details: http://www.bx.psu.edu/hg/galaxy/rev/8dfe971fcc27 changeset: 2457:8dfe971fcc27 user: guru date: Thu Jun 25 15:29:24 2009 -0400 description: Extract genomic DNA tool now uses only alignseq.loc to access sequence files. The twobit.loc file will henceforth be unnecessary, and all sequences from it should be moved to alignseq.loc.

1 file(s) affected in this change:

tools/extract/extract_genomic_dna.py

diffs (92 lines):

diff -r d3abf05d9272 -r 8dfe971fcc27 tools/extract/extract_genomic_dna.py --- a/tools/extract/extract_genomic_dna.py Fri Jun 19 11:21:13 2009 -0400 +++ b/tools/extract/extract_genomic_dna.py Thu Jun 25 15:29:24 2009 -0400 @@ -4,7 +4,7 @@ -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 + -g, --GALAXY_DATA_INDEX_DIR=N: the directory containing alignseq.loc """ from galaxy import eggs import pkg_resources @@ -29,33 +29,20 @@ reversed_s.reverse() return "".join( reversed_s )

-def check_nib_file( dbkey, GALAXY_DATA_INDEX_DIR ): - nib_file = "%s/alignseq.loc" % GALAXY_DATA_INDEX_DIR - nib_path = '' - for line in open( nib_file ): +def check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR ): + seq_file = "%s/alignseq.loc" % GALAXY_DATA_INDEX_DIR + seq_path = '' + for line in open( seq_file ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ) and line.startswith( 'seq' ): fields = line.split( '\t' ) if len( fields ) < 3: continue if fields[1] == dbkey: - nib_path = fields[2].strip() + seq_path = fields[2].strip() break - return nib_path + return seq_path

-def check_twobit_file( dbkey, GALAXY_DATA_INDEX_DIR ): - twobit_file = "%s/twobit.loc" % GALAXY_DATA_INDEX_DIR - twobit_path = '' - for line in open( twobit_file ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( "#" ): - fields = line.split( '\t' ) - if len( fields ) < 2: - continue - if fields[0] == dbkey: - twobit_path = fields[1].strip() - break - return twobit_path

def __main__(): options, args = doc_optparse.parse( __doc__ ) @@ -72,9 +59,8 @@ strand = None nibs = {} twobits = {} - nib_path = check_nib_file( dbkey, GALAXY_DATA_INDEX_DIR ) - twobit_path = check_twobit_file( dbkey, GALAXY_DATA_INDEX_DIR ) - if not os.path.exists( nib_path ) and not os.path.exists( twobit_path ): + seq_path = check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR ) + if not os.path.exists( seq_path ): # If this occurs, we need to fix the metadata validator. stop_err( "No sequences are available for '%s', request them by reporting this error." % dbkey )

@@ -116,11 +102,11 @@ strand = '+' sequence = ''

- if nib_path and os.path.exists( "%s/%s.nib" % ( nib_path, chrom ) ): + if seq_path and os.path.exists( "%s/%s.nib" % ( seq_path, chrom ) ): if chrom in nibs: nib = nibs[chrom] else: - nibs[chrom] = nib = bx.seq.nib.NibFile( file( "%s/%s.nib" % ( nib_path, chrom ) ) ) + nibs[chrom] = nib = bx.seq.nib.NibFile( file( "%s/%s.nib" % ( seq_path, chrom ) ) ) try: sequence = nib.get( start, end-start ) except: @@ -131,11 +117,11 @@ first_invalid_line = i + 1 invalid_line = line continue - elif twobit_path and os.path.exists( twobit_path ): + elif seq_path and os.path.exists( seq_path ): if chrom in twobits: t = twobits[chrom] else: - twobits[chrom] = t = bx.seq.twobit.TwoBitFile( file( twobit_path ) ) + twobits[chrom] = t = bx.seq.twobit.TwoBitFile( file( seq_path ) ) try: sequence = t[chrom][start:end] except: