details: http://www.bx.psu.edu/hg/galaxy/rev/cffa627364bb changeset: 3649:cffa627364bb user: Greg Von Kuster greg@bx.psu.edu date: Wed Apr 14 11:27:15 2010 -0400 description: Apply patch from Brad Chapman that resolves the following issue - resolves ticket # 319.
GFF and GFF3 sniffer functions in datatypes/intervals.py currently require the score column to be an integer between 0 and 1000 to assign a file as valid GFF. According to the GFF3 spec, the score values are not well defined and floating point values or numbers outside that range should also be valid.
The patch relaxes this requirement to allow detection of a wider range of GFF files.
diffstat:
lib/galaxy/datatypes/interval.py | 8 ++------ 1 files changed, 2 insertions(+), 6 deletions(-)
diffs (29 lines):
diff -r bb2f3963136d -r cffa627364bb lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py Wed Apr 14 11:21:00 2010 -0400 +++ b/lib/galaxy/datatypes/interval.py Wed Apr 14 11:27:15 2010 -0400 @@ -718,11 +718,9 @@ return False if hdr[5] != '.': try: - score = int(hdr[5]) + score = float( hdr[5] ) except: return False - if (score < 0 or score > 1000): - return False if hdr[6] not in data.valid_strand: return False return True @@ -822,11 +820,9 @@ return False if hdr[5] != '.': try: - score = int(hdr[5]) + score = float( hdr[5] ) except: return False - if (score < 0 or score > 1000): - return False if hdr[6] not in self.valid_gff3_strand: return False if hdr[7] not in self.valid_gff3_phase: