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PLEASE HELP me please m in great trouble
by aeman zahra 02 Apr '10

02 Apr '10

I am a student of Bs Bioinformatics. I have been using the open source galaxy platform to integrate tool and make a work flow as my Final semester project. My supervisor happens to be ill and thus is unable to facilitate me in any respect. I here by take this opportunity to request that If any of you could help me fixing my problem. I would extremely grateful. PROBLEM My project problem is that , first of all i am using perl code tools for galaxy because galaxy dose not support installed tools from command prompt. so m using perl code tools for example clustalw, wublast, muscle and many more. sir these perl code tools are running correctly on command prompt and give me desire output, but when i put them it to the galaxy by making there xml file it gives an error that error occour while running this job.. and sir actually galaxy took tool's correct output as an error. i dnt know how to resolve it i tried alot but couldnt resolve it.. sir breifly m telling you that how m embedding perl code tools into galaxy: 1.go to ebi site, there are some perl code tools like clustalw, muscle,ncbiblast etc 2.i took them and download them 3. go to command prompt and try to run them by giving commands like perl ncbiblast.pl -S aemanzahra(a)comsats.edu.pk -D uniprot -P blastp 4.when it runs correctly i put them and embed them into the galaxy. now in galaxy 1. insatlled galaxy 2. go in to tools directory 3. make a new directory of new tool ito tools directory e.g clustalw tool 4.go into clustalw tool and made two files in it. clustalw.pl in which perl code of clustalw tool is present. and secondly clustalw.xml is present of this tool that i made. 5.then run galaxy by sh run.sh command 6.galaxy web page opens 7. and i clicked on my added tool clustalw there and give it an input file of multiple sequences. 8. it runs. but after running it gives me an error that "error occour while running this job" but it took the output files of this tool as an error. "The tools run and three output files are created but the Galaxy takes them as errors." WHAT PROBLEM IS THERE? waitin for your reply regards aeman

1 0

Patch: show User menu's history and dataset options show independent of app.config.use_remote_user setting
by Ry4an Brase 30 Mar '10

30 Mar '10

It's not much, but we're using a remote_user setup and the History and Datasets menu items were not showing up under the User menu, which didn't seem to be by design. Attached is a micro patch to the template, which is also available here: http://bitbucket.org/Ry4an/galaxy-umn-msi-changes/src/tip/always-show-users… Also, What's the preferred patch submission mechanism? Patchbomb? Bitbucket pull-request? Thanks, -- Ry4an Brase 612-626-6575 University of Minnesota Supercomputing Institute for Advanced Computational Research http://www.msi.umn.edu

3 4

'Never ending' jobs in history
by Chris Cole 26 Mar '10

26 Mar '10

Hi, Occasionally, we see jobs that are constantly in the 'job running' state in the history. This is despite the fact that the job completed correctly. I can also see in the paster.log file that Galaxy has picked up on the fact that the job ended, but it just hasn't updated the UI. Clicking the eye for the 'running' history items does show the results of the run. This does not happen all the time. Is this a known issue and/or how can I resolve it? Thanks, Chris

2 6

Re: [galaxy-dev] Python crashing after latest changeset update (OSX) (Fixed)
by Roy Weckiewicz 25 Mar '10

25 Mar '10

Solved this problem by creating a new instance of galaxy via hg clone and creating a new MySQL database followed by the setup.sh, modifying universe_wsgi.ini to point to my MySQL database and finally run.sh which migrated the database and started the server without a Python crash. On Thu, Mar 25, 2010 at 4:35 PM, Roy Weckiewicz <roystefan(a)gmail.com> wrote: > Hello, > > > After doing a hg pull and update a few minutes ago, my Python (2.5.1) is > crashing on OSX (10.5.8) after I run.sh daemon. The galaxy log doesn't seem > to contain any information about the error and seems to start the galaxy > server just fine (localhost). I've attached osx error report details. Any > ideas? > > > > > Thank you, > > > Roy Weckiewicz > > -- > Roy Weckiewicz > Texas A&M University > -- Roy Weckiewicz Texas A&M University

1 0

Python crashing after latest changeset update (OSX)
by Roy Weckiewicz 25 Mar '10

25 Mar '10

Hello, After doing a hg pull and update a few minutes ago, my Python (2.5.1) is crashing on OSX (10.5.8) after I run.sh daemon. The galaxy log doesn't seem to contain any information about the error and seems to start the galaxy server just fine (localhost). I've attached osx error report details. Any ideas? Thank you, Roy Weckiewicz -- Roy Weckiewicz Texas A&M University

1 0

problems with using the <conditional> after upgrade
by Hotz, Hans-Rudolf 25 Mar '10

25 Mar '10

Hi (I am sorry, if this has been reported already, but I couldn't find it in the archive) This morning, I upgraded one of our local galaxy servers from changeset 2833 to 3545....so far, I haven't encountered any major problems, except for the cases, where we use a conditional, eg: <command> #if $range.mode=="part":#clustalw2 -infile=$input -outfile=$output -OUTORDER=$out_format1 -SEQNOS=$out_format2 -RANGE=$range.seq_range_start,$range.seq_range_end #else :#clustalw2 -infile=$input -outfile=$output -OUTORDER=$out_format1 -SEQNOS=$out_format2 #end if </command> which is pretty much the same as the example for the <conditional> tag set in the wiki (ToolConfigSyntax): <command interpreter="python"> #if $source.source_select=="database":#blat_wrapper.py 0 $source.dbkey $input_query $output1 $iden $tile_size $one_off #else:#blat_wrapper.py 1 $source.input_target $input_query $output1 $iden $tile_size $one_off #end if </command> However, I got the following error (after the upgrade): //// File "/work2/scratch/galaxy/galaxy_dist/eggs/Cheetah-2.2.2-py2.5-linux-x86_64-ucs 4.egg/Cheetah/Parser.py", line 2645, in popFromOpenDirectivesStack raise ParseError(self, msg="#end found, but nothing to end") ParseError: #end found, but nothing to end Line 4, column 1 Line|Cheetah Code ----|------------------------------------------------------------- 2 | #else:#clustalw2 -infile=$input -outfile=$output -OUTORDER=$out_format1 -SEQNOS=$out_format2 3 | #end if 4 | ^ //// after looking around in similar tool config files which have been changed in the distribution, I noticed that the colons are no longer present. I removed both ":" in front of "#clustalw2", resulting in: <command> #if $range.mode=="part" #clustalw2 -infile=$input -outfile=$output -OUTORDER=$out_format1 -SEQNOS=$out_format2 -RANGE=$range.seq_range_start,$range.seq_range_end #else #clustalw2 -infile=$input -outfile=$output -OUTORDER=$out_format1 -SEQNOS=$out_format2 #end if </command> and it worked! was this the correct fix? and if so, could you please update the wiki page, ie removing the two ":" in front of "#blat_wrapper.py" Thank you very much for your help Hans

