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commit/galaxy-central: dannon: =Use tabs instead of spaces for sample lines in bowtie_indices.loc.sample
by Bitbucket 23 Mar '12

23 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/732c10115fdf/ changeset: 732c10115fdf user: dannon date: 2012-03-23 13:24:42 summary: =Use tabs instead of spaces for sample lines in bowtie_indices.loc.sample affected #: 1 file diff -r 1adcc1b43718a0abc925061fdb6403a60bde2ddb -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e tool-data/bowtie_indices.loc.sample --- a/tool-data/bowtie_indices.loc.sample +++ b/tool-data/bowtie_indices.loc.sample @@ -7,11 +7,11 @@ # #<unique_build_id><dbkey><display_name><file_base_path> # -#So, for example, if you had hg18 indexed stored in -#/depot/data2/galaxy/bowtie/hg18/, +#So, for example, if you had hg18 indexed stored in +#/depot/data2/galaxy/bowtie/hg18/, #then the bowtie_indices.loc entry would look like this: # -#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18 +#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18 # #and your /depot/data2/galaxy/bowtie/hg18/ directory #would contain hg18.*.ebwt files: @@ -25,9 +25,9 @@ #index set you have stored. The "file" in the path does not actually #exist, but it is the prefix for the actual index files. For example: # -#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon -#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full -#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon +#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full +#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 #...etc... # #Note that for backwards compatibility with workflows, the unique ID of Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Remove the EMBOSS tools from Main's tool_conf.
by Bitbucket 23 Mar '12

23 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1adcc1b43718/ changeset: 1adcc1b43718 user: natefoo date: 2012-03-23 03:16:22 summary: Remove the EMBOSS tools from Main's tool_conf. affected #: 1 file diff -r 9e4fe7f46c621e1b79a33d223b3c9b807135b62c -r 1adcc1b43718a0abc925061fdb6403a60bde2ddb tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -218,115 +218,6 @@ <tool file="genome_diversity/select_restriction_enzymes.xml" /><tool file="genome_diversity/extract_flanking_dna.xml" /></section> - <section name="EMBOSS" id="EMBOSSLite"> - <tool file="emboss_5/emboss_antigenic.xml" /> - <tool file="emboss_5/emboss_backtranseq.xml" /> - <tool file="emboss_5/emboss_banana.xml" /> - <tool file="emboss_5/emboss_biosed.xml" /> - <tool file="emboss_5/emboss_btwisted.xml" /> - <tool file="emboss_5/emboss_cai_custom.xml" /> - <tool file="emboss_5/emboss_cai.xml" /> - <tool file="emboss_5/emboss_chaos.xml" /> - <tool file="emboss_5/emboss_charge.xml" /> - <tool file="emboss_5/emboss_checktrans.xml" /> - <tool file="emboss_5/emboss_chips.xml" /> - <tool file="emboss_5/emboss_cirdna.xml" /> - <tool file="emboss_5/emboss_codcmp.xml" /> - <tool file="emboss_5/emboss_coderet.xml" /> - <tool file="emboss_5/emboss_compseq.xml" /> - <tool file="emboss_5/emboss_cpgplot.xml" /> - <tool file="emboss_5/emboss_cpgreport.xml" /> - <tool file="emboss_5/emboss_cusp.xml" /> - <tool