[hg] galaxy 3661: Less blather from rgGRR and new functional tes...
details: http://www.bx.psu.edu/hg/galaxy/rev/92ce16e0e37e changeset: 3661:92ce16e0e37e user: fubar: ross Lazarus at gmail period com date: Thu Apr 15 21:20:04 2010 -0400 description: Less blather from rgGRR and new functional test output files to match Stretch lines_diff even further to accomodate an older version of plink for functional tests diffstat: lib/galaxy/datatypes/genetics.py | 24 +- test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt | 21 +- test-data/rgtestouts/rgGRR/rgGRRtest1.html | 32 +- test-data/rgtestouts/rgGRR/rgGRRtest1.svg | 517 +------ test-data/rgtestouts/rgGRR/rgGRRtest1_table.xls | 1560 +++++++++++----------- test-data/smallwgaP.xls | 103 + tools/rgenetics/rgGLM.xml | 2 +- tools/rgenetics/rgGRR.py | 8 +- tools/rgenetics/rgGRR.xml | 2 +- tools/rgenetics/rgQC.xml | 2 +- 10 files changed, 967 insertions(+), 1304 deletions(-) diffs (2456 lines): diff -r ed5535c4d48e -r 92ce16e0e37e lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py Thu Apr 15 15:58:08 2010 -0400 +++ b/lib/galaxy/datatypes/genetics.py Thu Apr 15 21:20:04 2010 -0400 @@ -86,8 +86,6 @@ site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) - if base_url.startswith( 'https://' ): - base_url = base_url.replace( 'https', 'http', 1 ) display_url = "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) display_url = urllib.quote_plus( display_url ) # was display_url = urllib.quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) ) @@ -264,7 +262,7 @@ stored in extra files path """ - MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", default="rgenetics", + MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", readonly=True, set_in_upload=True) composite_type = 'auto_primary_file' @@ -290,27 +288,15 @@ """ cannot do this until we are setting metadata """ - guessmt = {'.log':'text/plain','.ped':'text/plain', '.map':'text/plain','.out':'text/plain','.in':'text/plain'} - def fix(oldpath,newbase): - old,e = os.path.splitext(oldpath) - head,rest = os.path.split(old) - newpath = os.path.join(head,newbase) - newpath = '%s%s' % (newpath,e) - if oldpath <> newpath: - shutil.move(oldpath,newpath) - return newpath bn = dataset.metadata.base_name efp = dataset.extra_files_path flist = os.listdir(efp) - proper_base = bn - rval = ['<html><head><title>Files for Composite Dataset %s</title></head><p/>Composite %s contains the following files:<p/><ul>' % (dataset.name,dataset.name)] + rval = ['<html><head><title>Files for Composite Dataset %s</title></head><body><p/>Composite %s contains:<p/><ul>' % (dataset.name,dataset.name)] for i,fname in enumerate(flist): - newpath = fix(os.path.join(efp,fname),proper_base) - sfname = os.path.split(newpath)[-1] + sfname = os.path.split(fname)[-1] f,e = os.path.splitext(fname) - mt = guessmt.get(e,'application/binary') - rval.append( '<li><a href="%s" mimetype="%s">%s</a></li>' % ( sfname, mt, sfname) ) - rval.append( '</ul></html>' ) + rval.append( '<li><a