2 1

[hg] galaxy 3560: Next rev of codingSnps tool.
by Greg Von Kuster 24 Mar '10

24 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/4c95f1a101f1 changeset: 3560:4c95f1a101f1 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Mar 24 14:14:58 2010 -0400 description: Next rev of codingSnps tool. diffstat: tools/evolution/codingSnps.pl | 268 ++++++++++++++++++---------------------- tools/evolution/codingSnps.xml | 2 +- 2 files changed, 124 insertions(+), 146 deletions(-) diffs (423 lines): diff -r bc2e61c2dac1 -r 4c95f1a101f1 tools/evolution/codingSnps.pl --- a/tools/evolution/codingSnps.pl Tue Mar 23 15:43:58 2010 -0400 +++ b/tools/evolution/codingSnps.pl Wed Mar 24 14:14:58 2010 -0400 @@ -9,75 +9,32 @@ # those that cause a frameshift or substitution in the amino acid. ######################################################################### -my $uniq = 0; # flag for whether want uniq positions -my $syn = 0; # flag for if want synonomous changes rather than non-syn -my $seqFlag = "2bit"; # flag to set sequence type 2bit|nib -my $nibDir; # directory containg data -my $nibTag; # tag for directory above - -################################################################################ -# Parse command line arguments # -################################################################################ - -# make sure we have enough arguments if (!@ARGV or scalar @ARGV < 3) { - print STDERR "Usage: codingSnps.pl snps.bed genes.bed locfile.loc [chr=# start=# end=# snp=#] output_file\n"; + print "Usage: codingSnps.pl snps.bed genes.bed (/dir/nib/|Galaxy build= loc=) [chr=# start=# end=# snp=#] > codingSnps.txt\n"; exit; } - -# get first three command line arguments -my $snpFile = shift @ARGV; +my $uniq = 0; #flag for whether want uniq positions +my $syn = 0; #flag for if want synonomous changes rather than non-syn +my $snpFile = shift @ARGV; my $geneFile = shift @ARGV; -my $locFile = shift @ARGV; - -# read $locFile to get $nibDir (ignoring commets) -# FIXME: the last entry is the one you get -open(LF, "< $locFile") || die "open($locFile): $!\n"; -while(<LF>) { - s/#.*$//; - s/(?:^\s+|\s+$)//g; - next if (/^$/); - - # $tag and $path are set for each "valid" line in the file - ($nibTag, $nibDir) = split(/\t/); -} -close(LF); - -# bed like columns in default positions -my $col0 = 0; +my $nibDir = shift @ARGV; +if ($nibDir eq 'Galaxy') { getGalaxyInfo(); } +my $seqFlag = "2bit"; #flag to set sequence type 2bit|nib +my $col0 = 0; #bed like columns in default positions my $col1 = 1; my $col2 = 2; my $col3 = 3; - -# get column positions for chr, start, end, snp -# column positions 1 based coming in (for Galaxy) +#column positions 1 based coming in (for Galaxy) foreach (@ARGV) { - if (/^chr=(\d+)$/) { - $col0 = $1 - 1; - } elsif (/^start=(\d+)$/) { - $col1 = $1 - 1; - } elsif (/^end=(\d+)$/) { - $col2 = $1 - 1; - } elsif (/^snp=(\d+)$/) { - $col3 = $1 - 1; - } + if (/chr=(\d+)/) { $col0 = $1 -1; } + elsif (/start=(\d+)/) { $col1 = $1 -1; } + elsif (/end=(\d+)/) { $col2 = $1 -1; } + elsif (/snp=(\d+)/) { $col3 = $1 -1; } } - -# make sure the column positions are sane if ($col0 < 0 || $col1 < 0 || $col2 < 0 || $col3 < 0) { print STDERR "ERROR column numbers are given with origin 1\n"; exit 1; } - -# get the output_file from the command line arguments -my $outFile = $ARGV[$#ARGV]; - -open(OUTFILE, "> $outFile") || die "open($outFile): $!\n"; - -################################################################################ -# Initialization # -################################################################################ - my @genes; #bed lines for genes, sorted by chrom and start my %chrSt; #index in array where each chrom starts my %codon; #hash of codon amino acid conversions @@ -97,13 +54,7 @@ "V" => "A/C/G", "N" => "A/C/G/T" ); - fill_codon(); - -################################################################################ -# Main # -################################################################################ - open(FH, "cat $geneFile | sort -k1,1 -k2,2n |") or die "Couldn't open and sort $geneFile, $!\n"; my $i = 0; @@ -117,7 +68,7 @@ } close FH or die "Couldn't close $geneFile, $!\n"; -if ($ends) { print STDERR "TESTING using block ends rather than sizes\n"; } +if ($ends) { print STDERR "WARNING using block ends rather than sizes\n"; } #open snps sorted as well my $s1 = $col0 + 1; #sort order is origin 1 @@ -129,6 +80,7 @@ my %done; while(<FH>) { chomp; + if (/^\s*#/) { next; } #comment my @s = split(/\t/); #SNP fields if (!@s or !$s[$col0]) { die "ERROR missing SNP data, $_\n"; } my $size = $#s; @@ -200,14 +152,10 @@ } } close FH or die "Couldn't close $snpFile, $!\n"; -close(OUTFILE) || die "close($outFile): $!\n"; exit; -################################################################################ -# Subroutines # -################################################################################ - +######################################################################## sub processSnp { my $sref = shift; my $gref = shift; @@ -220,7 +168,7 @@ my $i = 0; my @st = split(/,/, $gref->[11]); my @size = split(/,/, $gref->[10]); - if (scalar @st ne $gref->[9]) { die "bad gene $gref->[3]\n"; } + if (scalar @st ne $gref->[9]) { return; } #cant do this gene #die "bad gene $gref->[3]\n"; } my @pos; my $in = 0; for($i = 0; $i < $gref->[9]; $i++) { @@ -246,12 +194,12 @@ my $c = ($copy =~ tr/-//); if ($c % 3 == 0) { return; } #not frameshift #handle bed4 to bed4 + 4 (pgSnp) - print OUTFILE "$sref->[$col0]\t$sref->[$col1]\t$sref->[$col2]\t$sref->[$col3]"; + print "$sref->[$col0]\t$sref->[$col1]\t$sref->[$col2]\t$sref->[$col3]"; #if ($sref->[4]) { print "\t$sref->[4]"; } #if ($sref->[5]) { print "\t$sref->[5]"; } #if ($sref->[6]) { print "\t$sref->[6]"; } #if ($sref->[7]) { print "\t$sref->[7]"; } - print OUTFILE "\t$gref->[3]\tframeshift\n"; + print "\t$gref->[3]\tframeshift\n"; $done{"$sref->[$col0] $sref->[$col1] $sref->[$col2]"}++; return; }elsif ($sref->[$col1] == $sref->[$col2]) { #insertion @@ -259,12 +207,12 @@ my $c = ($copy =~ tr/\[ACTG]+//); if ($c % 3 == 0) { return; } #not frameshift #handle bed4 to bed4 + 4 (pgSnp) - print OUTFILE "$sref->[$col0]\t$sref->[$col1]\t$sref->[$col2]\t$sref->[$col3]"; + print "$sref->[$col0]\t$sref->[$col1]\t$sref->[$col2]\t$sref->[$col3]"; #if ($sref->[4]) { print "\t$sref->[4]"; } #if ($sref->[5]) { print "\t$sref->[5]"; } #if ($sref->[6]) { print "\t$sref->[6]"; } #if ($sref->[7]) { print "\t$sref->[7]"; } - print OUTFILE "\t$gref->[3]\tframeshift\n"; + print "\t$gref->[3]\tframeshift\n"; $done{"$sref->[$col0] $sref->[$col1] $sref->[$col2]"}++; return; } @@ -310,6 +258,7 @@ my @vars = split(/\//, $sref->[$col3]); if ($gref->[5] eq '-') { #complement oldnts and revcomp vars $oldnts = compl($oldnts); + if (!$oldnts) { return; } #skip this one $oldnts = join('', (reverse(split(/ */, $oldnts)))); foreach (@vars) { $_ = reverse(split(/ */)); @@ -320,6 +269,7 @@ my @newnts; my $changed = ''; foreach my $v (@vars) { + if (!$v or length($v) != 1) { return; } #only simple changes my @new = split(/ */, $oldnts); $changed = splice(@new, $r, $len, split(/ */, $v)); #should only change single nt @@ -335,8 +285,8 @@ push(@newaa, $t); } if (!$change && $syn) { - print OUTFILE "$sref->[$col0]\t$sref->[$col1]\t$sref->[$col2]\t$sref->[$col3]"; - print OUTFILE "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\n"; + print "$sref->[$col0]\t$sref->[$col1]\t$sref->[$col2]\t$sref->[$col3]"; + print "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\n"; return; }elsif ($syn) { return; } #only want synonymous changes if (!$change) { return; } #no change in amino acids @@ -346,13 +296,14 @@ #print STDERR "oldnt $oldnts, strand $gref->[5]\n"; #exit; #} - print OUTFILE "$sref->[$col0]\t$sref->[$col1]\t$sref->[$col2]\t$sref->[$col3]"; + print "$sref->[$col0]\t$sref->[$col1]\t$sref->[$col2]\t$sref->[$col3]"; #if (defined $sref->[4]) { print "\t$sref->[4]"; } #if (defined $sref->[5]) { print "\t$sref->[5]"; } #if (defined $sref->[6]) { print "\t$sref->[6]"; } #if (defined $sref->[7]) { print "\t$sref->[7]"; } if ($gref->[5] eq '-') { $changed = compl($changed); } #use plus for ref - print OUTFILE "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\t$cdNum\t$changed\n"; + if (!$changed) { return; } #skip this one + print "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\t$cdNum\t$changed\n"; $done{"$sref->[$col0] $sref->[$col1] $sref->[$col2]"}++; } } @@ -415,7 +366,7 @@ my $end = shift; my $strand = '+'; $st--; #change to UCSC numbering - open (BIT, "twoBitToFa -seq=$chr -start=$st -end=$end $nibDir/$nibTag.2bit stdout |") or + open (BIT, "twoBitToFa -seq=$chr -start=$st -end=$end $nibDir stdout |") or die "Couldn't run twoBitToFa, $!\n"; my $seq = ''; while (<BIT>) { @@ -423,7 +374,7 @@ if (/^>/) { next; } #header $seq .= $_; } - close BIT or die "Couldn't finish nibFrag on $chr $st $end, $!\n"; + close BIT or die "Couldn't finish twoBitToFa on $chr $st $end, $!\n"; return $seq; } @@ -454,7 +405,7 @@ elsif ($n eq 'G') { $comp .= 'C'; } elsif ($n eq 'N') { $comp .= 'N'; } elsif ($n eq '-') { $comp .= '-'; } #deletion - else { die "Couldn't do complement of $n for $nts\n"; } + else { $comp = undef; } } return $comp; } @@ -473,69 +424,96 @@ } sub fill_codon { - $codon{GCA} = 'Ala'; - $codon{GCC} = 'Ala'; - $codon{GCG} = 'Ala'; - $codon{GCT} = 'Ala'; - $codon{CGG} = 'Arg'; - $codon{CGT} = 'Arg'; - $codon{CGC} = 'Arg'; - $codon{AGA} = 'Arg'; - $codon{AGG} = 'Arg'; - $codon{CGA} = 'Arg'; - $codon{AAC} = 'Asn'; - $codon{AAT} = 'Asn'; - $codon{GAC} = 'Asp'; - $codon{GAT} = 'Asp'; - $codon{TGC} = 'Cys'; - $codon{TGT} = 'Cys'; - $codon{CAG} = 'Gln'; - $codon{CAA} = 'Gln'; - $codon{GAA} = 'Glu'; - $codon{GAG} = 'Glu'; - $codon{GGG} = 'Gly'; - $codon{GGA} = 'Gly'; - $codon{GGC} = 'Gly'; - $codon{GGT} = 'Gly'; - $codon{CAC} = 'His'; - $codon{CAT} = 'His'; - $codon{ATA} = 'Ile'; - $codon{ATT} = 'Ile'; - $codon{ATC} = 'Ile'; - $codon{CTA} = 'Leu'; - $codon{CTC} = 'Leu'; - $codon{CTG} = 'Leu'; - $codon{CTT} = 'Leu'; - $codon{TTG} = 'Leu'; - $codon{TTA} = 'Leu'; - $codon{AAA} = 'Lys'; - $codon{AAG} = 'Lys'; - $codon{ATG} = 'Met'; - $codon{TTC} = 'Phe'; - $codon{TTT} = 'Phe'; - $codon{CCT} = 'Pro'; - $codon{CCA} = 'Pro'; - $codon{CCC} = 'Pro'; - $codon{CCG} = 'Pro'; - $codon{TCA} = 'Ser'; - $codon{AGC} = 'Ser'; - $codon{AGT} = 'Ser'; - $codon{TCC} = 'Ser'; - $codon{TCT} = 'Ser'; - $codon{TCG} = 'Ser'; - $codon{TGA} = 'Stop'; - $codon{TAG} = 'Stop'; - $codon{TAA} = 'Stop'; - $codon{ACT} = 'Thr'; - $codon{ACA} = 'Thr'; - $codon{ACC} = 'Thr'; - $codon{ACG} = 'Thr'; - $codon{TGG} = 'Trp'; - $codon{TAT} = 'Tyr'; - $codon{TAC} = 'Tyr'; - $codon{GTC} = 'Val'; - $codon{GTA} = 'Val'; - $codon{GTG} = 'Val'; - $codon{GTT} = 'Val'; +$codon{GCA} = 'Ala'; +$codon{GCC} = 'Ala'; +$codon{GCG} = 'Ala'; +$codon{GCT} = 'Ala'; +$codon{CGG} = 'Arg'; +$codon{CGT} = 'Arg'; +$codon{CGC} = 'Arg'; +$codon{AGA} = 'Arg'; +$codon{AGG} = 'Arg'; +$codon{CGA} = 'Arg'; +$codon{AAC} = 'Asn'; +$codon{AAT} = 'Asn'; +$codon{GAC} = 'Asp'; +$codon{GAT} = 'Asp'; +$codon{TGC} = 'Cys'; +$codon{TGT} = 'Cys'; +$codon{CAG} = 'Gln'; +$codon{CAA} = 'Gln'; +$codon{GAA} = 'Glu'; +$codon{GAG} = 'Glu'; +$codon{GGG} = 'Gly'; +$codon{GGA} = 'Gly'; +$codon{GGC} = 'Gly'; +$codon{GGT} = 'Gly'; +$codon{CAC} = 'His'; +$codon{CAT} = 'His'; +$codon{ATA} = 'Ile'; +$codon{ATT} = 'Ile'; +$codon{ATC} = 'Ile'; +$codon{CTA} = 'Leu'; +$codon{CTC} = 'Leu'; +$codon{CTG} = 'Leu'; +$codon{CTT} = 'Leu'; +$codon{TTG} = 'Leu'; +$codon{TTA} = 'Leu'; +$codon{AAA} = 'Lys'; +$codon{AAG} = 'Lys'; +$codon{ATG} = 'Met'; +$codon{TTC} = 'Phe'; +$codon{TTT} = 'Phe'; +$codon{CCT} = 'Pro'; +$codon{CCA} = 'Pro'; +$codon{CCC} = 'Pro'; +$codon{CCG} = 'Pro'; +$codon{TCA} = 'Ser'; +$codon{AGC} = 'Ser'; +$codon{AGT} = 'Ser'; +$codon{TCC} = 'Ser'; +$codon{TCT} = 'Ser'; +$codon{TCG} = 'Ser'; +$codon{TGA} = 'Stop'; +$codon{TAG} = 'Stop'; +$codon{TAA} = 'Stop'; +$codon{ACT} = 'Thr'; +$codon{ACA} = 'Thr'; +$codon{ACC} = 'Thr'; +$codon{ACG} = 'Thr'; +$codon{TGG} = 'Trp'; +$codon{TAT} = 'Tyr'; +$codon{TAC} = 'Tyr'; +$codon{GTC} = 'Val'; +$codon{GTA} = 'Val'; +$codon{GTG} = 'Val'; +$codon{GTT} = 'Val'; } - + +sub getGalaxyInfo { + my $build; + my $locFile; + foreach (@ARGV) { + if (/build=(.*)/) { $build = $1; } + elsif (/loc=(.*)/) { $locFile = $1; } + } + if (!$build or !$locFile) { + print STDERR "ERROR missing build or locfile for Galaxy input\n"; + exit 1; + } + # read $locFile to get $nibDir (ignoring commets) + open(LF, "< $locFile") || die "open($locFile): $!\n"; + while(<LF>) { + s/#.*$//; + s/(?:^\s+|\s+$)//g; + next if (/^$/); + + my @t = split(/\t/); + if ($t[0] eq $build) { $nibDir = $t[1]; } + } + close(LF); + if ($nibDir eq 'Galaxy') { + print STDERR "Failed to find sequence directory in locfile $locFile\n"; + } + $nibDir .= "/$build.2bit"; #we want full path and filename +} diff -r bc2e61c2dac1 -r 4c95f1a101f1 tools/evolution/codingSnps.xml --- a/tools/evolution/codingSnps.xml Tue Mar 23 15:43:58 2010 -0400 +++ b/tools/evolution/codingSnps.xml Wed Mar 24 14:14:58 2010 -0400 @@ -1,7 +1,7 @@ <tool id="codingSnps" name="Amino-acid changes"> <description>caused by a set of SNPs</description> <command interpreter="perl"> - codingSnps.pl $input1 $input2 ${GALAXY_DATA_INDEX_DIR}/codingSnps.loc chr=${input1.metadata.chromCol} start=${input1.metadata.startCol} end=${input1.metadata.endCol} snp=$col1 $out_file1 + codingSnps.pl $input1 $input2 Galaxy build=${input1.metadata.dbkey} loc=${GALAXY_DATA_INDEX_DIR}/codingSnps.loc chr=${input1.metadata.chromCol} start=${input1.metadata.startCol} end=${input1.metadata.endCol} snp=$col1 > $out_file1 </command> <inputs> <param format="interval" name="input1" type="data" label="SNPs"/>

