[Biopython-dev] GFF parser bug?
Eli Papa
elipapa at mit.edu
Sun Apr 25 19:09:51 EDT 2010
Hello,
While trying to use the GFF parser I ran into a value error.
I think it's probably due to one of the GFF3 fields in my file not being
specified as 'key=value', but just as 'value'.
Hope this helps,
eli
In [1]: from BCBio.GFF import GFFExaminer
In [2]: import pprint
In [3]: in_file = "V1.UC-9.scaftig.more500.gff"
In [4]: examiner = GFFExaminer()
In [5]: in_handle = open(in_file)
In [6]: pprint.pprint(examiner.parent_child_map(in_handle))
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
/data/elipapa/gutmetahit/SingleSample_GenePrediction/<ipython console>
in <module>()
/home/elipapa/lib/python/bcbio-0.1-py2.4.egg/BCBio/GFF/GFFParser.py in
_file_or_handle_inside(*args, **kwargs)
705 in_handle = open(in_file)
706 args = (args[0], in_handle) + args[2:]
--> 707 out = fn(*args, **kwargs)
708 if need_close:
709 in_handle.close()
/home/elipapa/lib/python/bcbio-0.1-py2.4.egg/BCBio/GFF/GFFParser.py in
parent_child_map(self, gff_handle)
789 if line.strip():
790 line_type, line_info = _gff_line_map(line,
--> 791 self._get_local_params())[0]
792 if (line_type == 'parent' or (line_type == 'child' and
793 line_info['id'])):
/home/elipapa/lib/python/bcbio-0.1-py2.4.egg/BCBio/GFF/GFFParser.py in
_gff_line_map(line, params)
158 # collect all of the base qualifiers for this item
159 if len(parts) > 8:
--> 160 quals, is_gff2 = _split_keyvals(gff_parts[8])
161 else:
162 quals, is_gff2 = dict(), False
/home/elipapa/lib/python/bcbio-0.1-py2.4.egg/BCBio/GFF/GFFParser.py in
_split_keyvals(keyval_str)
84 pieces.append(p.strip().split(" "))
85 key_vals = [(p[0], " ".join(p[1:])) for p in pieces]
---> 86 for key, val in key_vals:
87 # remove quotes in GFF2 files
88 if (len(val) > 0 and val[0] == '"' and val[-1] == '"'):
ValueError: need more than 1 value to unpack
*******
The gff file is as follows:
##gff-version 3
##sequence-region scaffold4215_3 1 6526
scaffold4215_3 glimmer gene 3 62 . - .
ID=GL0000006;Name=GL0000006;Lack 3'-end;
scaffold4215_3 glimmer mRNA 3 62 . - .
ID=GL0000006;Name=GL0000006;Parent=GL0000006;Lack 3'-end;
scaffold4215_3 glimmer CDS 3 62 2.84 - 0
Parent=GL0000006;Lack 3'-end;
scaffold4215_3 glimmer gene 124 1983 . - .
ID=GL0000007;Name=GL0000007;Complete;
[...]
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