file="emboss_5/emboss_cutseq.xml" /> - <tool file="emboss_5/emboss_dan.xml" /> - <tool file="emboss_5/emboss_degapseq.xml" /> - <tool file="emboss_5/emboss_descseq.xml" /> - <tool file="emboss_5/emboss_diffseq.xml" /> - <tool file="emboss_5/emboss_digest.xml" /> - <tool file="emboss_5/emboss_dotmatcher.xml" /> - <tool file="emboss_5/emboss_dotpath.xml" /> - <tool file="emboss_5/emboss_dottup.xml" /> - <tool file="emboss_5/emboss_dreg.xml" /> - <tool file="emboss_5/emboss_einverted.xml" /> - <tool file="emboss_5/emboss_epestfind.xml" /> - <tool file="emboss_5/emboss_equicktandem.xml" /> - <tool file="emboss_5/emboss_est2genome.xml" /> - <tool file="emboss_5/emboss_etandem.xml" /> - <tool file="emboss_5/emboss_extractfeat.xml" /> - <tool file="emboss_5/emboss_extractseq.xml" /> - <tool file="emboss_5/emboss_freak.xml" /> - <tool file="emboss_5/emboss_fuzznuc.xml" /> - <tool file="emboss_5/emboss_fuzzpro.xml" /> - <tool file="emboss_5/emboss_fuzztran.xml" /> - <tool file="emboss_5/emboss_garnier.xml" /> - <tool file="emboss_5/emboss_geecee.xml" /> - <tool file="emboss_5/emboss_getorf.xml" /> - <tool file="emboss_5/emboss_helixturnhelix.xml" /> - <tool file="emboss_5/emboss_hmoment.xml" /> - <tool file="emboss_5/emboss_iep.xml" /> - <tool file="emboss_5/emboss_infoseq.xml" /> - <tool file="emboss_5/emboss_isochore.xml" /> - <tool file="emboss_5/emboss_lindna.xml" /> - <tool file="emboss_5/emboss_marscan.xml" /> - <tool file="emboss_5/emboss_maskfeat.xml" /> - <tool file="emboss_5/emboss_maskseq.xml" /> - <tool file="emboss_5/emboss_matcher.xml" /> - <tool file="emboss_5/emboss_megamerger.xml" /> - <tool file="emboss_5/emboss_merger.xml" /> - <tool file="emboss_5/emboss_msbar.xml" /> - <tool file="emboss_5/emboss_needle.xml" /> - <tool file="emboss_5/emboss_newcpgreport.xml" /> - <tool file="emboss_5/emboss_newcpgseek.xml" /> - <tool file="emboss_5/emboss_newseq.xml" /> - <tool file="emboss_5/emboss_noreturn.xml" /> - <tool file="emboss_5/emboss_notseq.xml" /> - <tool file="emboss_5/emboss_nthseq.xml" /> - <tool file="emboss_5/emboss_octanol.xml" /> - <tool file="emboss_5/emboss_oddcomp.xml" /> - <tool file="emboss_5/emboss_palindrome.xml" /> - <tool file="emboss_5/emboss_pasteseq.xml" /> - <tool file="emboss_5/emboss_patmatdb.xml" /> - <tool file="emboss_5/emboss_pepcoil.xml" /> - <tool file="emboss_5/emboss_pepinfo.xml" /> - <tool file="emboss_5/emboss_pepnet.xml" /> - <tool file="emboss_5/emboss_pepstats.xml" /> - <tool file="emboss_5/emboss_pepwheel.xml" /> - <tool file="emboss_5/emboss_pepwindow.xml" /> - <tool file="emboss_5/emboss_pepwindowall.xml" /> - <tool file="emboss_5/emboss_plotcon.xml" /> - <tool file="emboss_5/emboss_plotorf.xml" /> - <tool file="emboss_5/emboss_polydot.xml" /> - <tool file="emboss_5/emboss_preg.xml" /> - <tool file="emboss_5/emboss_prettyplot.xml" /> - <tool file="emboss_5/emboss_prettyseq.xml" /> - <tool file="emboss_5/emboss_primersearch.xml" /> - <tool file="emboss_5/emboss_revseq.xml" /> - <tool file="emboss_5/emboss_seqmatchall.xml" /> - <tool file="emboss_5/emboss_seqret.xml" /> - <tool file="emboss_5/emboss_showfeat.xml" /> - <tool file="emboss_5/emboss_shuffleseq.xml" /> - <tool