[galaxy-commits] commit/galaxy-central: 6 new changesets

24 Oct 2013

6 new commits in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/1ce68c239d0e/
Changeset:   1ce68c239d0e
Branch:      extract_genomic_dna_tool_enhancements
User:        BjoernGruening
Date:        2013-10-18 18:31:44
Summary:     Add the value (nameCol) in a given BED file to the FASTA header.
Affected #:  2 files

diff -r febd7622924885dd0729ce00924289cc1f0eb741 -r 1ce68c239d0ee59bd469c4520bf754eaa80ac04c tools/extract/extract_genomic_dna.py

--- a/tools/extract/extract_genomic_dna.py
+++ b/tools/extract/extract_genomic_dna.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 """
 usage: %prog $input $out_file1
-    -1, --cols=N,N,N,N: Columns for start, end, strand in input file
+    -1, --cols=N,N,N,N,N: Columns for start, end, strand in input file
     -d, --dbkey=N: Genome build of input file
     -o, --output_format=N: the data type of the output file
     -g, --GALAXY_DATA_INDEX_DIR=N: the directory containing alignseq.loc
@@ -54,7 +54,13 @@
     #
     options, args = doc_optparse.parse( __doc__ )
     try:
-        chrom_col, start_col, end_col, strand_col = parse_cols_arg( options.cols )
+        if len(options.cols.split(',')) == 5:
+            # BED file
+            chrom_col, start_col, end_col, strand_col, name_col = parse_cols_arg( options.cols )
+        else:
+            # gff file
+            chrom_col, start_col, end_col, strand_col = parse_cols_arg( options.cols )
+            name_col = False
         dbkey = options.dbkey
         output_format = options.output_format
         gff_format = options.gff
@@ -144,6 +150,7 @@
             start = feature.start
             end = feature.end
             strand = feature.strand
+            name = ""
         else:
             # Processing lines, either interval or GFF format.
             line = feature.rstrip( '\r\n' )
@@ -153,6 +160,8 @@
                     chrom = fields[chrom_col]
                     start = int( fields[start_col] )
                     end = int( fields[end_col] )
+                    if name_col:
+                        name = fields[name_col]
                     if gff_format:
                         start, end = gff_util.convert_gff_coords_to_bed( [start, end] )
                     if includes_strand_col:
@@ -237,13 +246,16 @@
             sequence = reverse_complement( sequence )
 
         if output_format == "fasta" :
-            l = len( sequence )        
+            l = len( sequence )
             c = 0
             if gff_format:
                 start, end = gff_util.convert_bed_coords_to_gff( [ start, end ] )
             fields = [dbkey, str( chrom ), str( start ), str( end ), strand]
             meta_data = "_".join( fields )
-            fout.write( ">%s\n" % meta_data )
+            if name.strip():
+                fout.write( ">%s %s\n" % (meta_data, name) )
+            else:
+                fout.write( ">%s\n" % meta_data )
             while c < l:
                 b = min( c + 50, l )
                 fout.write( "%s\n" % str( sequence[c:b] ) )

diff -r febd7622924885dd0729ce00924289cc1f0eb741 -r 1ce68c239d0ee59bd469c4520bf754eaa80ac04c tools/extract/extract_genomic_dna.xml
--- a/tools/extract/extract_genomic_dna.xml
+++ b/tools/extract/extract_genomic_dna.xml
@@ -11,9 +11,9 @@
       #if isinstance( $input.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__):
         -1 1,4,5,7 --gff
       #else:
-        -1 ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}
+        -1 ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol},${input.metadata.nameCol}
       #end if
-            
+
       #if $seq_source.index_source == "cached":
         ## Genomic data from cache.
         -g ${GALAXY_DATA_INDEX_DIR}
@@ -52,8 +52,8 @@
       </data></outputs><requirements>
+      <requirement type="package">ucsc_tools</requirement><requirement type="binary">faToTwoBit</requirement>
-      <requirement type="package">ucsc_tools</requirement></requirements><tests><test>


https://bitbucket.org/galaxy/galaxy-central/commits/9c6732931369/
Changeset:   9c6732931369
Branch:      extract_genomic_dna_tool_enhancements
User:        BjoernGruening
Date:        2013-10-24 18:13:18
Summary:     bugfix and one test fix
Affected #:  3 files

diff -r 1ce68c239d0ee59bd469c4520bf754eaa80ac04c -r 9c67329313699a02108fe36dc0cee93fee362c70 test-data/extract_genomic_dna_out2.fasta
--- a/test-data/extract_genomic_dna_out2.fasta
+++ b/test-data/extract_genomic_dna_out2.fasta
@@ -1,6 +1,6 @@
->droPer1_super_1_139823_139913_-
+>droPer1_super_1_139823_139913_- AK028861
 CGTCGGCTTCTGCTTCTGCTGATGATGGTCGTTCTTCTTCCTTTACTTCT
 TCCTATTTTTCTTCCTTCCCTTACACTATATCTTCCTTTA
->droPer1_super_1_156750_156844_-
+>droPer1_super_1_156750_156844_- BC126698
 CCGGGCTGCGGCAAGGGATTCACCTGCTCCAAACAGCTCAAGGTGCACTC
 CCGCACGCACACGGGCGAGAAGCCCTATCACTGCGACATCTGCT