1 0

[hg] galaxy 3559: Add the add_scores tool.
by Greg Von Kuster 24 Mar '10

24 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/bc2e61c2dac1 changeset: 3559:bc2e61c2dac1 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Mar 23 15:43:58 2010 -0400 description: Add the add_scores tool. diffstat: test-data/add_scores_input1.interval | 20 +++++++++++ test-data/add_scores_input2.bed | 25 ++++++++++++++ test-data/add_scores_output1.interval | 20 +++++++++++ test-data/add_scores_output2.interval | 25 ++++++++++++++ tool-data/add_scores.loc.sample | 21 ++++++++++++ tool_conf.xml.sample | 1 + tools/evolution/add_scores.xml | 60 +++++++++++++++++++++++++++++++++++ 7 files changed, 172 insertions(+), 0 deletions(-) diffs (206 lines): diff -r dfaa18960944 -r bc2e61c2dac1 test-data/add_scores_input1.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/add_scores_input1.interval Tue Mar 23 15:43:58 2010 -0400 @@ -0,0 +1,20 @@ +chr20 74149 74150 G G +chr22 14642921 14642922 C A +chr20 74148 74149 T C +chr22 15452519 15452520 C C +chr22 15472687 15472688 C N +chr22 15508088 15508089 G G +chr22 15534573 15534574 C C +chr20 24770 24771 C C +chr20 24961 24962 T T +chr22 15451993 15451994 C C +chr22 14667850 14667851 G G +chr22 15452482 15452483 A G +chr20 71317 71318 T T +chr20 74223 74224 A A +chr22 15453065 15453066 A G +chr20 74284 74285 T T +chr20 74309 74310 A A +chr22 15472610 15472611 G N +chr20 86193 86194 C C +chr20 87418 87419 C C diff -r dfaa18960944 -r bc2e61c2dac1 test-data/add_scores_input2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/add_scores_input2.bed Tue Mar 23 15:43:58 2010 -0400 @@ -0,0 +1,25 @@ +chr1 90000 90001 A +chr2 90000 90001 A +chr3 90000 90001 A +chr4 90000 90001 A +chr5 90000 90001 A +chr6 90000 90001 A +chr7 90000 90001 A +chr8 90000 90001 A +chr9 90000 90001 A +chr10 90000 90001 A +chr11 90000 90001 A +chr12 90000 90001 A +chr13 90000 90001 A +chr14 90000 90001 A +chr15 90000 90001 A +chr16 90000 90001 A +chr17 90000 90001 A +chr18 90000 90001 A +chr19 90000 90001 A +chr20 90000 90001 A +chr21 90000 90001 A +chr22 90000 90001 A +chrX 90000 90001 A +chrY 90000 90001 A +chrM 9000 9001 A diff -r dfaa18960944 -r bc2e61c2dac1 test-data/add_scores_output1.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/add_scores_output1.interval Tue Mar 23 15:43:58 2010 -0400 @@ -0,0 +1,20 @@ +chr20 74149 74150 G G 0.885 +chr22 14642921 14642922 C A -1.844 +chr20 74148 74149 T C -3.161 +chr22 15452519 15452520 C C -1.138 +chr22 15472687 15472688 C N NA +chr22 15508088 15508089 G G -1.398 +chr22 15534573 15534574 C C 0.460 +chr20 24770 24771 C C -1.374 +chr20 24961 24962 T T -1.599 +chr22 15451993 15451994 C C 0.645 +chr22 14667850 14667851 G G 0.469 +chr22 15452482 15452483 A G -1.246 +chr20 71317 71318 T T -0.825 +chr20 74223 74224 A A -1.451 +chr22 15453065 15453066 A G -0.776 +chr20 74284 74285 T T -0.701 +chr20 74309 74310 A A -0.863 +chr22 15472610 15472611 G N NA +chr20 86193 86194 C C 0.887 +chr20 87418 87419 C C -1.703 diff -r dfaa18960944 -r bc2e61c2dac1 test-data/add_scores_output2.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/add_scores_output2.interval Tue Mar 23 15:43:58 2010 -0400 @@ -0,0 +1,25 @@ +chr1 90000 90001 A 0.431 +chr2 90000 90001 A 0.514 +chr3 90000 90001 A 0.808 +chr4 90000 90001 A 0.456 +chr5 90000 90001 A 0.446 +chr6 90000 90001 A 0.397 +chr7 90000 90001 A 0.446 +chr8 90000 90001 A NA +chr9 90000 90001 A 0.470 +chr10 90000 90001 A 0.463 +chr11 90000 90001 A 0.369 +chr12 90000 90001 A 0.557 +chr13 90000 90001 A NA +chr14 90000 90001 A NA +chr15 90000 90001 A NA +chr16 90000 90001 A 0.819 +chr17 90000 90001 A -0.993 +chr18 90000 90001 A 0.657 +chr19 90000 90001 A 0.372 +chr20 90000 90001 A 0.360 +chr21 90000 90001 A NA +chr22 90000 90001 A NA +chrX 90000 90001 A 0.414 +chrY 90000 90001 A 0.414 +chrM 9000 9001 A -0.587 diff -r dfaa18960944 -r bc2e61c2dac1 tool-data/add_scores.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/add_scores.loc.sample Tue Mar 23 15:43:58 2010 -0400 @@ -0,0 +1,21 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of gzipped genome files for use with add_scores. You will +#need to supply these files and then create a add_scores.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The add_scores.loc +#file has this format (white space characters are TAB characters): +# +#<build> <file_path> +# +#So, for example, if your add_scores.loc began like this: +# +#hg18 /afs/bx.psu.edu/depot/data/genome/hg18/misc/phyloP/ +# +#then your /afs/bx.psu.edu/depot/data/genome/hg18/misc/phyloP/ directory +#would need to contain the following gzipped files, among others: +# +#-rw-r--r-- 1 rico rico 161981190 2010-03-19 12:48 chr10.phyloP44way.primate.wigFix.gz +#-rw-r--r-- 1 rico rico 54091 2010-03-19 12:56 chr10_random.phyloP44way.primate.wigFix.gz +#-rw-r--r-- 1 rico rico 158621990 2010-03-19 12:46 chr11.phyloP44way.primate.wigFix.gz +# +hg18 /galaxy/data/hg18/misc/phyloP diff -r dfaa18960944 -r bc2e61c2dac1 tool_conf.xml.sample --- a/tool_conf.xml.sample Tue Mar 23 13:53:21 2010 -0400 +++ b/tool_conf.xml.sample Tue Mar 23 15:43:58 2010 -0400 @@ -162,6 +162,7 @@ <tool file="hyphy/hyphy_dnds_wrapper.xml" /> <tool file="evolution/mutate_snp_codon.xml" /> <tool file="evolution/codingSnps.xml" /> + <tool file="evolution/add_scores.xml" /> </section> <section name="Metagenomic analyses" id="tax_manipulation"> <tool file="taxonomy/gi2taxonomy.xml" /> diff -r dfaa18960944 -r bc2e61c2dac1 tools/evolution/add_scores.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/evolution/add_scores.xml Tue Mar 23 15:43:58 2010 -0400 @@ -0,0 +1,60 @@ +<tool id="add_scores" name="Add scores"> + <description>for interspecies conservation at each SNPs</description> + <command> + add_scores $input1 ${input1.metadata.dbkey} ${input1.metadata.chromCol} ${input1.metadata.startCol} ${GALAXY_DATA_INDEX_DIR}/add_scores.loc $out_file1 + </command> + <inputs> + <param format="interval" name="input1" type="data" label="SNPs"/> + </inputs> + <outputs> + <data format="input" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="input1" value="add_scores_input1.interval" dbkey="hg18" /> + <output name="output" file="add_scores_output1.interval" /> + </test> + <test> + <param name="input1" value="add_scores_input2.bed" dbkey="hg18" /> + <output name="output" file="add_scores_output2.interval" /> + </test> + </tests> + + <help> +This tool adds a column that measures interspecies conservation at each SNP position, using conservation scores for primates computed by the phyloP program. It currently works only for hg18. + +**Example** + +- input file, with SNPs:: + + chr22 16440426 14440427 C/T + chr22 15494851 14494852 A/G + chr22 14494911 14494912 A/T + chr22 14550435 14550436 A/G + chr22 14611956 14611957 G/T + chr22 14612076 14612077 A/G + chr22 14668537 14668538 C + chr22 14668703 14668704 A/T + chr22 14668775 14668776 G + chr22 14680074 14680075 A/T + etc. + +- output file, showing non-synonymous substitutions in coding regions:: + + chr22 16440426 14440427 C/T 0.509 + chr22 15494851 14494852 A/G 0.427 + chr22 14494911 14494912 A/T NA + chr22 14550435 14550436 A/G NA + chr22 14611956 14611957 G/T -2.142 + chr22 14612076 14612077 A/G 0.369 + chr22 14668537 14668538 C 0.419 + chr22 14668703 14668704 A/T -1.462 + chr22 14668775 14668776 G 0.470 + chr22 14680074 14680075 A/T 0.000 + chr22 14680074 14680075 A/T 0.303 + etc. + +"NA", means that the phyloP score was not available. + +</help> +</tool>

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[hg] galaxy 3558: Add the codingSnps tool.
by Greg Von Kuster 24 Mar '10