file="emboss_5/emboss_sigcleave.xml" /> - <tool file="emboss_5/emboss_sirna.xml" /> - <tool file="emboss_5/emboss_sixpack.xml" /> - <tool file="emboss_5/emboss_skipseq.xml" /> - <tool file="emboss_5/emboss_splitter.xml" /> - <tool file="emboss_5/emboss_supermatcher.xml" /> - <tool file="emboss_5/emboss_syco.xml" /> - <tool file="emboss_5/emboss_tcode.xml" /> - <tool file="emboss_5/emboss_textsearch.xml" /> - <tool file="emboss_5/emboss_tmap.xml" /> - <tool file="emboss_5/emboss_tranalign.xml" /> - <tool file="emboss_5/emboss_transeq.xml" /> - <tool file="emboss_5/emboss_trimest.xml" /> - <tool file="emboss_5/emboss_trimseq.xml" /> - <tool file="emboss_5/emboss_twofeat.xml" /> - <tool file="emboss_5/emboss_union.xml" /> - <tool file="emboss_5/emboss_vectorstrip.xml" /> - <tool file="emboss_5/emboss_water.xml" /> - <tool file="emboss_5/emboss_wobble.xml" /> - <tool file="emboss_5/emboss_wordcount.xml" /> - <tool file="emboss_5/emboss_wordmatch.xml" /> - </section><label text="NGS Toolbox Beta" id="ngs" /><section name="NGS: QC and manipulation" id="cshl_library_information"><label text="Illumina data" id="illumina" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Pack script.
by Bitbucket 23 Mar '12

23 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9e4fe7f46c62/ changeset: 9e4fe7f46c62 user: jgoecks date: 2012-03-23 02:17:09 summary: Pack script. affected #: 1 file diff -r b7d0ea8cf2334a840b9bef195c06b30e99fcbaba -r 9e4fe7f46c621e1b79a33d223b3c9b807135b62c static/scripts/packed/galaxy.panels.js --- a/static/scripts/packed/galaxy.panels.js +++ b/static/scripts/packed/galaxy.panels.js @@ -1,1 +1,1 @@ -!function(c,d){var e=function(){if(d("#DD-helper").length==0){d("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}};var b=150,h=800;var k=function(n){this.$panel=n.panel;this.$center=n.center;this.$drag=n.drag;this.$toggle=n.toggle;this.left=!n.right;this.hidden=false;this.hidden_by_tool=false;this.saved_size=null;this.init()};d.extend(k.prototype,{resize:function(n){this.$panel.css("width",n);if(this.left){this.$center.css("left",n)}else{this.$center.css("right",n)}if(document.recalc){document.recalc()}},do_toggle:function(){var n=this;if(this.hidden){this.$toggle.removeClass("hidden");if(this.left){this.$panel.css("left",-this.saved_size).show().animate({left:0},"fast",function(){n.resize(n.saved_size)})}else{this.$panel.css("right",-this.saved_size).show().animate({right:0},"fast",function(){n.resize(n.saved_size)})}n.hidden=false}else{n.saved_size=this.$panel.width();if(document.recalc){document.recalc()}if(this.left){this.$panel.animate({left:-this.saved_size},"fast")}else{this.$panel.animate({right:-this.saved_size},"fast")}if(this.left){this.$center.css("left",0)}else{this.$center.css("right",0)}n.hidden=true;n.$toggle.addClass("hidden")}this.hidden_by_tool=false},handle_minwidth_hint:function(n){var o=this.$center.width()-(this.hidden?this.saved_size:0);if(o<n){if(!this.hidden){this.do_toggle();this.hidden_by_tool=true}}else{if(this.hidden_by_tool){this.do_toggle();this.hidden_by_tool=false}}},force_panel:function(n){if((this.hidden&&n=="show")||(!this.hidden&&n=="hide")){this.do_toggle()}},init:function(){var n=this;this.$toggle.remove().appendTo("body");this.