1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/91a437977be1/ changeset: 91a437977be1 user: jgoecks date: 2012-03-08 17:09:14 summary: Enable fasta_to_len conversion to use only first word in title; this is standards compliant and used by default for automatic conversion. affected #: 2 files

diff -r 5ffd9f8983538741cf0597e6e61ccc70256ad585 -r 91a437977be1b1ae6eabd510e553f86f86f74ac0 lib/galaxy/datatypes/converters/fasta_to_len.py --- a/lib/galaxy/datatypes/converters/fasta_to_len.py +++ b/lib/galaxy/datatypes/converters/fasta_to_len.py @@ -9,7 +9,7 @@

assert sys.version_info[:2] >= ( 2, 4 )

-def compute_fasta_length( fasta_file, out_file, keep_first_char ): +def compute_fasta_length( fasta_file, out_file, keep_first_char, keep_first_word=False ):

infile = fasta_file out = open( out_file, 'w') @@ -32,6 +32,8 @@ continue if line[0] == '>': if first_entry == False: + if keep_first_word: + fasta_title = fasta_title.split()[0] out.write( "%s\t%d\n" % ( fasta_title[ 1:keep_first_char ], seq_len ) ) else: first_entry = False @@ -41,8 +43,10 @@ seq_len += len(line)

# last fasta-entry + if keep_first_word: + fasta_title = fasta_title.split()[0] out.write( "%s\t%d\n" % ( fasta_title[ 1:keep_first_char ], seq_len ) ) out.close()

-if __name__ == "__main__" : - compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3] ) \ No newline at end of file +if __name__ == "__main__" : + compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3], True ) \ No newline at end of file

diff -r 5ffd9f8983538741cf0597e6e61ccc70256ad585 -r 91a437977be1b1ae6eabd510e553f86f86f74ac0 tools/fasta_tools/fasta_compute_length.py --- a/tools/fasta_tools/fasta_compute_length.py +++ b/tools/fasta_tools/fasta_compute_length.py @@ -6,4 +6,4 @@ import sys from galaxy.datatypes.converters.fasta_to_len import compute_fasta_length

-compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3]) \ No newline at end of file +compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3], False ) \ No newline at end of file

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

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