 A 5 ..G., IIIDI +chr1 51 A 5 A..., IBIII +chr1 52 A 5 ...., IIII# +chr1 53 G 5 ..N., I$III +chr2 77 C 6 .G..., I$$III +chr2 78 G 6 ..N.., III@II +chr2 79 T 7 ..N..., I$IIIII +chr2 80 C 7 .G...., I#IIIII +chr2 81 G 7 ...A.., IIII#BI +chr2 82 A 8 ...G..., I$IDIIII +chr2 83 A 8 ...T..., IIIBD$II +chr2 84 T 8 ..A...., IBI#IIII +chr2 85 G 8 .GA...., IIBIII#I +chr2 86 C 9 ........, I$II#IIII +chr2 87 G 9 ....T..., IIIII$I$I +chr2 88 G 10 .N..G...., III$IIIIII +chr2 89 G 10 ...A..T.., IIIII#I@II diff -r 5cc5e94345b8 -r a9e25e05ae8d test-data/column_join_in6.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/column_join_in6.pileup Fri Mar 26 12:11:01 2010 -0400 @@ -0,0 +1,25 @@ +chr1 42 C 1 ^:. I +chr1 43 C 2 .^:. II +chr1 44 T 2 .. II +chr1 45 A 3 ..^:. III +chr1 46 G 4 ...^:. IIII +chr1 47 A 5 ....^:, IIIII +chr1 48 T 5 ...N, I#III +chr1 49 G 5 ...., IIIII +chr1 50 A 5 .G.., IIIII +chr1 51 G 5 ...., IIIII +chr2 52 T 5 .N.., II$II +chr2 53 A 5 ...., IIIII +chr2 54 T 5 ...., IIIII +chr2 55 T 5 ...., IIIII +chr2 56 C 5 ...., IIIBI +chr2 57 T 5 ...., IDIII +chr2 58 T 6 .N..., IIIIII +chr2 59 A 6 ....., IIII$I +chr3 60 C 6 ...G., I#IIII +chr3 61 T 6 ..N.., IIIIII +chr3 62 C 6 ...A., IIIIII +chr3 63 C 7 .N...., IIIIIII +chr3 64 A 7 ...G.., IIIII$I +chr3 65 T 7 ...AA., IIIII@@ +chr3 66 A 7 ....N., IIIIIII diff -r 5cc5e94345b8 -r a9e25e05ae8d test-data/column_join_in7.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/column_join_in7.pileup Fri Mar 26 12:11:01 2010 -0400 @@ -0,0 +1,32 @@ +chr2 1 T 6 .C..., I$$III +chr2 2 G 6 ..N.., III@II +chr2 3 C 7 ..C..., I$IIIII +chr2 4 G 7 .G...., I#IIIII +chr2 5 G 7 ...N.., IIII#BI +chr2 6 A 7 ..T..., I$IDIII +chr2 7 T 8 ...C..., IIIBD$II +chr2 8 A 8 ..A...., IBI#IIII +chr2 9 C 9 .GA..N.., I$IBIII#I +chr2 10 T 9 ........, I$II#IIII +chr2 11 C 10 .>>..T..., IIII@I$I$I +chr2 12 G 10 .N..G...., III$IIIIII +chr2 13 A 11 ....A..T.., IIIIII#I@II +chr2 14 G 11 ..N....... IICIBII@AII +chr2 15 C 11 A.....NG.. IIIIIDIIIII +chr2 16 T 11 ...C.....G I$IIIB@IIIC +chr2 17 C 12 G......TN.. IIAII@IIII$I +chr2 18 A 12 N......G..A IIIBIII$IIII +chr2 19 A 13 .......NN... IIIIIIBIII$$@ +chr2 20 C 13 ..GT.......N IIIIABIIC$III +chr1 1 C 1 ^:. I +chr1 2 G 2 .^:. $I +chr1 3 A 2 .. I% +chr1 4 C 2 .. I$ +chr1 5 T 3 ..^:. I#I +chr1 6 G 3 ..^:, I#I +chr1 7 C 4 .N., IIII +chr1 8 A 4 ..., I$II +chr1 9 T 5 ..C., I#IDI +chr1 10 G 5 N..., IBII@ +chr1 11 A 5 .C.., I$II# +chr1 12 C 5 ..N., I$III diff -r 5cc5e94345b8 -r a9e25e05ae8d test-data/column_join_in8.