href="%s">%s</a></li>' % ( sfname, sfname) ) + rval.append( '</ul></body></html>' ) f = file(dataset.file_name,'w') f.write("\n".join( rval )) f.write('\n') diff -r ed5535c4d48e -r 92ce16e0e37e test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt --- a/test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt Thu Apr 15 15:58:08 2010 -0400 +++ b/test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt Thu Apr 15 21:20:04 2010 -0400 @@ -1,22 +1,13 @@ -Reading genotypes for 40 subjects and 25 markers -Calculating 780 pairs, updating every 78 pairs... +Reading genotypes for 40 subjects and 5 markers +Calculating 780 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%) +T1: 0.00229454040527 T2: 0.0166795253754 T3: 0.000442743301392 TOT: 0.0201091766357 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 parentchild: mean(mean)=1.82 sdev(mean)=0.14, mean(sdev)=0.33 sdev(sdev)=0.22 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 parents: mean(mean)=1.62 sdev(mean)=0.21, mean(sdev)=0.53 sdev(sdev)=0.29 +Relstate unrelated: mean(mean)=1.60 sdev(mean)=0.23, mean(sdev)=0.54 sdev(sdev)=0.22 Relstate unknown: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 780 pairs are available of 780 Outliers: 0 diff -r ed5535c4d48e -r 92ce16e0e37e test-data/rgtestouts/rgGRR/rgGRRtest1.html --- a/test-data/rgtestouts/rgGRR/rgGRRtest1.html Thu Apr 15 15:58:08 2010 -0400 +++ b/test-data/rgtestouts/rgGRR/rgGRRtest1.html Thu Apr 15 21:20:04 2010 -0400 @@ -9,7 +9,7 @@ </head> <body> <div class="document"> -<h4><div>Output from rgGRR.py run at 25/03/2010 21:01:24<br> +<h4><div>Output from rgGRR.py run at 15/04/2010 13:12:45<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> @@ -18,43 +18,25 @@ <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 +</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 5 markers -Calculating 780 pairs, updating every 78 pairs... +Calculating 780 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%) +T1: 0.00229454040527 T2: 0.0166795253754 T3: 0.000442743301392 TOT: 0.0201091766357 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 parentchild: mean(mean)=1.82 sdev(mean)=0.14, mean(sdev)=0.33 sdev(sdev)=0.22 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 parents: mean(mean)=1.62 sdev(mean)=0.21, mean(sdev)=0.53 sdev(sdev)=0.29 -Relstate unrelated: mean(mean)=1.44 sdev(mean)=0.21, mean(sdev)=0.58 sdev(sdev)=0.15 +Relstate unrelated: mean(mean)=1.60 sdev(mean)=0.23, mean(sdev)=0.54 sdev(sdev)=0.22 Relstate unknown: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 diff -r ed5535c4d48e -r 92ce16e0e37e test-data/rgtestouts/rgGRR/rgGRRtest1.svg --- a/test-data/rgtestouts/rgGRR/rgGRRtest1.svg Thu Apr 15 15:58:08 2010 -0400 +++ b/test-data/rgtestouts/rgGRR/rgGRRtest1.svg Thu Apr 15 21:20:04 2010 -0400 @@ -5,9 +5,9 @@ xmlns="http://www.w3.org/2000/svg" version="1.2" xmlns:xlink="http://www.w3.org/1999/xlink" viewBox="0 0 1280 800" onload="init()"> - <script