diff -r 1ce68c239d0ee59bd469c4520bf754eaa80ac04c -r 9c67329313699a02108fe36dc0cee93fee362c70 tools/extract/extract_genomic_dna.py
--- a/tools/extract/extract_genomic_dna.py
+++ b/tools/extract/extract_genomic_dna.py
@@ -142,7 +142,8 @@
         if isinstance( feature, ( Header, Comment ) ):
             line_count += 1
             continue
-            
+
+        name = ""
         if gff_format and interpret_features:
             # Processing features.
             gff_util.convert_gff_coords_to_bed( feature )
@@ -150,7 +151,6 @@
             start = feature.start
             end = feature.end
             strand = feature.strand
-            name = ""
         else:
             # Processing lines, either interval or GFF format.
             line = feature.rstrip( '\r\n' )

diff -r 1ce68c239d0ee59bd469c4520bf754eaa80ac04c -r 9c67329313699a02108fe36dc0cee93fee362c70 tools/extract/extract_genomic_dna.xml
--- a/tools/extract/extract_genomic_dna.xml
+++ b/tools/extract/extract_genomic_dna.xml
@@ -60,7 +60,7 @@
       <param name="input" value="1.bed" dbkey="hg17" ftype="bed" /><param name="interpret_features" value="yes"/><param name="index_source" value="cached"/>
-      <param name="out_format" value="fasta"/>   
+      <param name="out_format" value="fasta"/><output name="out_file1" file="extract_genomic_dna_out1.fasta" /></test><test>


https://bitbucket.org/galaxy/galaxy-central/commits/af3fc6046bd6/
Changeset:   af3fc6046bd6
Branch:      extract_genomic_dna_tool_enhancements
User:        jmchilton
Date:        2013-10-25 06:03:57
Summary:     Update hg17 test case for extract_genomic_dna.xml tor reflect recent changes.

Cannot delete or modify previous output file - it is used as input for another tool. Use assertion testing to weaken test case. As this tool is migrated to the tool shed the hg17 test cases should probably be eliminated completely.
Affected #:  1 file

diff -r 9c67329313699a02108fe36dc0cee93fee362c70 -r af3fc6046bd693fdbf1ec26d119bf387d7a92bc2 tools/extract/extract_genomic_dna.xml
--- a/tools/extract/extract_genomic_dna.xml
+++ b/tools/extract/extract_genomic_dna.xml
@@ -61,7 +61,21 @@
       <param name="interpret_features" value="yes"/><param name="index_source" value="cached"/><param name="out_format" value="fasta"/>
-      <output name="out_file1" file="extract_genomic_dna_out1.fasta" />
+      <output name="out_file1">
+	<assert_contents>
+	  <!-- First few lines... -->
+	  <has_text text=">hg17_chr1_147962192_147962580_- CCDS989.1_cds_0_0_chr1_147962193_r" />
+	  <has_text text="ACTTGATCCTGCTCCCTCGGTGTCTGCATTGACTCCTCATGCTGGGACTG" />
+	  <has_text text="GACCCGTCAACCCCCCTGCTCGCTGCTCACGTACCTTCATCACTTTTAGT" />
+	  <has_text text="GATGATGCAACTTTCGAGGAATGGTTCCCCCAAGGGCGGCCCCCAAAAGT" />
+	  <!-- Last few lines... -->
+	  <has_text text="GCTGTGGCACAGAACATGGACTCTGTGTTTAAGGAGCTCTTGGGAAAGAC" />
+	  <has_text text="CTCTGTCCGCCAGGGCCTTGGGCCAGCATCTACCACCTCTCCCAGTCCTG" />
+	  <has_text text="GGCCCCGAAGCCCAAAGGCCCCGCCCAGCAGCCGCCTGGGCAGGAACAAA" />
+	  <has_text text="GGCTTCTCCCGGGGCCCTGGGGCCCCAGCCTCACCCTCAGCTTCCCACCC" />
+	  <has_text text="CCAGGGCCTAGACACGACCCCCAAGCCACACTGA" />
+	</assert_contents>
+      </output></test><test><param name="input" value="droPer1.bed" dbkey="droPer1" ftype="bed" />


https://bitbucket.org/galaxy/galaxy-central/commits/7b014440dda1/
Changeset:   7b014440dda1
Branch:      extract_genomic_dna_tool_enhancements
User:        jmchilton
Date:        2013-10-25 06:06:14
Summary:     Rev slightly the tool version of extract_genomic_dna.xml since output is slightly different.

