Error in the namedtuple when category names are not valid field names

[agbeltran]

There are no restrictions in the category names in ISA-TAB and the parser fails when they are not valid field names for the namedtuple.

rec = isatab.parse("/Users/agbeltran/workspace/datasets/harvard-CD133")
Traceback (most recent call last):
File "", line 1, in
File "bcbio/isatab/parser.py", line 57, in parse
rec = s_parser.parse(rec)
File "bcbio/isatab/parser.py", line 192, in parse
["Raw Data File", "Derived Data File", "Image File"])
File "bcbio/isatab/parser.py", line 228, in _parse_study
node.metadata)
File "bcbio/isatab/parser.py", line 246, in _line_keyvals
self._collapse_attributes)
File "bcbio/isatab/parser.py", line 260, in _line_by_type
val = collapse_quals_fn(line, header, hgroups[index])
File "bcbio/isatab/parser.py", line 275, in _collapse_attributes
Attrs = collections.namedtuple('Attrs', names)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/collections.py", line 253, in namedtuple
ValueError: Type names and field names cannot start with a number: '57B_antigen_expression_by_IHC'

[chapmanb]

Alejandra;
Thanks for the problem report. The approach I took was to prefix headers starting with numbers so they can be cleanly handled by namedtuples. The fix is here and your dataset now parses cleanly:

835754e

Thanks much