type="text/ecmascript" xlink:href="/static/scripts/tools/rgenetics/checkbox_and_radiobutton.js"/> - <script type="text/ecmascript" xlink:href="/static/scripts/tools/rgenetics/helper_functions.js"/> - <script type="text/ecmascript" xlink:href="/static/scripts/tools/rgenetics/timer.js"/> + <script type="text/ecmascript" xlink:href="/static/scripts/checkbox_and_radiobutton.js"/> + <script type="text/ecmascript" xlink:href="/static/scripts/helper_functions.js"/> + <script type="text/ecmascript" xlink:href="/static/scripts/timer.js"/> <script type="text/ecmascript"> <![CDATA[ var checkBoxes = new Array(); @@ -247,492 +247,99 @@ <!-- Plot Title --> <g style="fill:black; stroke:none" font-size="18" font-family="Arial"> - <text x="425" 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117_2 1.200000 0.577350 0.469098 -0.467231 25 5 -101_1 117_3 1.200000 0.577350 0.469098 0.077804 25 5 -101_1 12_1 1.200000 0.577350 0.469098 -0.467230 25 5 -101_1 12_2 1.200000 0.577350 0.469098 -0.467230 25 5 -101_1 12_3 1.200000 0.577350 1.071833 -0.655899 25 5 -101_1 13_1 1.200000 0.577350 -0.133637 -0.504142 25 5 -101_1 13_2 1.200000 0.577350 -0.255930 0.042025 25 5 -101_1 13_3 1.200000 0.577350 1.071832 -0.655899 25 5 -101_1 1334_1 1.200000 0.577350 -0.133636 0.045908 25 5 -101_1 1334_10 1.200000 0.577350 -0.334548 -0.566551 25 5 -101_1 1334_11 1.200000 0.577350 -0.937282 0.679102 25 5 -101_1 1334_12 1.200000 0.577350 -0.334548 -0.007823 25 5 -101_1 1334_13 1.200000 0.577350 -0.133636 -0.504142 25 5 -101_1 1334_2 1.200000 0.577350 -0.736370 1.194476 25 5 -101_1 1340_1 1.200000 0.577350 -0.535459 -0.084293 25 5 -101_1 1340_10 1.200000 0.577350 -0.535459 -0.084293 25 5 -101_1 1340_11 1.200000 0.577350 -0.133636 -0.504142 25 5 -101_1 1340_12 1.200000 0.577350 0.469098 -0.467231 25 5 -101_1 1340_2 1.200000 0.577350 0.469098 -0.467231 25 5 -101_1 1340_9 1.200000 0.577350 -2.142751 0.999931 25 5 -101_1 1341_1 1.200000 0.577350 0.163363 -0.455013 25 5 -101_1 1341_11 1.200000 0.577350 -0.334549 0.481281 25 5 -101_1 1341_12 1.200000 0.577350 -0.937282 -0.925605 25 5 -101_1 1341_13 1.200000 0.577350 -0.736371 0.779435 25 5 -101_1 1341_14 1.200000 0.577350 -0.736371 0.779435 25 5 -101_1 1341_2 1.200000 0.577350 -0.736371 0.779435 25 5 -101_1 1344_1 1.200000 0.577350 -0.535459 0.413356 25 5 -101_1 1344_12 1.200000 0.577350 0.469098 -0.467231 25 5 -101_1 1344_13 1.200000 0.577350 0.469098 -0.467231 25 5 -101_1 1345_12 1.200000 0.577350 -0.736370 -0.774446 25 5 -101_2 101_3 1.200000 0.577350 0.236040 -0.228179 25 5 -101_2 105_1 1.200000 0.577350 0.670010 -0.504142 25 5 -101_2 105_2 1.200000 0.577350 0.943250 -0.598443 25 5 -101_2 105_3 1.200000 0.577350 1.136125 -0.693367 25 5 -101_2 112_1 1.200000 0.577350 -0.599751 0.780517 25 5 -101_2 112_2 1.200000 0.577350 -0.792626 0.696771 25 5 -101_2 112_3 1.200000 0.577350 -0.406876 -0.598443 25 5 -101_2 117_1 1.200000 0.577350 0.171750 0.062100 25 5 -101_2 117_2 1.200000 0.577350 0.557499 -0.483424 