$drag.on("dragstart",function(o,p){d("#DD-helper").show();p.width=n.$panel.width()}).on("dragend",function(){d("#DD-helper").hide()}).on("drag",function(p,q){var o;if(n.left){o=q.width+q.deltaX}else{o=q.width-q.deltaX}o=Math.min(h,Math.max(b,o));n.resize(o)});n.$toggle.on("click",function(){n.do_toggle()})}});var f=function(n){this.$overlay=n.overlay;this.$dialog=n.dialog;this.$header=this.$dialog.find(".modal-header");this.$body=this.$dialog.find(".modal-body");this.$footer=this.$dialog.find(".modal-footer");this.$backdrop=n.backdrop};d.extend(f.prototype,{setContent:function(p){if(p.title){this.$header.find(".title").html(p.title);this.$header.show()}else{this.$header.hide()}this.$footer.hide();console.log(this.$footer,p.buttons);var o=this.$footer.find(".buttons").html("");if(p.buttons){d.each(p.buttons,function(r,s){o.append(d("<button></button> ").text(r).click(s)).append(" ")});this.$footer.show()}var q=this.$footer.find(".extra_buttons").html("");if(p.extra_buttons){d.each(p.extra_buttons,function(r,s){q.append(d("<button></button>").text(r).click(s)).append(" ")});this.$footer.show()}var n=p.body;if(n=="progress"){n=d("<div class='progress progress-striped active'><div class='bar' style='width: 100%'></div></div>")}this.$body.html(n)},show:function(n,o){if(!this.$dialog.is(":visible")){if(n.backdrop){this.$backdrop.addClass("in")}else{this.$backdrop.removeClass("in")}this.$overlay.show();this.$dialog.show();this.$body.css("min-width",this.$body.width())}if(o){o()}},hide:function(){var n=this;n.$dialog.fadeOut(function(){n.$overlay.hide();n.$backdrop.removeClass("in");n.$body.children().remove();n.$body.css("min-width",undefined)})}});var m;d(function(){m=new f({overlay:d("#overlay"),dialog:d("#dialog-box"),backdrop:d("#overlay-background")})});function a(){m.hide()}function l(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:true},q)}function g(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:false},q)}function j(p){var q=p.width||"600";var o=p.height||"400";var n=p.scroll||"auto";d("#overlay-background").bind("click.overlay",function(){a();d("#overlay-background").unbind("click.overlay")});l(null,d("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='"+image_path+"/closebox.png'><iframe style='margin: 0; 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commit/galaxy-central: jgoecks: Reinstate dialog-box class in modal.
by Bitbucket 22 Mar '12

22 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b7d0ea8cf233/ changeset: b7d0ea8cf233 user: jgoecks date: 2012-03-22 23:53:55 summary: Reinstate dialog-box class in modal. affected #: 1 file diff -r 423d7f6e7b80cc294a9324133a49e1cd385c36ae -r b7d0ea8cf2334a840b9bef195c06b30e99fcbaba templates/base_panels.mako --- a/templates/base_panels.mako +++ b/templates/base_panels.mako @@ -178,7 +178,7 @@ <div id="overlay-background" class="modal-backdrop fade ${overlay_class}"></div> - <div id="dialog-box" class="modal" border="0" ${display}> + <div id="dialog-box" class="modal dialog-box" border="0" ${display}><div class="modal-header"><span><h3 class='title'>${title}</h3></span></div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Remove debugging statement.
by Bitbucket 22 Mar '12

22 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/423d7f6e7b80/ changeset: 423d7f6e7b80 user: jgoecks date: 2012-03-22 23:00:54 summary: Remove debugging statement. affected #: 1 file diff -r bb19e940a03c7120674b2ba1ebf1588cbea95f74 -r 423d7f6e7b80cc294a9324133a49e1cd385c36ae static/scripts/galaxy.panels.js --- a/static/scripts/galaxy.panels.js +++ b/static/scripts/galaxy.panels.js @@ -140,7 +140,6 @@ } // Buttons this.$footer.hide(); - console.log( this.$footer, options.buttons ); var $buttons = this.$footer.find( ".buttons" ).html( "" ); if ( options.buttons ) { $.each( options.buttons, function( name, value ) { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: richard_burhans: fix get_file_peek() to better support datasets with very long lines
by Bitbucket 22 Mar '12

22 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/bb19e940a03c/ changeset: bb19e940a03c user: richard_burhans date: 2012-03-22 21:15:24 summary: fix get_file_peek() to better support datasets with very long lines affected #: 1 file diff -r fa40b8f3f385f67d57294d98a036e483775d873f -r bb19e940a03c7120674b2ba1ebf1588cbea95f74 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -433,13 +433,13 @@ if line and not line.startswith( '#' ): data_lines += 1 return data_lines - def set_peek( self, dataset, line_count=None, is_multi_byte=False, skipchars=[] ): + def set_peek( self, dataset, line_count=None, is_multi_byte=False, WIDTH=256, skipchars=[] ): """ Set the peek. This method is used by various subclasses of Text. """ if not dataset.dataset.purged: # The file must exist on disk for the get_file_peek() method - dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte, skipchars=skipchars ) + dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte, WIDTH=WIDTH, skipchars=skipchars ) if line_count is None: # See if line_count is stored in the metadata if dataset.metadata.data_lines: @@ -567,6 +567,11 @@ ## >>> get_file_peek(fname) ## 'chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 +\n' """ + # Set size for file.readline() to a negative number to force it to + # read until either a newline or EOF. Needed for datasets with very + # long lines. + if WIDTH == 'unlimited': + WIDTH = -1 lines = [] count = 0 file_type = None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: richard_burhans: changes to aaChanges tool
by Bitbucket 22 Mar '12

22 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/fa40b8f3f385/ changeset: fa40b8f3f385 user: richard_burhans date: 2012-03-22 18:19:31 summary: changes to aaChanges tool affected #: 2 files diff -r 1f6c7be22ba9059d8fd8e05148466bb005a7fbd1 -r fa40b8f3f385f67d57294d98a036e483775d873f tools/evolution/codingSnps.pl --- a/tools/evolution/codingSnps.pl +++ b/tools/evolution/codingSnps.pl @@ -7,11 +7,15 @@ # 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. +# Output columns: +# chrom, start, end, allele as given (amb code translated) +# Gene ID from genes file, ref amino acid:variant amino acids, +# codon number, (in strand of gene)ref nt, refCodon:variantCodons ######################################################################### my $seqFlag = "2bit"; #flag to set sequence type 2bit|nib if (!@ARGV or scalar @ARGV < 3) { - print "Usage: codingSnps.pl snps.bed genes.bed (/dir/*$seqFlag|Galaxy build= loc=) [chr=# start=# end=# snp=# keepColumns=1] > codingSnps.txt\n"; + print "Usage: codingSnps.pl snps.bed genes.bed (/dir/*$seqFlag|Galaxy build= loc=) [chr=# start=# end=# snp=# strand=#|-|+ keepColumns=1 synon=1 unique=1] > codingSnps.txt\n"; exit; } my $uniq = 0; #flag for whether want uniq positions @@ -25,6 +29,7 @@ my $col1 = 1; my $col2 = 2; my $col3 = 3; +my $strand = -1; #column positions 1 based coming in (for Galaxy) foreach (@ARGV) { if (/chr=(\d+)/) { $col0 = $1 -1; } @@ -32,6 +37,10 @@ elsif (/end=(\d+)/) { $col2 = $1 -1; } elsif (/snp=(\d+)/) { $col3 = $1 -1; } elsif (/keepColumns=1/) { $keep = 1; } + elsif (/synon=1/) { $syn = 1; } + elsif (/unique=1/) { $uniq = 1; } + elsif (/strand=(\d+)/) { $strand = $1 -1; } #0 based column + elsif (/strand=-/) { $strand = -99; } #special case of all minus } if ($col0 < 0 || $col1 < 0 || $col2 < 0 || $col3 < 0) { print STDERR "ERROR column numbers are given with origin 1\n"; @@ -42,6 +51,7 @@ 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 $origAll; #alleles from input file (before changes for strand) my %amb = ( "R" => "A/G", @@ -90,6 +100,10 @@ print STDERR "ERROR file has fewer columns than requested, requested columns (0 based) $col0 $col1 $col2 $col3, file has $size\n"; exit 1; } + if ($strand >= 0 && $strand > $size) { + print STDERR "ERROR file has fewer columns than requested, requested strand in $strand (0 based), 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; @@ -100,6 +114,11 @@ } if ($s[$col3] eq 'N' && $ignoreN) { next; } if (exists $amb{$s[$col3]}) { $s[$col3] = $amb{$s[$col3]}; } + if (($strand >= 0 && $s[$strand] eq '-') or $strand == -99) { + #reverse complement nts + $origAll = $s[$col3]; + $s[$col3] = reverseCompAlleles($s[$col3]); + }else { undef $origAll } if (!@g && exists $chrSt{$s[$col0]}) { #need to fetch first gene row $i = $chrSt{$s[$col0]}; @g = split(/\t/, $genes[$i]); @@ -287,36 +306,45 @@ } #now compute amino acids my $oldaa = getaa($oldnts); + my $codon = "$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, $t); + push(@newaa, "$t"); + $codon .= "$v/"; } + $codon =~ s/\/$//; if (!$change && $syn) { if (!$keep) { print "$sref->[$col0]\t$sref->[$col1]\t$sref->[$col2]\t$sref->[$col3]"; - print "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\n"; + print "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\t$cdNum\t$changed\t$codon\n"; }else { my @s = @{$sref}; print join("\t", @s), - "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\n"; + "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\t$cdNum\t$changed\t$codon\n"; } + $done{"$sref->[$col0] $sref->[$col1] $sref->[$col2]"}++; return; }elsif ($syn) { return; } #only want synonymous changes if (!$change) { return; } #no change in amino acids if (!$keep) { - print "$sref->[$col0]\t$sref->[$col1]\t$sref->[$col2]\t$sref->[$col3]"; - if ($gref->[5] eq '-') { $changed = compl($changed); } #use plus for ref + my $a = $sref->[$col3]; + if (($strand >= 0 && $origAll) or $strand == -99) { $a = $origAll; } + print "$sref->[$col0]\t$sref->[$col1]\t$sref->[$col2]\t$a"; + #my $minus = $changed; #in case minus strand and change back + #if ($gref->[5] eq '-') { $changed = compl($changed); } #use plus for ref if (!$changed) { return; } #skip this one - print "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\t$cdNum\t$changed\n"; + print "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\t$cdNum\t$changed\t$codon\n"; }else { my @s = @{$sref}; + if (($strand >= 0 && $origAll) or $strand == -99) { $s[$col3] = $origAll; } print join("\t", @s); - if ($gref->[5] eq '-') { $changed = compl($changed); } #use plus for ref + #my $minus = $changed; #in case minus strand and change back + #if ($gref->[5] eq '-') { $changed = compl($changed); } #use plus for ref if (!$changed) { return; } #skip this one - print "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\t$cdNum\t$changed\n"; + print "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\t$cdNum\t$changed\t$codon\n"; } $done{"$sref->[$col0] $sref->[$col1] $sref->[$col2]"}++; } @@ -418,6 +446,19 @@ return $comp; } +sub reverseCompAlleles { + my $all = shift; + my @nt = split(/\//, $all); + my $rv = ''; + foreach my $n (@nt) { + $n = reverse(split(/ */, $n)); #needed for indels + $n = compl($n); + $rv .