24 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/dfaa18960944 changeset: 3558:dfaa18960944 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Mar 23 13:53:21 2010 -0400 description: Add the codingSnps tool. diffstat: test-data/codingSnps_input1.interval | 21 + test-data/codingSnps_input2.bed | 20 + test-data/codingSnps_output.interval | 21 + tool-data/codingSnps.loc.sample | 25 + tool_conf.xml.sample | 1 + tools/evolution/codingSnps.pl | 541 +++++++++++++++++++++++++++++++++++ tools/evolution/codingSnps.xml | 89 +++++ tools/evolution/codingSnps_filter.py | 43 ++ 8 files changed, 761 insertions(+), 0 deletions(-) diffs (799 lines): diff -r a67ca0795efb -r dfaa18960944 test-data/codingSnps_input1.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/codingSnps_input1.interval Tue Mar 23 13:53:21 2010 -0400 @@ -0,0 +1,21 @@ +chr1 1415785 1415786 C C S N C N C N C +chr1 1420777 1420778 C C Y N C N C N C +chr1 1469195 1469196 A G R R G G G G G +chr1 1541789 1541790 T C Y Y N Y N T N +chr1 1548654 1548655 T T C N C N N N N +chr1 1549089 1549090 T C A A T A N A N +chr1 1551984 1551985 C C Y N C N N N N +chr1 1571349 1571350 G A R N N N N N N +chr1 1571354 1571355 G G R N N N N N N +chr1 1589750 1589751 A G G N G N G N G +chr1 1675899 1675900 G A C C G C G C N +chr1 1714578 1714579 G G R N A N G N G +chr1 1837838 1837839 T C Y N T N T N C +chr1 1839388 1839389 A A T T A T A T A +chr1 1839389 1839390 T T Y N T N T N C +chr1 1839603 1839604 G G R N G N G N R +chr1 1843968 1843969 A G G G R R A A G +chr1 1844405 1844406 C C Y Y C C N C Y +chr1 1876878 1876879 A G G N N N N N N +chr1 1886192 1886193 G N R N G N N N N +chr1 1890091 1890092 T C Y Y C C N C N diff -r a67ca0795efb -r dfaa18960944 test-data/codingSnps_input2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/codingSnps_input2.bed Tue Mar 23 13:53:21 2010 -0400 @@ -0,0 +1,20 @@ +chr1 67051161 67163158 ENST00000371026 0 - 67052400 67163102 0 17 1290,157,227,99,122,158,152,87,203,195,156,140,157,113,185,175,226, 0,9470,13929,14921,20694,21100,22735,24819,27578,34593,49256,58479,61890,78263,80338,92310,111771, +chr1 67075869 67163055 ENST00000371023 0 - 67075923 67162979 0 10 198,203,195,156,140,157,113,185,175,123, 0,2870,9885,24548,33771,37182,53555,55630,67602,87063, +chr1 1843259 1849228 ENST00000378596 0 - 1843585 1847183 0 10 428,135,161,133,155,130,156,120,56,1278, 0,628,1024,1406,1814,2430,3822,4267,4496,4691, +chr1 1874611 1925136 ENST00000270720 0 - 1876876 1912255 0 18 2538,165,90,67,119,174,156,199,158,103,111,174,105,99,144,85,86,137, 0,3307,5807,6651,10436,11575,13058,15322,17346,18667,19624,20712,32073,33624,35199,35576,37577,50388, +chr1 1838889 1840572 ENST00000310991 0 - 1839180 1840564 0 5 572,179,42,44,92, 0,662,1302,1454,1591, +chr1 1838888 1840096 ENST00000378602 0 - 1839180 1839855 0 2 573,545, 0,663, +chr1 1672537 1699769 ENST00000344463 0 - 1674202 1686705 0 14 1822,83,158,100,155,103,86,155,204,143,169,84,219,182, 0,2328,2812,3045,3305,4135,5019,5264,5868,7862,8495,10713,13989,27050, +chr1 1836125 1838593 ENST00000307786 0 + 1836579 1838492 0 6 481,51,175,145,101,148, 0,858,1614,1925,2147,2320, +chr1 1672530 1701368 ENST00000378625 0 - 1674202 1686705 0 14 1829,83,158,100,155,103,86,155,204,143,169,84,219,165, 0,2335,2819,3052,3312,4142,5026,5271,5875,7869,8502,10720,13996,28673, +chr1 1672537 1699769 ENST00000341426 0 - 1674202 1686705 0 12 1822,83,158,100,155,103,86,106,130,84,219,182, 0,2328,2812,3045,3305,4135,5019,5264,5942,10713,13989,27050, +chr1 1540746 1555847 ENST00000378710 0 + 1540873 1555773 0 19 130,107,311,172,107,195,143,105,163,134,149,157,161,127,234,179,182,66,313, 0,1004,7885,8270,9291,9487,9782,11146,11333,11570,11792,12169,12515,12769,12985,13629,13881,14135,14788, +chr1 1672530 1700089 ENST00000341991 0 - 1674202 1686705 0 12 1829,83,158,100,155,103,86,106,130,84,219,45, 0,2335,2819,3052,3312,4142,5026,5271,5949,10720,13996,27514, +chr1 1540746 1555847 ENST00000355826 0 + 1540873 1555773 0 20 130,107,311,172,107,195,143,108,105,163,134,149,157,161,127,234,179,182,66,313, 0,1004,7885,8270,9291,9487,9782,10042,11146,11333,11570,11792,12169,12515,12769,12985,13629,13881,14135,14788, +chr1 1836125 1838593 ENST00000378604 0 + 1836579 1838492 0 5 481,175,145,101,148, 0,1614,1925,2147,2320, +chr1 1540746 1555847 ENST00000357882 0 + 1540873 1555773 0 19 130,107,311,172,107,143,108,105,163,134,149,157,161,127,234,179,182,66,313, 0,1004,7885,8270,9291,9782,10042,11146,11333,11570,11792,12169,12515,12769,12985,13629,13881,14135,14788, +chr1 1540746 1555847 ENST00000357882 0 + 1540873 1555773 0 19 130,107,311,172,107,143,108,105,163,134,149,157,161,127,234,179,182,66,313, 0,1004,7885,8270,9291,9782,10042,11146,11333,11570,11792,12169,12515,12769,12985,13629,13881,14135,14788, +chr1 67075991 67163158 ENST00000395250 0 - 67075991 67113089 0 11 27,45,203,195,156,140,157,113,185,175,226, 0,31,2748,9763,24426,33649,37060,53433,55508,67480,86941, +chr1 201326404 201403155 ENST00000309502 0 + 201364592 201401651 0 6 81,18,100,155,398,2144, 0,1039,37175,37624,38131,74607, +chr1 8335052 8508585 ENST00000377464 0 - 8337733 8508430 0 17 2715,181,147,721,223,1379,114,162,200,93,163,81,99,100,125,49,181, 0,3013,3694,5790,7358,7706,9357,10277,11650,12340,13406,70321,113519,142657,144999,156220,173352, +chr1 8335054 8800286 ENST00000400908 0 - 8337733 8638943 0 23 2713,181,147,721,223,1379,114,162,200,93,163,81,99,100,125,49,105,97,106,126,71,469,481, 0,3011,3692,5788,7356,7704,9355,10275,11648,12338,13404,70319,113517,142655,144997,156218,188805,204066,205009,262152,271901,303564,464751, diff -r a67ca0795efb -r dfaa18960944 test-data/codingSnps_output.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/codingSnps_output.interval Tue Mar 23 13:53:21 2010 -0400 @@ -0,0 +1,21 @@ +chr1 1541789 1541790 C/T ENST00000355826 Phe:Leu/Phe 15 T +chr1 1541789 1541790 C/T ENST00000357882 Phe:Leu/Phe 15 T +chr1 1541789 1541790 C/T ENST00000357882 Phe:Leu/Phe 15 T +chr1 1541789 1541790 C/T ENST00000378710 Phe:Leu/Phe 15 T +chr1 1548654 1548655 C ENST00000355826 Met:Thr 45 T +chr1 1548654 1548655 C ENST00000357882 Met:Thr 45 T +chr1 1548654 1548655 C ENST00000357882 Met:Thr 45 T +chr1 1548654 1548655 C ENST00000378710 Met:Thr 45 T +chr1 1675899 1675900 C ENST00000341991 Asn:Lys 262 G +chr1 1675899 1675900 C ENST00000378625 Asn:Lys 407 G +chr1 1675899 1675900 C ENST00000341426 Asn:Lys 262 G +chr1 1675899 1675900 C ENST00000344463 Asn:Lys 407 G +chr1 1837838 1837839 C/T ENST00000307786 Trp:Arg/Trp 60 T +chr1 1837838 1837839 C/T ENST00000378604 Trp:Arg/Trp 43 T +chr1 1839388 1839389 T ENST00000378602 Met:Lys 126 A +chr1 1839388 1839389 T ENST00000310991 Met:Lys 141 A +chr1 1839389 1839390 C/T ENST00000378602 Met:Val/Met 126 T +chr1 1839389 1839390 C/T ENST00000310991 Met:Val/Met 141 T +chr1 1844405 1844406 C/T ENST00000378596 Glu:Glu/Lys 187 C +chr1 1876878 1876879 G ENST00000270720 Stop:Gln 763 A +chr1 1890091 1890092 C/T ENST00000270720 Ile:Val/Ile 363 T diff -r a67ca0795efb -r dfaa18960944 tool-data/codingSnps.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/codingSnps.loc.sample Tue Mar 23 13:53:21 2010 -0400 @@ -0,0 +1,25 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of nib genome files for use with codingSnps. You will +#need to supply these files and then create a codingSnps.