25 5 -101_2 117_3 1.200000 0.577350 0.557499 0.042491 25 5 -101_2 12_1 1.200000 0.577350 0.557499 -0.483423 25 5 -101_2 12_2 1.200000 0.577350 0.557499 -0.483423 25 5 -101_2 12_3 1.200000 0.577350 1.136124 -0.693367 25 5 -101_2 13_1 1.200000 0.577350 -0.021126 -0.483423 25 5 -101_2 13_2 1.200000 0.577350 -0.255930 0.042025 25 5 -101_2 13_3 1.200000 0.577350 1.136124 -0.693367 25 5 -101_2 1334_1 1.200000 0.577350 -0.021125 0.042491 25 5 -101_2 1334_10 1.200000 0.577350 -0.214001 -0.528970 25 5 -101_2 1334_11 1.200000 0.577350 -0.792626 0.696771 25 5 -101_2 1334_12 1.200000 0.577350 -0.214001 0.002982 25 5 -101_2 1334_13 1.200000 0.577350 -0.021126 -0.483424 25 5 -101_2 1334_2 1.200000 0.577350 -0.599751 1.178851 25 5 -101_2 1340_1 1.200000 0.577350 -0.406876 -0.057030 25 5 -101_2 1340_10 1.200000 0.577350 -0.406876 -0.057030 25 5 -101_2 1340_11 1.200000 0.577350 -0.021126 -0.483424 25 5 -101_2 1340_12 1.200000 0.577350 0.557499 -0.483423 25 5 -101_2 1340_2 1.200000 0.577350 0.557499 -0.483423 25 5 -101_2 1340_9 1.200000 0.577350 -1.949876 1.086115 25 5 -101_2 1341_1 1.200000 0.577350 0.268187 -0.455013 25 5 -101_2 1341_11 1.200000 0.577350 -0.214002 0.471641 25 5 -101_2 1341_12 1.200000 0.577350 -0.792626 -0.816040 25 5 -101_2 1341_13 1.200000 0.577350 -0.599751 0.780517 25 5 -101_2 1341_14 1.200000 0.577350 -0.599751 0.780517 25 5 -101_2 1341_2 1.200000 0.577350 -0.599751 0.780517 25 5 -101_2 1344_1 1.200000 0.577350 -0.406876 0.418047 25 5 -101_2 1344_12 1.200000 0.577350 0.557499 -0.483423 25 5 -101_2 1344_13 1.200000 0.577350 0.557499 -0.483423 25 5 -101_2 1345_12 1.200000 0.577350 -0.599751 -0.693367 25 5 -101_3 105_1 1.200000 0.577350 -1.540017 1.879362 25 5 -101_3 105_2 1.200000 0.577350 0.171750 -0.460872 25 5 -101_3 105_3 1.200000 0.577350 -0.792627 -0.242861 25 5 -101_3 112_1 1.200000 0.577350 -0.599750 0.780517 25 5 -101_3 112_2 1.200000 0.577350 -0.792626 2.157894 25 5 -101_3 112_3 1.200000 0.577350 -0.021126 -0.483423 25 5 -101_3 117_1 1.200000 0.577350 -0.599751 1.178851 25 5 -101_3 117_2 1.200000 0.577350 1.329000 -0.816040 25 5 -101_3 117_3 1.200000 0.577350 0.171750 0.062100 25 5 -101_3 12_1 1.200000 0.577350 2.486250 -2.592124 25 5 -101_3 12_2 1.200000 0.577350 2.486250 -2.592124 25 5 -101_3 12_3 1.200000 0.577350 1.136124 -0.693367 25 5 -101_3 13_1 1.200000 0.577350 1.521875 -0.969866 25 5 -101_3 13_2 1.200000 0.577350 -0.255930 0.546459 25 5 -101_3 13_3 1.200000 0.577350 1.136125 -0.693367 25 5 -101_3 1334_1 1.200000 0.577350 -0.021126 -0.483424 25 5 -101_3 1334_10 1.200000 0.577350 -0.599750 -0.693367 25 5 -101_3 1334_11 1.200000 0.577350 -0.792626 2.157894 25 5 -101_3 1334_12 1.200000 0.577350 -0.599751 0.345553 25 5 -101_3 1334_13 1.200000 0.577350 -0.406876 -0.598443 25 5 -101_3 1334_2 1.200000 0.577350 -0.985501 1.388993 25 5 -101_3 1340_1 1.200000 0.577350 -0.406876 -0.598443 25 5 -101_3 1340_10 1.200000 0.577350 -0.406876 -0.598443 25 5 -101_3 1340_11 1.200000 0.577350 -0.406876 -0.598443 