Hi,
for some strange gff files i get the following error:
Traceback (most recent call last):
File
"/media/data/web/galaxy-central/lib/galaxy/jobs/runners/local.py", line
149, in run_job
job_wrapper.finish( stdout, stderr, exit_code )
File "/media/data/web/galaxy-central/lib/galaxy/jobs/__init__.py",
line 373, in finish
dataset.datatype.set_meta( dataset, overwrite = False ) #call
datatype.set_meta directly for the initial set_meta call during dataset
creation
File
"/media/data/web/galaxy-central/lib/galaxy/datatypes/interval.py", line
829, in set_meta
if valid_start and valid_end and start < end and strand in
self.valid_gff3_strand and phase in self.valid_gff3_phase:
UnboundLocalError: local variable 'start' referenced before assignment
start and end are not defined when elems[3] and elems[4] are '.'
Attached is a patch that should fix it.
Cheers,
Bjoern
diff -r 9207ba35fa0c lib/galaxy/datatypes/interval.py
--- a/lib/galaxy/datatypes/interval.py Sun Sep 09 18:24:51 2012 -0400
+++ b/lib/galaxy/datatypes/interval.py Wed Sep 26 23:52:02 2012 +0200
@@ -808,22 +808,25 @@
for i, line in enumerate( file ( dataset.file_name ) ):
line = line.rstrip('\r\n')
if line and not line.startswith( '#' ):
elems = line.split( '\t' )
valid_start = False
valid_end = False
if len( elems ) == 9:
try:
start = int( elems[3] )
- valid_start = True
+ valid_start = True
except:
if elems[3] == '.':
- valid_start = True
+ valid_start = True
+ start = 0
try:
end = int( elems[4] )
valid_end = True
except:
if elems[4] == '.':
valid_end = True
+ end = 0
strand = elems[6]
phase = elems[7]
if valid_start and valid_end and start < end and strand in self.valid_gff3_strand and phase in self.valid_gff3_phase:
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