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The codingSnps.loc +#file has this format (white space characters are TAB characters): +# +#<build> <file_path> +# +#So, for example, if your codingSnps.loc began like this: +# +#hg18 /afs/bx.psu.edu/depot/data/genome/hg18/ + +# +#then your /afs/bx.psu.edu/depot/data/genome/hg18/ directory +#would need to contain the following 2bit file: +# +# +#-rw-r--r-- 1 g2data g2data 807604784 Dec 8 13:21 hg18.2bit + +#Your codingSnps.loc file should include an entry per line for +#each file you have stored that you want to be available. Note that +#your files should all have the extension '2bit'. + +hg18 /afs/bx.psu.edu/depot/data/genome/hg18 diff -r a67ca0795efb -r dfaa18960944 tool_conf.xml.sample --- a/tool_conf.xml.sample Tue Mar 23 13:15:56 2010 -0400 +++ b/tool_conf.xml.sample Tue Mar 23 13:53:21 2010 -0400 @@ -161,6 +161,7 @@ <tool file="hyphy/hyphy_nj_tree_wrapper.xml" /> <tool file="hyphy/hyphy_dnds_wrapper.xml" /> <tool file="evolution/mutate_snp_codon.xml" /> + <tool file="evolution/codingSnps.xml" /> </section> <section name="Metagenomic analyses" id="tax_manipulation"> <tool file="taxonomy/gi2taxonomy.xml" /> diff -r a67ca0795efb -r dfaa18960944 tools/evolution/codingSnps.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/evolution/codingSnps.pl Tue Mar 23 13:53:21 2010 -0400 @@ -0,0 +1,541 @@ +#!/usr/bin/perl -w +use strict; + +######################################################################### +# codingSnps.pl +# This takes a bed file with the names being / separated nts +# and a gene bed file with cds start and stop. +# It then checks for changes in coding regions, reporting +# those that cause a frameshift or substitution in the amino acid. +######################################################################### + +my $uniq = 0; # flag for whether want uniq positions +my $syn = 0; # flag for if want synonomous changes rather than non-syn +my $seqFlag = "2bit"; # flag to set sequence type 2bit|nib +my $nibDir; # directory containg data +my $nibTag; # tag for directory above + +################################################################################ +# Parse command line arguments # +################################################################################ + +# make sure we have enough arguments +if (!@ARGV or scalar @ARGV < 3) { + print STDERR "Usage: codingSnps.pl snps.bed genes.bed locfile.loc [chr=# start=# end=# snp=#] output_file\n"; + exit; +} + +# get first three command line arguments +my $snpFile = shift @ARGV; +my $geneFile = shift @ARGV; +my $locFile = shift @ARGV; + +# read $locFile to get $nibDir (ignoring commets) +# FIXME: the last entry is the one you get +open(LF, "< $locFile") || die "open($locFile): $!\n"; +while(<LF>) { + s/#.*$//; + s/(?:^\s+|\s+$)//g; + next if (/^$/); + + # $tag and $path are set for each "valid" line in the file + ($nibTag, $nibDir) = split(/\t/); +} +close(LF); + +# bed like columns in default positions +my $col0 = 0; +my $col1 = 1; +my $col2 = 2; +my $col3 = 3; + +# get column positions for chr, start, end, snp +# column positions 1 based coming in (for Galaxy) +foreach (@ARGV) { + if (/^chr=(\d+)$/) { + $col0 = $1 - 1; + } elsif (/^start=(\d+)$/) { + $col1 = $1 - 1; + } elsif (/^end=(\d+)$/) { + $col2 = $1 - 1; + } elsif (/^snp=(\d+)$/) { + $col3 = $1 - 1; + } +} + +# make sure the column positions are sane +if ($col0 < 0 || $col1 < 0 || $col2 < 0 || $col3 < 0) { + print STDERR "ERROR column numbers are given with origin 1\n"; + exit 1; +} + +# get the output_file from the command line arguments +my $outFile = $ARGV[$#ARGV]; + +open(OUTFILE, "> $outFile") || die "open($outFile): $!\n"; + +################################################################################ +# Initialization # +################################################################################ + +my @genes; #bed lines for genes, sorted by chrom and start +my %chrSt; #index in array where each chrom starts +my %codon; #hash of codon amino acid conversions +my $ends = 0; #ends vs sizes in bed 11 position, starts relative to chrom +my $ignoreN = 1; #skip N + +my %amb = ( +"R" => "A/G", +"Y" => "C/T", +"S" => "C/G", +"W" => "A/T", +"K" => "G/T", +"M" => "A/C", +"B" => "C/G/T", +"D" => "A/G/T", +"H" => "A/C/T", +"V" => "A/C/G", +"N" => "A/C/G/T" +); + +fill_codon(); + +################################################################################ +# Main # +################################################################################ + +open(FH, "cat $geneFile | sort -k1,1 -k2,2n |") + or die "Couldn't open and sort $geneFile, $!\n"; +my $i = 0; +while(<FH>) { + chomp; + if (/refGene.cdsEnd|ccdsGene.exonEnds/) { $ends = 1; next; } + push(@genes, "$_"); + my @f = split(/\t/); + if (!exists $chrSt{$f[0]}) { $chrSt{$f[0]} = $i; } + $i++; +} +close FH or die "Couldn't close $geneFile, $!\n"; + +if ($ends) { print STDERR "TESTING using block ends rather than sizes\n"; } + +#open snps sorted as well +my $s1 = $col0 + 1; #sort order is origin 1 +my $s2 = $col1 + 1; +open(FH, "cat $snpFile | sort -k$s1,$s1 -k$s2,${s2}n |") + or die "Couldn't open and sort $snpFile, $!\n"; +$i = 0; +my @g; #one genes fields, should be used repeatedly +my %done; +while(<FH>) { + chomp; + my @s = split(/\t/); #SNP fields + if (!@s or !$s[$col0]) { die "ERROR missing SNP data, $_\n"; } + my $size = $#s; + if ($col0 > $size || $col1 > $size || $col2 > $size || $col3 > $size) { + print STDERR "ERROR file has fewer columns than requested, requested columns (0 based) $col0 $col1 $col2 $col3, file has $size\n"; + exit 1; + } + if ($s[$col1] =~ /\D/) { + print STDERR "ERROR the start point must be an integer not $s[$col1]\n"; + exit 1; + } + if ($s[$col2] =~ /\D/) { + print STDERR "ERROR the start point must be an integer not $s[$col2]\n"; + exit 1; + } + if ($s[$col3] eq 'N' && $ignoreN) { next; } + if (exists $amb{$s[$col3]}) { $s[$col3] = $amb{$s[$col3]}; } + if (!@g && exists $chrSt{$s[$col0]}) { #need to fetch first gene row + $i = $chrSt{$s[$col0]}; + @g = split(/\t/, $genes[$i]); + }elsif (!@g) { + next; #no gene for this chrom + }elsif ($s[$col0] ne $g[0] && exists $chrSt{$s[$col0]}) { #new chrom + $i = $chrSt{$s[$col0]}; + @g = split(/\t/, $genes[$i]); + }elsif ($s[$col0] ne $g[0]) { + next; #no gene for this chrom + }elsif ($s[$col1] < $g[1] && $i == $chrSt{$s[$col0]}) { + next; #before any genes + }elsif ($s[$col1] > $g[2] && ($i == $#genes or $genes[$i+1] !~ $s[$col0])) { + next; #after all genes on chr + }else { + while ($s[$col1] > $g[2] && $i < $#genes) { + $i++; + @g = split(/\t/, $genes[$i]); + if ($s[$col0] ne $g[0]) { last; } #end of gene + } + if ($s[$col0] ne $g[0] or $s[$col1] < $g[1] or $s[$col1] > $g[2]) { + next; #no overlap with genes + } + } + + processSnp(\@s, \@g); + if ($uniq && exists $done{"$s[$col0] $s[$col1] $s[$col2]"}) { next; } + + my $k = $i + 1; #check for more genes without losing data of first + if ($k <= $#genes) { + my @g2 = split(/\t/, $genes[$k]); + while (@g2 && $k <= $#genes) { + @g2 = split(/\t/, $genes[$k]); + if ($s[$col0] ne $g2[0]) { + undef @g2; + last; #not same chrom + }else { + while ($s[$col1] > $g2[2] && $k <= $#genes) { + $k++; + @g2 = split(/\t/, $genes[$k]); + if ($s[$col0] ne $g2[0]) { last; } #end of chrom + } + if ($s[$col0] ne $g2[0] or $s[$col1] < $g2[1] or $s[$col1] > $g2[2]) { + undef @g2; + last; #no overlap with more genes + } + processSnp(\@s, \@g2); + if ($uniq && exists $done{"$s[$col0] $s[$col1] $s[$col2]"}) { last; } + } + $k++; + } + } +} +close FH or die "Couldn't close $snpFile, $!\n"; +close(OUTFILE) || die "close($outFile): $!