25 5 -101_3 1340_12 1.200000 0.577350 -0.599750 -0.693367 25 5 -101_3 1340_2 1.200000 0.577350 -0.599751 0.345552 25 5 -101_3 1340_9 1.200000 0.577350 -0.406876 1.948414 25 5 -101_3 1341_1 1.200000 0.577350 -1.339106 0.413355 25 5 -101_3 1341_11 1.200000 0.577350 -1.371251 1.881413 25 5 -101_3 1341_12 1.200000 0.577350 -1.564126 0.158748 25 5 -101_3 1341_13 1.200000 0.577350 -0.599750 0.780517 25 5 -101_3 1341_14 1.200000 0.577350 -0.599750 0.780517 25 5 -101_3 1341_2 1.200000 0.577350 -0.599750 0.780517 25 5 -101_3 1344_1 1.200000 0.577350 -0.792626 2.157893 25 5 -101_3 1344_12 1.200000 0.577350 -0.599751 0.345552 25 5 -101_3 1344_13 1.200000 0.577350 -0.599751 0.345552 25 5 -101_3 1345_12 1.200000 0.577350 -1.371251 0.327238 25 5 -105_1 105_2 1.200000 0.577350 -1.155984 0.612530 25 5 -105_1 105_3 1.200000 0.577350 -0.936806 0.621689 25 5 -105_1 112_1 1.200000 0.577350 -1.540017 1.127651 25 5 -105_1 112_2 1.200000 0.577350 -0.133636 1.738452 25 5 -105_1 112_3 1.200000 0.577350 -1.339105 0.859974 25 5 -105_1 117_1 1.200000 0.577350 0.067275 0.991299 25 5 -105_1 117_2 1.200000 0.577350 -1.138194 0.991299 25 5 -105_1 117_3 1.200000 0.577350 -0.736371 0.779434 25 5 -105_1 12_1 1.200000 0.577350 -1.540017 1.879362 25 5 -105_1 12_2 1.200000 0.577350 -1.540017 1.879362 25 5 -105_1 12_3 1.200000 0.577350 -0.535459 0.859974 25 5 -105_1 13_1 1.200000 0.577350 -1.740928 1.738452 25 5 -105_1 13_2 1.200000 0.577350 -1.094517 0.648831 25 5 -105_1 13_3 1.200000 0.577350 -0.937282 0.679103 25 5 -105_1 1334_1 1.200000 0.577350 -0.937283 1.102364 25 5 -105_1 1334_10 1.200000 0.577350 -1.138194 0.991300 25 5 -105_1 1334_11 1.200000 0.577350 -0.133636 1.738452 25 5 -105_1 1334_12 1.200000 0.577350 -1.138194 0.991300 25 5 -105_1 1334_13 1.200000 0.577350 -0.937282 0.213207 25 5 -105_1 1334_2 1.200000 0.577350 -1.540016 1.879362 25 5 -105_1 1340_1 1.200000 0.577350 -1.339106 0.859974 25 5 -105_1 1340_10 1.200000 0.577350 -1.339106 0.859974 25 5 -105_1 1340_11 1.200000 0.577350 -0.937282 0.213207 25 5 -105_1 1340_12 1.200000 0.577350 -0.334548 -0.566551 25 5 -105_1 1340_2 1.200000 0.577350 0.469098 -0.467231 25 5 -105_1 1340_9 1.200000 0.577350 -2.946397 2.337655 25 5 -105_1 1341_1 1.200000 0.577350 0.582657 -0.481725 25 5 -105_1 1341_11 1.200000 0.577350 0.469098 0.077804 25 5 -105_1 1341_12 1.200000 0.577350 -0.535459 1.268636 25 5 -105_1 1341_13 1.200000 0.577350 -1.540017 1.127651 25 5 -105_1 1341_14 1.200000 0.577350 -1.540017 1.127651 25 5 -105_1 1341_2 1.200000 0.577350 -1.540017 1.127651 25 5 -105_1 1344_1 1.200000 0.577350 0.268187 1.397944 25 5 -105_1 1344_12 1.200000 0.577350 0.469098 -0.467231 25 5 -105_1 1344_13 1.200000 0.577350 0.469098 -0.467231 25 5 -105_1 1345_12 1.200000 0.577350 -0.334549 1.325597 25 5 -105_2 105_3 1.200000 0.577350 0.722984 0.122716 25 5 -105_2 112_1 1.200000 0.577350 -0.021126 0.507014 25 5 -105_2 112_2 1.200000 0.577350 -0.214001 0.471641 25 5 -105_2 112_3 1.200000 0.577350 0.943249 -0.598443 25 5 -105_2 117_1 1.200000 0.577350 0.750376 -0.528970 25 5 -105_2 117_2 1.200000 0.577350 1.521875 -0.969866 25 5 -105_2 117_3 1.200000 0.577350 1.521875 -0.969867 25 5 -105_2 12_1 1.200000 0.577350 0.364625 -0.460872 25 5 -105_2 12_2 1.200000 0.577350 0.364625 -0.460872 25 5 -105_2 12_3 1.200000 0.577350 0.943251 -0.598443 25 5 -105_2 13_1 1.200000 0.577350 -0.214002 -0.528970 25 5 -105_2 13_2 1.200000 0.577350 0.163363 0.111360 25 5 -105_2 13_3 1.200000 0.577350 0.943249 -0.598444 25 5 -105_2 1334_1 1.200000 0.577350 1.328999 -0.816040 25 5 -105_2 1334_10 1.200000 0.577350 0.364624 -0.460872 25 5 -105_2 1334_11 1.200000 0.577350 -0.214001 0.471641 25 5 -105_2 1334_12 1.200000 0.577350 -0.021126 0.042491 25 5 -105_2 1334_13 1.200000 0.577350 0.943249 -0.598443 25 5 -105_2 1334_2 1.200000 0.577350 -0.792626 1.101688 25 5 -105_2 1340_1 1.200000 0.577350 0.557499 -0.483424 25 5 -105_2 1340_10 1.200000 0.577350 0.557499 -0.483424 25 5 -105_2 1340_11 1.200000 0.577350 0.943249 -0.598443 25 5 -105_2 1340_12 1.200000 0.577350 1.907625 -1.394354 25 5 -105_2 1340_2 1.200000 0.577350 1.521875 -0.969866 25 5 -105_2 1340_9 1.200000 0.577350 -1.371251 1.163511 25 5 -105_2 1341_1 1.200000 0.577350 1.272743 -0.774447 25 5 -105_2 1341_11 1.200000 0.577350 0.364624 0.524595 25 5 -105_2 1341_12 1.200000 0.577350 -0.599751 -0.693367 25 5 -105_2 1341_13 1.200000 0.577350 -0.021126 0.507014 25 5 -105_2 1341_14 1.200000 0.577350 -0.021126 0.507014 25 5 -105_2 1341_2 1.200000 0.577350 -0.021126 0.507014 25 5 -105_2 1344_1 1.200000 0.577350 0.171750 0.062100 25 5 -105_2 1344_12 1.200000 0.577350 1.521875 -0.969866 25 5 -105_2 1344_13 1.200000 0.577350 1.521875 -0.969866 25 5 -105_2 1345_12 1.200000 0.577350 -0.406876 -0.598443 25 5 -105_3 112_1 1.200000 0.577350 0.943249 -0.057030 25 5 -105_3 112_2 1.200000 0.577350 -0.406876 -0.057030 25 5 -105_3 112_3 1.200000 0.577350 0.750375 -0.528970 25 5 -105_3 117_1 1.200000 0.577350 -0.599751 -0.138508 25 5 -105_3 117_2 1.200000 0.577350 -0.214002 0.002982 25 5 -105_3 117_3 1.200000 0.577350 0.171749 0.062100 25 5 -105_3 12_1 1.200000 0.577350 -0.599752 -0.138508 25 5 -105_3 12_2 1.200000 0.577350 -0.599752 -0.138508 25 5 -105_3 12_3 1.200000 0.577350 0.364625 -0.460872 25 5 -105_3 13_1 1.200000 0.577350 0.364624 -0.460872 25 5 -105_3 13_2 1.200000 0.577350 1.211597 -0.732039 25 5 -105_3 13_3 1.200000 0.577350 -0.406876 -0.057030 25 5 -105_3 1334_1 1.200000 0.577350 -0.021126 -0.483423 25 5 -105_3 1334_10 1.200000 0.577350 0.943250 -0.598444 25 5 -105_3 1334_11 1.200000 0.577350 -0.406876 -0.057030 25 5 -105_3 1334_12 1.200000 0.577350 1.329000 -0.816040 25 5 -105_3 1334_13 1.200000 0.577350 1.136125 -0.693367 25 5 -105_3 1334_2 1.200000 0.577350 0.943249 -0.598443 25 5 -105_3 1340_1 1.200000 0.577350 0.750375 -0.528970 25 5 -105_3 1340_10 1.200000 0.577350 0.750375 -0.528970 25 5 -105_3 1340_11 1.200000 0.577350 1.136125 -0.693367 25 5 -105_3 1340_12 1.200000 0.577350 0.557499 -0.483423 25 5 -105_3 1340_2 