Update tool help to reflect new output format.
Affected #:  1 file

diff -r af3fc6046bd693fdbf1ec26d119bf387d7a92bc2 -r 7b014440dda1d9dddb292598fb804510b5274438 tools/extract/extract_genomic_dna.xml
--- a/tools/extract/extract_genomic_dna.xml
+++ b/tools/extract/extract_genomic_dna.xml
@@ -1,4 +1,4 @@
-<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.2.2">
+<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.2.3"><description>using coordinates from assembled/unassembled genomes</description><command interpreter="python">
       extract_genomic_dna.py $input $out_file1 -o $out_format -d $dbkey 
@@ -166,14 +166,14 @@
 
 Extracting sequences with **FASTA** output data type returns::
 
-    >hg17_chr7_127475281_127475310_+
+    >hg17_chr7_127475281_127475310_+ NM_000230
     GTAGGAATCGCAGCGCCAGCGGTTGCAAG
-    >hg17_chr7_127485994_127486166_+
+    >hg17_chr7_127485994_127486166_+ NM_000230
     GCCCAAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCG
     GATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATC
     CAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAG
     GATCAATGACATTTCACACACG
-    >hg17_chr7_127486011_127486166_+
+    >hg17_chr7_127486011_127486166_+ D49487
     TGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGG
     CCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGA
     CACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCAC


https://bitbucket.org/galaxy/galaxy-central/commits/57e9ebe8ea6b/
Changeset:   57e9ebe8ea6b
User:        jmchilton
Date:        2013-10-25 06:08:48
Summary:     Merge pull request #239 changes into default.
Affected #:  3 files

diff -r d4e60067889e2bd8873010fa0fc887e725a4b695 -r 57e9ebe8ea6ba6686a489560cde62b309d2e5271 test-data/extract_genomic_dna_out2.fasta
--- a/test-data/extract_genomic_dna_out2.fasta
+++ b/test-data/extract_genomic_dna_out2.fasta
@@ -1,6 +1,6 @@
->droPer1_super_1_139823_139913_-
+>droPer1_super_1_139823_139913_- AK028861
 CGTCGGCTTCTGCTTCTGCTGATGATGGTCGTTCTTCTTCCTTTACTTCT
 TCCTATTTTTCTTCCTTCCCTTACACTATATCTTCCTTTA
->droPer1_super_1_156750_156844_-
+>droPer1_super_1_156750_156844_- BC126698
 CCGGGCTGCGGCAAGGGATTCACCTGCTCCAAACAGCTCAAGGTGCACTC
 CCGCACGCACACGGGCGAGAAGCCCTATCACTGCGACATCTGCT

diff -r d4e60067889e2bd8873010fa0fc887e725a4b695 -r 57e9ebe8ea6ba6686a489560cde62b309d2e5271 tools/extract/extract_genomic_dna.py
--- a/tools/extract/extract_genomic_dna.py
+++ b/tools/extract/extract_genomic_dna.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 """
 usage: %prog $input $out_file1
-    -1, --cols=N,N,N,N: Columns for start, end, strand in input file
+    -1, --cols=N,N,N,N,N: Columns for start, end, strand in input file
     -d, --dbkey=N: Genome build of input file
     -o, --output_format=N: the data type of the output file
     -g, --GALAXY_DATA_INDEX_DIR=N: the directory containing alignseq.loc
@@ -54,7 +54,13 @@
     #
     options, args = doc_optparse.parse( __doc__ )
     try:
-        chrom_col, start_col, end_col, strand_col = parse_cols_arg( options.cols )
+        if len(options.cols.split(',')) == 5:
+            # BED file
+            chrom_col, start_col, end_col, strand_col, name_col = parse_cols_arg( options.cols )
+        else:
+            # gff file
+            chrom_col, start_col, end_col, strand_col = parse_cols_arg( options.cols )
+            name_col = False
         dbkey = options.dbkey
         output_format = options.output_format
         gff_format = options.gff
@@ -136,7 +142,8 @@
         if isinstance( feature, ( Header, Comment ) ):
             line_count += 1
             continue
-            
+
+        name = ""
         if gff_format and interpret_features:
             # Processing features.
             gff_util.convert_gff_coords_to_bed( feature )
@@ -153,6 +160,8 @@
                     chrom = fields[chrom_col]
                     start = int( fields[start_col] )
                     end = int( fields[end_col] )
+                    if name_col:
+                        name = fields[name_col]
                     if gff_format:
                         start, end = gff_util.convert_gff_coords_to_bed( [start, end] )
                     if includes_strand_col:
@@ -237,13 +246,16 @@
             sequence = reverse_complement( sequence )
 