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/column_join_in8.pileup Fri Mar 26 12:11:01 2010 -0400 @@ -0,0 +1,23 @@ +chr1 42 T 1 ^:. I +chr1 43 G 2 .^:. $I +chr1 44 T 2 .. I% +chr1 45 C 3 ..^:. III +chr1 46 G 3 ..^:. I#I +chr1 47 T 4 ...^:, I#II +chr1 48 A 4 .N., IIII +chr1 49 C 5 ...., IIIII +chr1 50 A 5 ..G., IIIDI +chr1 51 A 5 A..., IBIII +chr1 52 A 5 ...., IIII# +chr1 53 G 5 ..N., I$III +chr2 77 C 6 .G..., I$$III +chr2 78 G 6 ..N.., III@II +chr2 79 T 7 ..N..., I$IIIII +chr2 80 C 7 .G...., I#IIIII +chr2 81 G 7 ...A.., IIII#BI +chr2 82 A 8 ...G..., I$IDIIII +chr2 83 A 8 ...T..., IIIBD$II +chr2 84 T 8 ..A...., IBI#IIII +chr2 85 G 8 .GA...., IIBIII#I +chr2 86 C 9 ........, I$II#IIII +chr2 87 G 9 ....T..., IIIII$I$I diff -r 5cc5e94345b8 -r a9e25e05ae8d test-data/column_join_in9.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/column_join_in9.pileup Fri Mar 26 12:11:01 2010 -0400 @@ -0,0 +1,25 @@ +chr1 43 C 2 .^:. II +chr3 65 T 7 ...AA., IIIII@@ +chr1 44 T 2 .. II +chr2 54 T 5 ...., IIIII +chr1 45 A 3 ..^:. III +chr1 47 A 5 ....^:, IIIII +chr1 50 A 5 .G.., IIIII +chr1 51 G 5 ...., IIIII +chr2 52 T 5 .N.., II$II +chr2 53 A 5 ...., IIIII +chr3 60 C 6 ...G., I#IIII +chr3 61 T 6 ..N.., IIIIII +chr1 49 G 5 ...., IIIII +chr2 55 T 5 ...., IIIII +chr2 56 C 5 ...., IIIBI +chr2 58 T 6 .N..., IIIIII +chr2 59 A 6 ....., IIII$I +chr3 62 C 6 ...A., IIIIII +chr1 42 C 1 ^:. I +chr3 63 C 7 .N...., IIIIIII +chr1 48 T 5 ...N, I#III +chr1 46 G 4 ...^:. IIII +chr3 64 A 7 ...G.., IIIII$I +chr3 66 A 7 ....N., IIIIIII +chr2 57 T 5 ...., IDIII diff -r 5cc5e94345b8 -r a9e25e05ae8d test-data/column_join_out1.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/column_join_out1.pileup Fri Mar 26 12:11:01 2010 -0400 @@ -0,0 +1,60 @@ +chr1 1 T T 87 25 G G 25 25 +chr1 2 A T 87 25 T T 25 25 +chr1 3 A G 87 25 T T 27 25 +chr1 4 A T 55 25 A A 36 25 +chr1 5 C A 54 25 A A 36 25 +chr1 6 G T 87 25 T T 36 25 +chr1 7 A C 87 25 G G 42 25 +chr1 8 G A 87 25 T T 45 25 +chr1 9 A T 87 25 A A 51 25 +chr1 10 G A 57 25 G G 54 25 +chr1 11 C A 57 25 C C 57 25 +chr1 12 T A 99 25 T T 60 25 +chr1 13 A C 99 25 T T 78 25 +chr1 14 G C 55 25 A A 56 25 +chr1 15 T G 68 25 A A 87 25 +chr4 1 T T 90 25 +chr4 2 A A 87 25 +chr4 3 A A 34 25 +chr4 4 T T 55 25 +chr4 5 A A 54 25 +chr4 6 T T 87 25 +chr4 7 A A 80 25 +chr4 8 A A 87 25 +chr4 9 A A 87 25 +chr4 10 G G 57 25 +chr4 11 C C 57 25 +chr4 12 A A 99 25 +chr4 13 A A 99 25 +chr4 14 G G 55 25 +chr4 15 G G 68 25 +chrM 1 A G 25 25 T G 25 25 +chrM 2 C T 25 25 C A 25 25 +chrM 3 T G 27 25 C A 25 25 +chrM 4 G C 36 25 G A 36 25 +chrM 5 T A 38 25 A T 36 25 +chrM 6 T A 39 25 A G 36 25 +chrM 7 G C 43 25 C G 42 25 +chrM 8 A C 46 25 T T 45 25 +chrM 9 T G 53 25 C A 51 25 +chrM 10 T G 56 25 G G 54 25 +chrM 11 C G 57 25 T C 57 25 +chrM 12 T C 61 25 A T 60 25 +chrM 13 T G 79 25 A T 78 25 +chrM 14 A C 58 25 G A 56 25 +chrM 15 G A 87 25 G A 87 25 +chrM 16 G C 88 25 +chrM 17 A C 88 25 +chrM 18 G A 89 25 +chrM 19 G T 58 25 +chrM 20 T C 55 25 +chrM 21 C T 87 25 +chrM 22 C A 87 25 +chrM 23 A G 87 25 +chrM 24 A T 89 25 +chrM 25 G A 57 25 +chrM 26 C G 58 25 +chrM 27 T A 99 25 +chrM 28 A C 99 25 +chrM 29 G C 58 25 +chrM 30 T T 65 25 diff -r 5cc5e94345b8 -r a9e25e05ae8d test-data/column_join_out2.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/column_join_out2.pileup Fri Mar 26 12:11:01 2010 -0400 @@ -0,0 +1,65 @@ +chr1 1 C 1 +chr1 2 G 2 +chr1 3 A 2 +chr1 4 C 2 +chr1 5 T 3 +chr1 6 G 3 +chr1 7 C 4 +chr1 8 A 4 +chr1 9 T 5 +chr1 10 G 5 +chr1 11 A 5 +chr1 12 C 5 +chr1 42 T 1 C 1 +chr1 43 G 2 C 2 +chr1 44 T 2 T 2 +chr1 45 C 3 A 3 +chr1 46 G 3 G 4 +chr1 47 T 4 A 5 +chr1 48 A 4 T 5 +chr1 49 C 5 G 5 +chr1 50 A 5 A 5 +chr1 51 A 5 G 5 +chr1 52 A 5 +chr1 53 G 5 +chr2 1 T 6 +chr2 2 G 6 +chr2 3 C 7 +chr2 4 G 7 +chr2 5 G 7 +chr2 6 A 7 +chr2 7 T 8 +chr2 8 A 8 +chr2 9 C 9 +chr2 10 T 9 +chr2 11 C 10 +chr2 12 G 10 +chr2 13 A 11 +chr2 52 T 5 +chr2 53 A 5 +chr2 54 T 5 +chr2 55 T 5 +chr2 56 C 5 +chr2 57 T 5 +chr2 58 T 6 +chr2 59 A 6 +chr2 77 C 6 +chr2 78 G 6 +chr2 79 T 7 +chr2 80 C 7 +chr2 81 G 7 +chr2 82 A 8 +chr2 83 A 8 +chr2 84 T 8 +chr2 85 G 8 +chr2 86 C 9 +chr2 87 G 9 +chr2 88 G 10 +chr2 89 G 10 +chr3 60 C 6 +chr3 61 T 6 +chr3 62 C 6 +chr3 63 C 7 +chr3 64 A 7 +chr3 65 T 7 +chr3 66 A 7 diff -r 5cc5e94345b8 -r a9e25e05ae8d test-data/column_join_out3.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/column_join_out3.pileup Fri Mar 26 12:11:01 2010 -0400 @@ -0,0 +1,70 @@ +chr1 1 C 1 ^:. +chr1 2 G 2 .^:. +chr1 3 A 2 .. +chr1 4 C 2 .. +chr1 5 T 3 ..^:. +chr1 6 G 3 ..^:, +chr1 7 C 4 .N., +chr1 8 A 4 ..., +chr1 9 T 5 ..C., +chr1 10 G 5 N..., +chr1 11 A 5 .C.., +chr1 12 C 5 ..N., +chr1 42 T 1 ^:. C 1 ^:. +chr1 43 G 2 .^:. C 2 .^:. +chr1 44 T 2 .. T 2 .. +chr1 45 C 3 ..^:. A 3 ..^:. +chr1 46 G 3 ..^:. G 4 ...^:. +chr1 47 T 4 ...^:, A 5 ....^:, +chr1 48 A 4 .N., T 5 ...N, +chr1 49 C 5 ...., G 5 ...., +chr1 50 A 5 ..G., A 5 .G.., +chr1 51 A 5 A..., G 5 ...., +chr1 52 A 5 ...., +chr1 53 G 5 ..N., +chr2 1 T 6 .C..., +chr2 2 G 6 ..N.., +chr2 3 C 7 ..C..., +chr2 4 G 7 .G...., +chr2 5 G 7 ...N.., +chr2 6 A 7 ..T..., +chr2 7 T 8 ...C..., +chr2 8 A 8 ..A...., +chr2 9 C 9 .GA..N.., +chr2 10 T 9 ........, +chr2 11 C 10 .