1:26 p.m.
details: http://www.bx.psu.edu/hg/galaxy/rev/78e84936b7a3
changeset: 1470:78e84936b7a3
user: Greg Von Kuster <greg(a)bx.psu.edu>
date: Tue Aug 12 09:18:47 2008 -0400
description:
Fix for Extract Genomic DNA when input file metadata missing strand column value.
2 file(s) affected in this change:
tools/extract/extract_genomic_dna.py
tools/extract/extract_genomic_dna.xml
diffs (79 lines):
diff -r b9142bbae4ad -r 78e84936b7a3 tools/extract/extract_genomic_dna.py
--- a/tools/extract/extract_genomic_dna.py Fri Aug 08 13:42:32 2008 -0400
+++ b/tools/extract/extract_genomic_dna.py Tue Aug 12 09:18:47 2008 -0400
@@ -1,7 +1,10 @@
#!/usr/bin/env python
"""
-usage: extract_genomic_dna.py $input $out_file1 ${input.metadata.chromCol}
${input.metadata.startCol} ${input.metadata.endCol} ${input.metadata.strandCol} $dbkey
$out_format GALAXY_DATA_INDEX_DIR
-by Wen-Yu Chung
+usage: %prog $input $out_file1
+ -1, --cols=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 and twobit.loc
"""
from galaxy import eggs
import pkg_resources
@@ -10,6 +13,7 @@
from bx.cookbook import doc_optparse
import bx.seq.nib
import bx.seq.twobit
+from galaxy.tools.util.galaxyops import *
assert sys.version_info[:2] >= ( 2, 4 )
@@ -54,32 +58,18 @@
return twobit_path
def __main__():
- input_filename = sys.argv[1]
- output_filename = sys.argv[2]
- includes_strand_col = False
+ options, args = doc_optparse.parse( __doc__ )
+ try:
+ chrom_col, start_col, end_col, strand_col = parse_cols_arg( options.cols )
+ dbkey = options.dbkey
+ output_format = options.output_format
+ GALAXY_DATA_INDEX_DIR = options.GALAXY_DATA_INDEX_DIR
+ input_filename, output_filename = args
+ except:
+ doc_optparse.exception()
+
+ includes_strand_col = strand_col >= 0
strand = None
- # If any of the following exceptions are thrown, we need to improve the metadata
validator.
- try:
- chrom_col = int( sys.argv[3] ) - 1
- except:
- stop_err( "Chrom column not properly set, click the pencil icon in your
history item to set it." )
- try:
- start_col = int( sys.argv[4] ) - 1
- except:
- stop_err( "Start column not properly set, click the pencil icon in your
history item to set it." )
- try:
- end_col = int( sys.argv[5] ) - 1
- except:
- stop_err( "End column not properly set, click the pencil icon in your
history item to set it." )
- try:
- strand_col = int( sys.argv[6] ) - 1
- if strand_col >= 0:
- includes_strand_col = True
- except:
- pass
- dbkey = sys.argv[7]
- output_format = sys.argv[8]
- GALAXY_DATA_INDEX_DIR = sys.argv[9]
nibs = {}
twobits = {}
nib_path = check_nib_file( dbkey, GALAXY_DATA_INDEX_DIR )
diff -r b9142bbae4ad -r 78e84936b7a3 tools/extract/extract_genomic_dna.xml
--- a/tools/extract/extract_genomic_dna.xml Fri Aug 08 13:42:32 2008 -0400
+++ b/tools/extract/extract_genomic_dna.xml Tue Aug 12 09:18:47 2008 -0400
@@ -1,6 +1,6 @@
<tool id="Extract genomic DNA 1" name="Extract Genomic DNA"
version="2.1.0">
<description>using coordinates from assembled/unassembled
genomes</description>
- <command interpreter="python">extract_genomic_dna.py $input $out_file1
${input.metadata.chromCol} ${input.metadata.startCol} ${input.metadata.endCol}
${input.metadata.strandCol} $dbkey $out_format ${GALAXY_DATA_INDEX_DIR}</command>
+ <command interpreter="python">extract_genomic_dna.py $input $out_file1
-1
${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}
-d $dbkey -o $out_format -g ${GALAXY_DATA_INDEX_DIR}</command>
<inputs>
<param format="interval" name="input" type="data"
label="Fetch sequences corresponding to Query">
<validator type="unspecified_build" />