Mercurial > repos > jjohnson > gmap
changeset 5:f4b4c1712e39
GSNAP - added datatypes for tally related data and gnsap default output
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Tue, 08 Nov 2011 13:07:25 -0600 |
parents | f49f5a460c74 |
children | 3be0e0a858fe |
files | gmap/lib/galaxy/datatypes/gmap.py |
diffstat | 1 files changed, 48 insertions(+), 0 deletions(-) [+] |
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--- a/gmap/lib/galaxy/datatypes/gmap.py Tue Nov 08 13:02:32 2011 -0600 +++ b/gmap/lib/galaxy/datatypes/gmap.py Tue Nov 08 13:07:25 2011 -0600 @@ -217,6 +217,13 @@ """ file_ext = 'snps.iit' +class TallyIntervalIndexTree( IntervalIndexTree ): + """ + A GMAP Interval Index Tree Map + created by iit_store + """ + file_ext = 'tally.iit' + class IntervalAnnotation( Text ): """ Class describing a GMAP Interval format: @@ -422,3 +429,44 @@ return False +class TallyAnnotation(IntervalAnnotation): + file_ext = 'gsnap_tally' + """ + Output produced by gsnap_tally + Example: + >144 chr20:57268791..57268935 + G0 + A1(1@7|1Q-3) + A2(1@36,1@1|1Q2,1Q-8) + C2 0.889,0.912,0.889,0.889,0.933,0.912,0.912,0.889,0.889,0.889 -2.66,-2.89,-2.66,-2.66,-3.16,-2.89,-2.89,-2.66,-2.66,-2.66 + C1 T1 0.888,0.9,0.888,0.9,0.913,0.9,0.911,0.888,0.9,0.913 -2.66,-2.78,-2.66,-2.78,-2.91,-2.78,-2.89,-2.66,-2.78,-2.91 + """ + def sniff( self, filename ): # TODO + """ + Determines whether the file is a gmap splice site annotation file + """ + try: + pat = '^>(\d+)\s((\S+):(\d+)\.\.(\d+))$' #>total chr:position..position + pat2 = '^[GATCN]\d.*$' #BaseCountDeatails + fh = open( filename ) + count = 0 + while True and count < 10: + line = fh.readline() + if not line: + break #EOF + line = line.strip() + if line: #first non-empty line + count += 1 + if re.match(pat,line) == None and re.match(pat2,line) == None: # Failed to match + return False + finally: + fh.close() + return False + +class GsnapResult( Text ): + """ + The default output format for gsnap. Can be used as input for gsnap_tally. + """ + file_ext = 'gsnap' + +