>>..T..., +chr2 12 G 10 .N..G...., +chr2 13 A 11 ....A..T.., +chr2 14 G 11 ..N....... +chr2 15 C 11 A.....NG.. +chr2 16 T 11 ...C.....G +chr2 17 C 12 G......TN.. +chr2 18 A 12 N......G..A +chr2 19 A 13 .......NN... +chr2 20 C 13 ..GT.......N +chr2 52 T 5 .N.., +chr2 53 A 5 ...., +chr2 54 T 5 ...., +chr2 55 T 5 ...., +chr2 56 C 5 ...., +chr2 57 T 5 ...., +chr2 58 T 6 .N..., +chr2 59 A 6 ....., +chr2 77 C 6 .G..., +chr2 78 G 6 ..N.., +chr2 79 T 7 ..N..., +chr2 80 C 7 .G...., +chr2 81 G 7 ...A.., +chr2 82 A 8 ...G..., +chr2 83 A 8 ...T..., +chr2 84 T 8 ..A...., +chr2 85 G 8 .GA...., +chr2 86 C 9 ........, +chr2 87 G 9 ....T..., +chr3 60 C 6 ...G., +chr3 61 T 6 ..N.., +chr3 62 C 6 ...A., +chr3 63 C 7 .N...., +chr3 64 A 7 ...G.., +chr3 65 T 7 ...AA., +chr3 66 A 7 ....N., diff -r 5cc5e94345b8 -r a9e25e05ae8d test/functional/test_get_data.py --- a/test/functional/test_get_data.py Fri Mar 26 12:02:22 2010 -0400 +++ b/test/functional/test_get_data.py Fri Mar 26 12:11:01 2010 -0400 @@ -575,5 +575,22 @@ self.check_history_for_string( 'Pasted Entry' ) self.check_history_for_string( 'hello world' ) self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0165_upload_file( self ): + """Test uploading 1.pileup, NOT setting the file format""" + self.check_history_for_string( 'Your history is empty' ) + history = sa_session.query( galaxy.model.History ) \ + .filter( and_( galaxy.model.History.table.c.deleted==False, + galaxy.model.History.table.c.user_id==admin_user.id ) ) \ + .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ + .first() + self.upload_file( '1.pileup' ) + hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \ + .first() + assert hda is not None, "Problem retrieving hda from database" + self.verify_dataset_correctness( '1.pileup', hid=str( hda.hid ) ) + self.check_history_for_string( '1.pileup format: <span class="pileup">pileup</span>, database: \? Info: uploaded file' ) + self.check_metadata_for_string( 'value="1.pileup" value="\?" Change data type selected value="pileup" selected="yes"' ) + self.delete_history( id=self.security.encode_id( history.id ) ) def test_9999_clean_up( self ): self.logout() diff -r 5cc5e94345b8 -r a9e25e05ae8d tool_conf.xml.sample --- a/tool_conf.xml.sample Fri Mar 26 12:02:22 2010 -0400 +++ b/tool_conf.xml.sample Fri Mar 26 12:11:01 2010 -0400 @@ -61,6 +61,7 @@ <tool file="filters/compare.xml"/> <tool file="new_operations/subtract_query.xml"/> <tool file="stats/grouping.xml" /> + <tool file="new_operations/column_join.xml" /> </section> <section name="Convert Formats" id="convert"> <tool file="filters/axt_to_concat_fasta.xml" />

1 0