= "$n/"; + } + $rv =~ s/\/$//; + return $rv; +} + sub getaa { my $nts = shift; #in multiples of 3 my $aa = ''; diff -r 1f6c7be22ba9059d8fd8e05148466bb005a7fbd1 -r fa40b8f3f385f67d57294d98a036e483775d873f tools/evolution/codingSnps.xml --- a/tools/evolution/codingSnps.xml +++ b/tools/evolution/codingSnps.xml @@ -2,7 +2,7 @@ <description>amino-acid changes caused by a set of SNPs</description><command interpreter="perl"> - 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=$col1 keepColumns=$keep > $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=$col1 keepColumns=$keep strand=${strand_source.strand_col} > $out_file1 </command><inputs> @@ -17,6 +17,22 @@ <option value="0" selected="true">No</option><option value="1">Yes</option></param> + <conditional name="strand_source"> + <param name="strand_choice" type="select" label="Strand info"> + <option value="data_column">a column in the dataset</option> + <option value="all_pos" selected="true">all on sense/forward/+ strand</option> + <option value="all_neg">all on antisense/reverse/- strand</option> + </param> + <when value="data_column"> + <param name="strand_col" type="data_column" data_ref="input1" label="Column with strand"/> + </when> + <when value="all_pos"> + <param name="strand_col" type="hidden" value="+"/> + </when> + <when value="all_neg"> + <param name="strand_col" type="hidden" value="-"/> + </when> + </conditional></inputs><outputs> @@ -36,14 +52,26 @@ <param name="input1" ftype="interval" value="codingSnps_input1.interval" dbkey="hg18" /><param name="col1" value="6" /><param name="input2" ftype="interval" value="codingSnps_inputGenes1.bed" dbkey="hg18" /> + <param name="strand_choice" value="all_pos" /> + <param name="strand_col" value="+" /><output name="output" file="codingSnps_output1.interval" /></test><test><param name="input1" ftype="interval" value="codingSnps_input2.interval" dbkey="hg18" /><param name="input2" ftype="interval" value="codingSnps_inputGenes2.bed" dbkey="hg18" /><param name="col1" value="4" /> + <param name="strand_choice" value="all_pos" /> + <param name="strand_col" value="+" /><output name="output" file="codingSnps_output2.interval" /></test> + <test> + <param name="input1" ftype="interval" value="codingSnps_input2.interval" dbkey="hg18" /> + <param name="input2" ftype="interval" value="codingSnps_inputGenes2.bed" dbkey="hg18" /> + <param name="col1" value="4" /> + <param name="strand_choice" value="all_neg" /> + <param name="strand_col" value="-" /> + <output name="output" file="codingSnps_output3.interval" /> + </test></tests><help> @@ -79,8 +107,9 @@ the first 12 columns standard BED columns. The output is the same as the first input file with several columns added: the name field from the line of the gene input file -used, the amino acids, the codon number, and the reference nucleotide that -changed in the amino acid. +used, the amino acids, the codon number, the reference nucleotide that +changed in the amino acid (in the same strand as the gene), and the codons +that go with the amino acids. The amino acids are listed with the reference amino acid first, then a colon, and then the amino acids for the alleles. If a SNP is not in a coding region or is synonymous then it is not included in the output file. @@ -128,15 +157,15 @@ - output file, showing non-synonymous substitutions in coding regions:: - chr22 15825725 15825726 G/T uc002zlw.1 Gln:Pro/Gln 469 T - chr22 15827035 15827036 G uc002zlw.1 Glu:Asp 414 C - chr22 15827135 15827136 C/G uc002zlw.1 Gly:Gly/Ala 381 C - chr22 15830928 15830929 A/G uc002zlw.1 Ala:Ser/Pro 281 C - chr22 15830951 15830952 G uc002zlw.1 Leu:Pro 273 A - chr22 15830955 15830956 C/T uc002zlw.1 Ser:Gly/Ser 272 T - chr22 15848885 15848886 C/T uc002zlw.1 Ser:Trp/Stop 217 G - chr22 15848885 15848886 C/T uc010gqs.1 Ser:Trp/Stop 200 G - chr22 15849048 15849049 A/C uc002zlw.1 Gly:Stop/Gly 163 C + chr22 15825725 15825726 G/T uc002zlw.1 Gln:Pro/Gln 469 A CAA:CCA/CAA + chr22 15827035 15827036 G uc002zlw.1 Glu:Asp 414 G GAG:GAC + chr22 15827135 15827136 C/G uc002zlw.1 Gly:Gly/Ala 381 G GGT:GGT/GCT + chr22 15830928 15830929 A/G uc002zlw.1 Ala:Ser/Pro 281 G GCA:TCA/CCA + chr22 15830951 15830952 G uc002zlw.1 Leu:Pro 273 T CTT:CCT + chr22 15830955 15830956 C/T uc002zlw.1 Ser:Gly/Ser 272 A AGC:GGC/AGC + chr22 15848885 15848886 C/T uc002zlw.1 Ser:Trp/Stop 217 C TCG:TGG/TAG + chr22 15848885 15848886 C/T uc010gqs.1 Ser:Trp/Stop 200 C TCG:TGG/TAG + chr22 15849048 15849049 A/C uc002zlw.1 Gly:Stop/Gly 163 G GGA:TGA/GGA etc. </help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: richard_burhans: Updates to Human Genome Variation tools