         if output_format == "fasta" :
-            l = len( sequence )        
+            l = len( sequence )
             c = 0
             if gff_format:
                 start, end = gff_util.convert_bed_coords_to_gff( [ start, end ] )
             fields = [dbkey, str( chrom ), str( start ), str( end ), strand]
             meta_data = "_".join( fields )
-            fout.write( ">%s\n" % meta_data )
+            if name.strip():
+                fout.write( ">%s %s\n" % (meta_data, name) )
+            else:
+                fout.write( ">%s\n" % meta_data )
             while c < l:
                 b = min( c + 50, l )
                 fout.write( "%s\n" % str( sequence[c:b] ) )

diff -r d4e60067889e2bd8873010fa0fc887e725a4b695 -r 57e9ebe8ea6ba6686a489560cde62b309d2e5271 tools/extract/extract_genomic_dna.xml
--- a/tools/extract/extract_genomic_dna.xml
+++ b/tools/extract/extract_genomic_dna.xml
@@ -1,4 +1,4 @@
-<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.2.2">
+<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.2.3"><description>using coordinates from assembled/unassembled genomes</description><command interpreter="python">
       extract_genomic_dna.py $input $out_file1 -o $out_format -d $dbkey 
@@ -11,9 +11,9 @@
       #if isinstance( $input.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__):
         -1 1,4,5,7 --gff
       #else:
-        -1 ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}
+        -1 ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol},${input.metadata.nameCol}
       #end if
-            
+
       #if $seq_source.index_source == "cached":
         ## Genomic data from cache.
         -g ${GALAXY_DATA_INDEX_DIR}
@@ -52,16 +52,30 @@
       </data></outputs><requirements>
+      <requirement type="package">ucsc_tools</requirement><requirement type="binary">faToTwoBit</requirement>
-      <requirement type="package">ucsc_tools</requirement></requirements><tests><test><param name="input" value="1.bed" dbkey="hg17" ftype="bed" /><param name="interpret_features" value="yes"/><param name="index_source" value="cached"/>
-      <param name="out_format" value="fasta"/>   
-      <output name="out_file1" file="extract_genomic_dna_out1.fasta" />
+      <param name="out_format" value="fasta"/>
+      <output name="out_file1">
+	<assert_contents>
+	  <!-- First few lines... -->
+	  <has_text text=">hg17_chr1_147962192_147962580_- CCDS989.1_cds_0_0_chr1_147962193_r" />
+	  <has_text text="ACTTGATCCTGCTCCCTCGGTGTCTGCATTGACTCCTCATGCTGGGACTG" />
+	  <has_text text="GACCCGTCAACCCCCCTGCTCGCTGCTCACGTACCTTCATCACTTTTAGT" />
+	  <has_text text="GATGATGCAACTTTCGAGGAATGGTTCCCCCAAGGGCGGCCCCCAAAAGT" />
+	  <!-- Last few lines... -->
+	  <has_text text="GCTGTGGCACAGAACATGGACTCTGTGTTTAAGGAGCTCTTGGGAAAGAC" />
+	  <has_text text="CTCTGTCCGCCAGGGCCTTGGGCCAGCATCTACCACCTCTCCCAGTCCTG" />
+	  <has_text text="GGCCCCGAAGCCCAAAGGCCCCGCCCAGCAGCCGCCTGGGCAGGAACAAA" />
+	  <has_text text="GGCTTCTCCCGGGGCCCTGGGGCCCCAGCCTCACCCTCAGCTTCCCACCC" />
+	  <has_text text="CCAGGGCCTAGACACGACCCCCAAGCCACACTGA" />
+	</assert_contents>
+      </output></test><test><param name="input" value="droPer1.bed" dbkey="droPer1" ftype="bed" />
@@ -152,14 +166,14 @@
 
 Extracting sequences with **FASTA** output data type returns::
 
-    >hg17_chr7_127475281_127475310_+
+    >hg17_chr7_127475281_127475310_+ NM_000230
     GTAGGAATCGCAGCGCCAGCGGTTGCAAG
-    >hg17_chr7_127485994_127486166_+
+    >hg17_chr7_127485994_127486166_+ NM_000230
     GCCCAAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCG
     GATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATC
     CAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAG
     GATCAATGACATTTCACACACG
-    >hg17_chr7_127486011_127486166_+
+    >hg17_chr7_127486011_127486166_+ D49487
     TGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGG
     CCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGA
     CACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCAC


https://bitbucket.org/galaxy/galaxy-central/commits/7286338fd77e/
Changeset:   7286338fd77e
Branch:      extract_genomic_dna_tool_enhancements
User:        jmchilton
Date:        2013-10-25 06:09:25
Summary:     Close branch extract_genomic_dna_tool_enhancements.
Affected #:  0 files

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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[galaxy-commits] commit/galaxy-central: 6 new changesets

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