\n"; + +exit; + +################################################################################ +# Subroutines # +################################################################################ + +sub processSnp { + my $sref = shift; + my $gref = shift; + #overlaps gene, but maybe not coding seq + #inside cds + if ($sref->[$col1] + 1 < $gref->[6] or $sref->[$col2] > $gref->[7]) { + return; #outside of coding + } + #now check exon + my $i = 0; + my @st = split(/,/, $gref->[11]); + my @size = split(/,/, $gref->[10]); + if (scalar @st ne $gref->[9]) { die "bad gene $gref->[3]\n"; } + my @pos; + my $in = 0; + for($i = 0; $i < $gref->[9]; $i++) { + my $sta = $gref->[1] + $st[$i] + 1; #1 based position + my $end = $sta + $size[$i] - 1; # + if ($ends) { $end = $size[$i]; $sta = $st[$i] + 1; } #ends instead of sizes + if ($end < $gref->[6]) { next; } #utr only + if ($sta > $gref->[7]) { next; } #utr only + #shorten to coding only + if ($sta < $gref->[6]) { $sta = $gref->[6] + 1; } + if ($end > $gref->[7]) { $end = $gref->[7]; } + if ($sref->[$col1] + 1 >= $sta && $sref->[$col2] <= $end) { $in = 1; } + elsif ($sref->[$col1] == $sref->[$col2] && $sref->[$col2] <= $end && $sref->[$col2] >= $sta) { $in = 1; } + push(@pos, ($sta .. $end)); #add exon worth of positions + } + #@pos has coding positions for whole gene (chr coors), + #and $in has whether we need to continue + if (!$in) { return; } #not in coding exon + if ((scalar @pos) % 3 != 0) { return; } #partial gene? not even codons + if ($sref->[$col3] =~ /^-+\/[ACTG]+$/ or $sref->[$col3] =~ /^[ACTG]+\/-+$/ or + $sref->[$col3] =~ /^-+$/) { #indel or del + my $copy = $sref->[$col3]; + my $c = ($copy =~ tr/-//); + if ($c % 3 == 0) { return; } #not frameshift + #handle bed4 to bed4 + 4 (pgSnp) + print OUTFILE "$sref->[$col0]\t$sref->[$col1]\t$sref->[$col2]\t$sref->[$col3]"; + #if ($sref->[4]) { print "\t$sref->[4]"; } + #if ($sref->[5]) { print "\t$sref->[5]"; } + #if ($sref->[6]) { print "\t$sref->[6]"; } + #if ($sref->[7]) { print "\t$sref->[7]"; } + print OUTFILE "\t$gref->[3]\tframeshift\n"; + $done{"$sref->[$col0] $sref->[$col1] $sref->[$col2]"}++; + return; + }elsif ($sref->[$col1] == $sref->[$col2]) { #insertion + my $copy = $sref->[$col3]; + my $c = ($copy =~ tr/\[ACTG]+//); + if ($c % 3 == 0) { return; } #not frameshift + #handle bed4 to bed4 + 4 (pgSnp) + print OUTFILE "$sref->[$col0]\t$sref->[$col1]\t$sref->[$col2]\t$sref->[$col3]"; + #if ($sref->[4]) { print "\t$sref->[4]"; } + #if ($sref->[5]) { print "\t$sref->[5]"; } + #if ($sref->[6]) { print "\t$sref->[6]"; } + #if ($sref->[7]) { print "\t$sref->[7]"; } + print OUTFILE "\t$gref->[3]\tframeshift\n"; + $done{"$sref->[$col0] $sref->[$col1] $sref->[$col2]"}++; + return; + } + #check for amino acid substitutions + my $s = $sref->[$col1] + 1; + my $e = $sref->[$col2]; + my $len = $sref->[$col2] - $sref->[$col1]; + if ($gref->[5] eq '-') { + @pos = reverse(@pos); + my $t = $s; + $s = $e; + $e = $t; + } + $i = 0; + my $found = 0; + foreach (@pos) { + if ($s == $_) { + $found = 1; + last; + } + $i++; + } + if ($found) { + my $fs = $i; #keep original start index + #have index where substitution starts + my $cp = $i % 3; + $i -= $cp; #i is now first position in codon + my $cdNum = int($i / 3) + 1; + my $ls = $i; + if (!defined $ls) { die "ERROR not defined ls for $fs $sref->[$col2]\n"; } + if (!@pos) { die "ERROR not defined array pos\n"; } + if (!defined $pos[$ls]) { die "ERROR not defined pos at $ls\n"; } + if (!defined $e) { die "ERROR not defined e for $pos[0] $pos[1] $pos[2]\n"; } + while ($ls <= $#pos && $pos[$ls] ne $e) { + $ls++; + } + my $i2 = $ls + (2 - ($ls % 3)); + if ($i2 > $#pos) { return; } #not a full codon, partial gene? + + if ($i2 - $i < 2) { die "not a full codon positions $i to $i2 for $sref->[3]\n"; } + my $oldnts = getnts($sref->[$col0], @pos[$i..$i2]); + if (!$oldnts) { die "Failed to get sequence for $sref->[$col0] $pos[$i] .. $pos[$i2]\n"; } + my @vars = split(/\//, $sref->[$col3]); + if ($gref->[5] eq '-') { #complement oldnts and revcomp vars + $oldnts = compl($oldnts); + $oldnts = join('', (reverse(split(/ */, $oldnts)))); + foreach (@vars) { + $_ = reverse(split(/ */)); + $_ = compl($_); + } + } + my $r = $fs - $i; #difference in old indexes gives new index + my @newnts; + my $changed = ''; + foreach my $v (@vars) { + my @new = split(/ */, $oldnts); + $changed = splice(@new, $r, $len, split(/ */, $v)); + #should only change single nt + push(@newnts, join("", @new)); + } + #now compute amino acids + my $oldaa = getaa($oldnts); + my @newaa; + my $change = 0; #flag for if there is a change + foreach my $v (@newnts) { + my $t = getaa($v); + if ($t ne $oldaa) { $change = 1; } + push(@newaa, $t); + } + if (!$change && $syn) { + print OUTFILE "$sref->[$col0]\t$sref->[$col1]\t$sref->[$col2]\t$sref->[$col3]"; + print OUTFILE "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\n"; + return; + }elsif ($syn) { return; } #only want synonymous changes + if (!$change) { return; } #no change in amino acids +#if (abs($pos[$i] - $pos[$i2]) > 200) { +#print STDERR "TESTING found mutation at splice site $sref->[0]\t$sref->[1]\t$sref->[2]\n"; +#print STDERR "old $oldaa, new ", join(', ', @newaa), "\n"; +#print STDERR "oldnt $oldnts, strand $gref->[5]\n"; +#exit; +#} + print OUTFILE "$sref->[$col0]\t$sref->[$col1]\t$sref->[$col2]\t$sref->[$col3]"; + #if (defined $sref->[4]) { print "\t$sref->[4]"; } + #if (defined $sref->[5]) { print "\t$sref->[5]"; } + #if (defined $sref->[6]) { print "\t$sref->[6]"; } + #if (defined $sref->[7]) { print "\t$sref->[7]"; } + if ($gref->[5] eq '-') { $changed = compl($changed); } #use plus for ref + print OUTFILE "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\t$cdNum\t$changed\n"; + $done{"$sref->[$col0] $sref->[$col1] $sref->[$col2]"}++; + } +} + +sub getnts { + my $chr = shift; + my @pos = @_; #list of positions not necessarily in order + #list may be reversed or have gaps(introns), at least 3 bps + my $seq = ''; + if (scalar @pos < 3) { die "too small region for $chr $pos[0]\n"; } + if ($pos[0] < $pos[1]) { #not reversed + my $s = $pos[0]; + for(my $i = 1; $i <= $#pos; $i++) { + if ($pos[$i] == $pos[$i-1] + 1) { next; } + if ($seqFlag eq '2bit') { + $seq .= fetchSeq2bit($chr, $s, $pos[$i-1]); + }else { + $seq .= fetchSeqNib($chr, $s, $pos[$i-1]); + } + $s = $pos[$i]; + } + if (length $seq != scalar @pos) { #still need to fetch seq +#if (abs($pos[$#pos]-$pos[0]) > 200) { +#print STDERR "TESTING have split codon $chr $pos[0] $pos[$#pos]\n"; +#exit; +#} + if ($seqFlag eq '2bit') { + $seq .= fetchSeq2bit($chr, $s, $pos[$#pos]); + }else { + $seq .= fetchSeqNib($chr, $s, $pos[$#pos]); + } + } + }else { #reversed + my $s = $pos[$#pos]; + for(my $i = $#pos -1; $i >= 0; $i--) { + if ($pos[$i] == $pos[$i+1] + 1) { next; } + if ($seqFlag eq '2bit') { + $seq .= fetchSeq2bit($chr, $s, $pos[$i+1]); + }else { + $seq .= fetchSeqNib($chr, $s, $pos[$i+1]); + } + $s = $pos[$i]; + } + if (length $seq != scalar @pos) { #still need to fetch seq +#if (abs($pos[$#pos]-$pos[0]) > 200) { +#print STDERR "TESTING have split codon $pos[0] .. $pos[$#pos]\n"; +#} + if ($seqFlag eq '2bit') { + $seq .= fetchSeq2bit($chr, $s, $pos[0]); + }else { + $seq .= fetchSeqNib($chr, $s, $pos[0]); + } + } + } +} + +sub fetchSeq2bit { + my $chr = shift; + my $st = shift; + my $end = shift; + my $strand = '+'; + $st--; #change to UCSC numbering + open (BIT, "twoBitToFa -seq=$chr -start=$st -end=$end $nibDir/$nibTag.2bit stdout |") or + die "Couldn't run twoBitToFa, $!\n"; + my $seq = ''; + while (<BIT>) { + chomp; + if (/^>/) { next; } #header + $seq .= $_; + } + close BIT or die "Couldn't finish nibFrag on $chr $st $end, $!\n"; + return $seq; +} + +sub fetchSeqNib { + my $chr = shift; + my $st = shift; + my $end = shift; + my $strand = '+'; + $st--; #change to UCSC numbering + open (NIB, "nibFrag -upper $nibDir/${chr}.nib $st $end $strand stdout |") or die "Couldn't run nibFrag, $!\n"; + my $seq = ''; + while (<NIB>) { + chomp; + if (/^>/) { next; } #header + $seq .