1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8227055957e5/ changeset: 8227055957e5 user: dan date: 2011-10-20 22:38:14 summary: Update sff extractor to version 0.2.10. affected #: 2 files (-1 bytes) --- a/tools/filters/sff_extract.py Thu Oct 20 10:24:19 2011 -0400 +++ b/tools/filters/sff_extract.py Thu Oct 20 16:38:14 2011 -0400 @@ -27,7 +27,7 @@ __author__ = 'Jose Blanca and Bastien Chevreux' __copyright__ = 'Copyright 2008, Jose Blanca, COMAV, and Bastien Chevreux' __license__ = 'GPLv3 or later' -__version__ = '0.2.8' +__version__ = '0.2.10' __email__ = 'jblanca@btc.upv.es' __status__ = 'beta' @@ -298,7 +298,8 @@ #we check that we're removing the asked tag if tag is not None and tag != last_tag: - raise RuntimeError("The given xml tag wasn't the last one in the file") + etxt=join('The given xml tag (',tag,') was not the last one in the file'); + raise RuntimeError(etxt) # while we are at it: also remove all white spaces in that line :-) i -= 1 @@ -843,7 +844,7 @@ if len(boundaries) == 3: # case: mask char on both sides of sequence #print "bounds3" - data['clip_adapter_left']=1+boundaries[0][1] + data['clip_adapter_left']=boundaries[0][1] data['clip_adapter_right']=boundaries[2][0] elif len(boundaries) == 2: # case: mask char left or right of sequence @@ -851,7 +852,7 @@ if maskedseq[0] == maskchar : # case: mask char left #print "left" - data['clip_adapter_left']=1+boundaries[0][1] + data['clip_adapter_left']=boundaries[0][1] else: # case: mask char right #print "right" @@ -1192,7 +1193,11 @@ ''' left, right = return_merged_clips(data) seq = data['bases'] - new_seq = ''.join((seq[:left-1].lower(), seq[left-1:right], seq[right:].lower())) + if left >= right: + new_seq = seq.lower() + else: + new_seq = ''.join((seq[:left-1].lower(), seq[left-1:right], seq[right:].lower())) + return new_seq def clip_read(data): @@ -1209,14 +1214,14 @@ -def tests_for_ssaha(linker_fname): +def tests_for_ssaha(): '''Tests whether SSAHA2 can be successfully called.''' try: print "Testing whether SSAHA2 is installed and can be launched ... ", sys.stdout.flush() fh = open('/dev/null', 'w') - retcode = subprocess.call(["ssaha2", "-v"], stdout = fh) + retcode = subprocess.call(["ssaha2"], stdout = fh) fh.close() print "ok." except : @@ -1247,6 +1252,8 @@ '''Launches SSAHA2 on the linker and query file, string SSAHA2 output into the output filehandle''' + tests_for_ssaha() + try: print "Searching linker sequences with SSAHA2 (this may take a while) ... ", sys.stdout.flush() --- a/tools/filters/sff_extractor.xml Thu Oct 20 10:24:19 2011 -0400 +++ b/tools/filters/sff_extractor.xml Thu Oct 20 16:38:14 2011 -0400 @@ -1,4 +1,4 @@ -<tool id="Sff_extractor" name="SFF converter" version="1.0.0"> +<tool id="Sff_extractor" name="SFF converter" version="1.0.1"><description></description><command interpreter="python"> #if str($fastq_output) == "fastq_false" #sff_extract.py $clip --seq_file=$out_file3 --qual_file=$out_file4 --xml_file=$out_file2 $input 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.