1.200000 0.577350 0.557499 -0.483423 25 5 -105_3 1340_9 1.200000 0.577350 -0.406876 -0.057030 25 5 -105_3 1341_1 1.200000 0.577350 -0.133637 -0.504142 25 5 -105_3 1341_11 1.200000 0.577350 0.171749 0.062100 25 5 -105_3 1341_12 1.200000 0.577350 -0.021125 -0.483423 25 5 -105_3 1341_13 1.200000 0.577350 0.943249 -0.057030 25 5 -105_3 1341_14 1.200000 0.577350 0.943249 -0.057030 25 5 -105_3 1341_2 1.200000 0.577350 0.943249 -0.057030 25 5 -105_3 1344_1 1.200000 0.577350 -1.178375 0.471641 25 5 -105_3 1344_12 1.200000 0.577350 0.557499 -0.483423 25 5 -105_3 1344_13 1.200000 0.577350 0.557499 -0.483423 25 5 -105_3 1345_12 1.200000 0.577350 0.171749 -0.460872 25 5 -112_1 112_2 1.200000 0.577350 0.220453 0.351043 25 5 -112_1 112_3 1.200000 0.577350 -1.042010 0.617297 25 5 -112_1 117_1 1.200000 0.577350 -1.564126 1.758837 25 5 -112_1 117_2 1.200000 0.577350 -1.178376 0.471641 25 5 -112_1 117_3 1.200000 0.577350 -0.792626 0.696771 25 5 -112_1 12_1 1.200000 0.577350 -0.406876 0.846466 25 5 -112_1 12_2 1.200000 0.577350 -0.406876 0.846466 25 5 -112_1 12_3 1.200000 0.577350 0.943249 -0.598443 25 5 -112_1 13_1 1.200000 0.577350 0.557499 0.042491 25 5 -112_1 13_2 1.200000 0.577350 2.469478 -2.533568 25 5 -112_1 13_3 1.200000 0.577350 -0.214002 1.284973 25 5 -112_1 1334_1 1.200000 0.577350 0.943249 -0.598443 25 5 -112_1 1334_10 1.200000 0.577350 -0.406876 -0.598443 25 5 -112_1 1334_11 1.200000 0.577350 1.328999 -0.816040 25 5 -112_1 1334_12 1.200000 0.577350 0.364625 -0.460872 25 5 -112_1 1334_13 1.200000 0.577350 0.557499 -0.483423 25 5 -112_1 1334_2 1.200000 0.577350 -0.021126 -0.483423 25 5 -112_1 1340_1 1.200000 0.577350 1.714749 -1.159963 25 5 -112_1 1340_10 1.200000 0.577350 1.714749 -1.159963 25 5 -112_1 1340_11 1.200000 0.577350 0.557499 -0.483423 25 5 -112_1 1340_12 1.200000 0.577350 -0.021126 -0.483423 25 5 -112_1 1340_2 1.200000 0.577350 -0.021125 -0.483423 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+rs13328662 1 3147312 1.000 0.000000 0.134 0.872571 0.110 0.957031 1.000 0.000000 +rs16823529 1 3161070 1.000 0.000000 0.534 0.272621 0.541 0.266883 1.000 0.000000 +rs12075867 1 3161113 1.000 0.000000 0.191 0.719422 0.193 0.713768 1.000 0.000000 +rs2817148 1 3161293 1.000 0.000000 0.009 2.050269 0.006 2.244583 1.000 0.000000 +rs2651891 1 3163073 1.000 0.000000 0.009 2.050269 0.006 2.244583 1.000 0.000000 +rs16823551 1 3164773 1.000 0.000000 0.005 2.260982 0.004 2.447453 1.000 0.000000 +rs10157420 1 3169654 1.000 0.000000 0.413 0.383840 0.432 0.364919 1.000 0.000000 +rs6424069 1 3170187 1.000 0.000000 0.004 2.354381 0.003 2.495257 1.000 0.000000 + diff -r ed5535c4d48e -r 92ce16e0e37e tools/rgenetics/rgGLM.xml --- a/tools/rgenetics/rgGLM.xml Thu Apr 15 15:58:08 2010 -0400 +++ b/tools/rgenetics/rgGLM.xml Thu Apr 15 21:20:04 2010 -0400 @@ -68,7 +68,7 @@ <param name='maf' value='0.0' /> <param name='logistic' value='0' /> <output name='out_file1' file='rgGLMtest1_GLM.xls' ftype='tabular' compare="diff" /> - <output name='logf' file='rgGLMtest1_GLM_log.txt' ftype='txt' compare="diff" lines_diff='33'/> + <output name='logf' file='rgGLMtest1_GLM_log.txt' ftype='txt' compare="diff" lines_diff='36'/> <output name='gffout' file='rgGLMtest1_GLM_topTable.gff' compare="diff" ftype='gff' /> </test> </tests> diff -r ed5535c4d48e -r 92ce16e0e37e tools/rgenetics/rgGRR.py --- a/tools/rgenetics/rgGRR.py Thu Apr 15 15:58:08 2010 -0400 +++ b/tools/rgenetics/rgGRR.py Thu Apr 15 21:20:04 2010 -0400 @@ -639,7 +639,7 @@ skip = set() ndone = 0 ## How many have been done so far - logf.write('Calculating %d pairs, updating every %d pairs...\n' % (tot, nprog)) + logf.write('Calculating %d pairs...\n' % (tot)) logf.write('Estimated time is %2.2f to %2.2f seconds ...\n' % (estimatedTimeFast, estimatedTimeSlow)) t1sum = 0 @@ -695,10 +695,6 @@ for s2 in xrange(s1+1, nSubjects): if s2 in emptyRows: continue - if nprog and ndone % nprog == 0 and ndone > 1: - dur = time.time() - started - pct = float(ndone)/tot*100.0 - logf.write('%f sec at pair %d of %d (%3.2f%%): %f marker*pairs/sec\n' % (dur, ndone, tot, pct, ndone/dur*nrsSamples)) t1s = time.time() (fid2,iid2,did2,mid2,sex2,phe2,iid2,d_sid2,m_sid2) = scache.setdefault(s2, ped.getSubject(s2)) @@ -848,9 +844,7 @@ continue outliers = [(scalefactor*int(abs(x[3]))+ int(abs(x[2])),x) for x in outliers] # decorate outliers.sort() - logf.write('### outliers after decorated sort=%s' % outliers) outliers.reverse() # largest deviation first - logf.write('### outliers after decorated sort=%s' % outliers) outliers = [x[1] for x in outliers] # undecorate nrows = len(outliers) truncated = 0 diff -r ed5535c4d48e -r 92ce16e0e37e tools/rgenetics/rgGRR.xml --- a/tools/rgenetics/rgGRR.xml Thu Apr 15 15:58:08 2010 -0400 +++ b/tools/rgenetics/rgGRR.xml Thu Apr 15 21:20:04 2010 -0400 @@ -29,7 +29,7 @@ <param name='n' value='100' /> <param name='Z' value='6' /> <output name='out_file1' file='rgtestouts/rgGRR/rgGRRtest1.html' ftype='html' compare="diff" lines_diff='30'> - <extra_files type="file" name='Log_rgGRRtest1.txt' value="rgtestouts/rgGRR/Log_rgGRRtest1.txt" compare="diff" lines_diff="30"/> + <extra_files type="file" name='Log_rgGRRtest1.txt' value="rgtestouts/rgGRR/Log_rgGRRtest1.txt" compare="diff" lines_diff="70"/> <extra_files type="file" name='rgGRRtest1.svg' value="rgtestouts/rgGRR/rgGRRtest1.svg" compare="diff" lines_diff="1000" /> <extra_files type="file" name='rgGRRtest1_table.xls' value="rgtestouts/rgGRR/rgGRRtest1_table.xls" compare="diff" lines_diff="100" /> </output> diff -r ed5535c4d48e -r 92ce16e0e37e tools/rgenetics/rgQC.xml --- a/tools/rgenetics/rgQC.xml Thu Apr 15 15:58:08 2010 -0400 +++ b/tools/rgenetics/rgQC.xml Thu Apr 15 21:20:04 2010 -0400 @@ -27,7 +27,7 @@ <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='250'> + <output name='html_file' file='rgtestouts/rgQC/rgQCtest1.html' ftype='html' lines_diff='260'> <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" />
participants (1)
-
Greg Von Kuster