= $_; + } + close NIB or die "Couldn't finish nibFrag on $chr $st $end, $!\n"; + return $seq; +} + +sub compl { + my $nts = shift; + my $comp = ''; + foreach my $n (split(/ */, $nts)) { + if ($n eq 'A') { $comp .= 'T'; } + elsif ($n eq 'T') { $comp .= 'A'; } + elsif ($n eq 'C') { $comp .= 'G'; } + elsif ($n eq 'G') { $comp .= 'C'; } + elsif ($n eq 'N') { $comp .= 'N'; } + elsif ($n eq '-') { $comp .= '-'; } #deletion + else { die "Couldn't do complement of $n for $nts\n"; } + } + return $comp; +} + +sub getaa { + my $nts = shift; #in multiples of 3 + my $aa = ''; + my @n = split(/ */, $nts); + while (@n) { + my @t = splice(@n, 0, 3); + my $n = uc(join("", @t)); + if (!exists $codon{$n}) { $aa .= 'N'; next; } + $aa .= $codon{$n}; + } + return $aa; +} + +sub fill_codon { + $codon{GCA} = 'Ala'; + $codon{GCC} = 'Ala'; + $codon{GCG} = 'Ala'; + $codon{GCT} = 'Ala'; + $codon{CGG} = 'Arg'; + $codon{CGT} = 'Arg'; + $codon{CGC} = 'Arg'; + $codon{AGA} = 'Arg'; + $codon{AGG} = 'Arg'; + $codon{CGA} = 'Arg'; + $codon{AAC} = 'Asn'; + $codon{AAT} = 'Asn'; + $codon{GAC} = 'Asp'; + $codon{GAT} = 'Asp'; + $codon{TGC} = 'Cys'; + $codon{TGT} = 'Cys'; + $codon{CAG} = 'Gln'; + $codon{CAA} = 'Gln'; + $codon{GAA} = 'Glu'; + $codon{GAG} = 'Glu'; + $codon{GGG} = 'Gly'; + $codon{GGA} = 'Gly'; + $codon{GGC} = 'Gly'; + $codon{GGT} = 'Gly'; + $codon{CAC} = 'His'; + $codon{CAT} = 'His'; + $codon{ATA} = 'Ile'; + $codon{ATT} = 'Ile'; + $codon{ATC} = 'Ile'; + $codon{CTA} = 'Leu'; + $codon{CTC} = 'Leu'; + $codon{CTG} = 'Leu'; + $codon{CTT} = 'Leu'; + $codon{TTG} = 'Leu'; + $codon{TTA} = 'Leu'; + $codon{AAA} = 'Lys'; + $codon{AAG} = 'Lys'; + $codon{ATG} = 'Met'; + $codon{TTC} = 'Phe'; + $codon{TTT} = 'Phe'; + $codon{CCT} = 'Pro'; + $codon{CCA} = 'Pro'; + $codon{CCC} = 'Pro'; + $codon{CCG} = 'Pro'; + $codon{TCA} = 'Ser'; + $codon{AGC} = 'Ser'; + $codon{AGT} = 'Ser'; + $codon{TCC} = 'Ser'; + $codon{TCT} = 'Ser'; + $codon{TCG} = 'Ser'; + $codon{TGA} = 'Stop'; + $codon{TAG} = 'Stop'; + $codon{TAA} = 'Stop'; + $codon{ACT} = 'Thr'; + $codon{ACA} = 'Thr'; + $codon{ACC} = 'Thr'; + $codon{ACG} = 'Thr'; + $codon{TGG} = 'Trp'; + $codon{TAT} = 'Tyr'; + $codon{TAC} = 'Tyr'; + $codon{GTC} = 'Val'; + $codon{GTA} = 'Val'; + $codon{GTG} = 'Val'; + $codon{GTT} = 'Val'; +} + diff -r a67ca0795efb -r dfaa18960944 tools/evolution/codingSnps.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/evolution/codingSnps.xml Tue Mar 23 13:53:21 2010 -0400 @@ -0,0 +1,89 @@ +<tool id="codingSnps" name="Amino-acid changes"> + <description>caused by a set of SNPs</description> + <command interpreter="perl"> + codingSnps.pl $input1 $input2 ${GALAXY_DATA_INDEX_DIR}/codingSnps.loc chr=${input1.metadata.chromCol} start=${input1.metadata.startCol} end=${input1.metadata.endCol} snp=$col1 $out_file1 + </command> + <inputs> + <param format="interval" name="input1" type="data" label="SNPs"/> + <param format="interval" name="input2" type="data" label="genes"/> + <param name="col1" label="Column with SNPs" type="data_column" data_ref="input1" /> + </inputs> + <outputs> + <data format="input" name="out_file1" /> + </outputs> + <code file="codingSnps_filter.py"></code> + <requirements> + <requirement type="binary">twoBitToFa</requirement> + </requirements> + <tests> + <test> + <param name="input1" value="codingSnps_input1.interval" dbkey="hg18" /> + <param name="input2" value="codingSnps_input2.bed" dbkey="hg18" /> + <param name="col1" value="6" /> + <output name="output" file="codingSnps_output.interval" /> + </test> + </tests> + + <help> +This tool identifies which SNPs create amino-acid changes in the specified coding regions. + +**Example** + +- first input file, with SNPs:: + + chr22 14440426 14440427 C/T + chr22 14494851 14494852 A/G + chr22 14494911 14494912 A/T + chr22 14550435 14550436 A/G + chr22 14611956 14611957 G/T + chr22 14612076 14612077 A/G + chr22 14668537 14668538 C + chr22 14668703 14668704 A/T + chr22 14668775 14668776 G + chr22 14680074 14680075 A/T + etc. + + alternatively indicating polymorphisms using ambiguous-nucleotide symbols: + + chr22 14440426 14440427 Y + chr22 14494851 14494852 R + chr22 14494911 14494912 W + chr22 14550435 14550436 R + chr22 14611956 14611957 K + chr22 14612076 14612077 R + chr22 14668537 14668538 C + chr22 14668703 14668704 W + chr22 14668775 14668776 G + chr22 14680074 14680075 W + etc. + +- second input file, with UCSC annotations for human genes:: + + chr22 14504263 14572999 uc002zkr.2 0 - 14504263 14504263 0 5 710,91,136,138,94, 0,38133,62547,62901,68642, + chr22 14527995 14572999 uc010gqo.1 0 - 14527995 14527995 0 4 3826,91,136,94, 0,14401,38815,44910, + chr22 14542065 14552264 uc002zkt.2 0 + 14542065 14542065 0 3 323,88,313, 0,2416,9886, + chr22 14559619 14561004 uc002zku.2 0 - 14559619 14559619 0 1 1385, 0, + chr22 14567164 14572999 uc002zkv.2 0 - 14567164 14567164 0 5 138,112,115,111,94, 0,1867,2099,3516,5741, + chr22 14620243 14620281 uc002zkw.1 0 - 14620243 14620243 0 1 38, 0, + chr22 14620300 14620339 uc002zkx.1 0 - 14620300 14620300 0 1 39, 0, + chr22 14621086 14621125 uc002zky.1 0 + 14621086 14621086 0 1 39, 0, + chr22 14622000 14622030 uc002zkz.1 0 - 14622000 14622000 0 1 30, 0, + chr22 14623380 14623414 uc002zla.1 0 - 14623380 14623380 0 1 34, 0, + etc. + +- output file, showing non-synonymous substitutions in coding regions:: + + chr22 15452482 15452483 G uc002zlp.1 Trp:Arg 320 A + chr22 15644564 15644565 T uc002zlv.1 His:Asn 442 G + chr22 15645123 15645124 C uc002zlv.1 Phe:Leu 255 A + chr22 15645193 15645194 A/G uc002zlv.1 Pro:Leu/Pro 232 G + chr22 15660821 15660822 A/G uc002zlv.1 Thr:Met/Thr 143 G + chr22 15969208 15969209 C/T uc002zly.1 Ala:Ala/Val 367 C + chr22 15969208 15969209 C/T uc010gqt.1 Ala:Ala/Val 315 C + chr22 15999075 15999076 C/G uc002zmd.1 Arg:Arg/Ser 180 C + chr22 15999075 15999076 C/G uc002zme.1 Arg:Arg/Ser 161 C + chr22 15999075 15999076 C/G uc002zmf.1 Arg:Arg/Ser 369 C + etc. + +</help> +</tool> diff -r a67ca0795efb -r dfaa18960944 tools/evolution/codingSnps_filter.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/evolution/codingSnps_filter.py Tue Mar 23 13:53:21 2010 -0400 @@ -0,0 +1,43 @@ +# runs after the job (and after the default post-filter) +import os +from galaxy import eggs +from galaxy import jobs +from galaxy.tools.parameters import DataToolParameter +# Older py compatibility +try: + set() +except: + from sets import Set as set + +def validate_input( trans, error_map, param_values, page_param_map ): + dbkeys = set() + data_param_names = set() + data_params = 0 + for name, param in page_param_map.iteritems(): + if isinstance( param, DataToolParameter ): + # for each dataset parameter + if param_values.get(name, None) != None: + dbkeys.add( param_values[name].dbkey ) + data_params += 1 + # check meta data + try: + param = param_values[name] + startCol = int( param.metadata.startCol ) + endCol = int( param.metadata.endCol ) + chromCol = int( param.metadata.chromCol ) + if param.metadata.strandCol is not None: + strandCol = int ( param.metadata.strandCol ) + else: + strandCol = 0 + except: + error_msg = "The attributes of this dataset are not properly set. " + \ + "Click the pencil icon in the history item to set the chrom, start, end and strand columns." + error_map[name] = error_msg + data_param_names.add( name ) + if len( dbkeys ) > 1: + for name in data_param_names: + error_map[name] = "All datasets must belong to same genomic build, " \ + "this dataset is linked to build '%s'" % param_values[name].dbkey + if data_params != len(data_param_names): + for name in data_param_names: + error_map[name] = "A dataset of the appropriate type is required"