by Bitbucket 22 Mar '12

22 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1f6c7be22ba9/ changeset: 1f6c7be22ba9 user: richard_burhans date: 2012-03-22 18:03:01 summary: Updates to Human Genome Variation tools Rename Human Genome Variation to Phenotype Association affected #: 76 files Diff too large to display. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 22 Mar '12

22 Mar '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b00471c0ffe8/ changeset: b00471c0ffe8 user: jgoecks date: 2012-03-22 15:10:18 summary: Remove debugging statement. affected #: 1 file diff -r 4d48285fcaa65c7895768069ea197acf9d66b1ed -r b00471c0ffe864c1223d39ca4fd5b4836d73f4c7 templates/base_panels.mako --- a/templates/base_panels.mako +++ b/templates/base_panels.mako @@ -69,7 +69,7 @@ %if self.has_right_panel: var rp = new Panel( { panel: $("#right"), center: $("#center"), drag: $("#right > .unified-panel-footer > .drag" ), toggle: $("#right > .unified-panel-footer > .panel-collapse" ), right: true } ); - window.handle_minwidth_hint = function( x ) { console.log( "hint", x ); rp.handle_minwidth_hint( x ) }; + window.handle_minwidth_hint = function( x ) { rp.handle_minwidth_hint( x ) }; force_right_panel = function( x ) { rp.force_panel( x ) }; %endif https://bitbucket.org/galaxy/galaxy-central/changeset/164eef0d7693/ changeset: 164eef0d7693 user: jgoecks date: 2012-03-22 15:40:47 summary: Add spacing for checkboxes, radio buttons; use webkit default of 0.5ex affected #: 1 file diff -r b00471c0ffe864c1223d39ca4fd5b4836d73f4c7 -r 164eef0d76931e20135fdb908136e599d351599e static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -14,6 +14,7 @@ button,input[type="button"],input[type="reset"],input[type="submit"]{cursor:pointer;-webkit-appearance:button;} input[type="search"]{-webkit-appearance:textfield;-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box;} input[type="search"]::-webkit-search-decoration,input[type="search"]::-webkit-search-cancel-button{-webkit-appearance:none;} +input[type="checkbox"],input[type="radio"]{margin-left:0.5ex;margin-right:0.5ex;} textarea{overflow:auto;vertical-align:top;} body{margin:0;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-size:12px;line-height:16px;color:#111111;background-color:#ffffff;} a{color:#303030;text-decoration:none;} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Convert dbkeys from string to dict before checking for dbkey when including chrom info in jobs. Thanks Andrew Warren.
by Bitbucket 22 Mar '12

22 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4d48285fcaa6/ changeset: 4d48285fcaa6 user: jgoecks date: 2012-03-22 14:58:42 summary: Convert dbkeys from string to dict before checking for dbkey when including chrom info in jobs. Thanks Andrew Warren. affected #: 1 file diff -r ee4a47ed53712fe87c5372f667c9058147415c04 -r 4d48285fcaa65c7895768069ea197acf9d66b1ed lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -195,7 +195,7 @@ else: # For custom builds, chrom info resides in converted dataset; for built-in builds, chrom info resides in tool-data/shared. chrom_info = None - if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in trans.user.preferences[ 'dbkeys' ] ): + if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ): # Custom build. custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ input_dbkey ] if 'fasta' in custom_build_dict: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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