1 0

[hg] galaxy 3557: lims: fixed a bug in the csv importer for samples
by Greg Von Kuster 24 Mar '10

24 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/a67ca0795efb changeset: 3557:a67ca0795efb user: rc date: Tue Mar 23 13:15:56 2010 -0400 description: lims: fixed a bug in the csv importer for samples diffstat: lib/galaxy/web/controllers/requests.py | 14 ++++++++++++-- lib/galaxy/web/controllers/requests_admin.py | 11 ++++++++++- 2 files changed, 22 insertions(+), 3 deletions(-) diffs (59 lines): diff -r 8f6fa47b21c4 -r a67ca0795efb lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Tue Mar 23 12:45:08 2010 -0400 +++ b/lib/galaxy/web/controllers/requests.py Tue Mar 23 13:15:56 2010 -0400 @@ -438,18 +438,28 @@ current_samples, details, edit_mode, libraries = self.__update_samples( trans, request, **kwd ) if params.get('import_samples_button', False) == 'Import samples': try: + lib_widget, folder_widget = self.__library_widgets(trans, request.user, + len(current_samples), + libraries, None, **kwd) file_obj = params.get('file_data', '') import csv reader = csv.reader(file_obj.file) for row in reader: - current_samples.append([row[0], row[1:]]) - return trans.fill_template( '/requests/show_request.mako', + current_samples.append(dict(name=row[0], + barcode='', + library=None, + folder=None, + lib_widget=lib_widget, + folder_widget=folder_widget, + field_values=row[1:])) + return trans.fill_template( '/admin/requests/show_request.mako', request=request, request_details=self.request_details(trans, request.id), current_samples=current_samples, sample_copy=self.__copy_sample(current_samples), details=details, edit_mode=edit_mode) + except: return trans.response.send_redirect( web.url_for( controller='requests', action='list', diff -r 8f6fa47b21c4 -r a67ca0795efb lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Tue Mar 23 12:45:08 2010 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Tue Mar 23 13:15:56 2010 -0400 @@ -946,11 +946,20 @@ current_samples, details, edit_mode, libraries = self.__update_samples( trans, request, **kwd ) if params.get('import_samples_button', False) == 'Import samples': try: + lib_widget, folder_widget = self.__library_widgets(trans, request.user, + len(current_samples), + libraries, None, **kwd) file_obj = params.get('file_data', '') import csv reader = csv.reader(file_obj.file) for row in reader: - current_samples.append([row[0], row[1:]]) + current_samples.append(dict(name=row[0], + barcode='', + library=None, + folder=None, + lib_widget=lib_widget, + folder_widget=folder_widget, + field_values=row[1:])) return trans.fill_template( '/admin/requests/show_request.mako', request=request, request_details=self.request_details(trans, request.id),

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