can't handle abi / ab1 files

[Daniel Brami]

Hi,
trim_quality chokes on ab1 /abi files:

here is my trim_quality.error:
Traceback (most recent call last):
File "/sgi/asmopt/python27/lib/python2.7/site-packages/crumbs/utils/bin_utils.py", line 61, in main
return(funct())
File "/sgi/asmopt/python27/bin/trim_quality", line 86, in run
args['out_format'], workers=workers)
File "/sgi/asmopt/python27/lib/python2.7/site-packages/crumbs/seqio.py", line 143, in write_trim_packets
seqs_diverted=ORPHAN_SEQS)
File "/sgi/asmopt/python27/lib/python2.7/site-packages/crumbs/seqio.py", line 104, in _write_filter_trim_packets
return write_seqs(seqs, passed_fhand, file_format=file_format)
File "/sgi/asmopt/python27/lib/python2.7/site-packages/crumbs/seqio.py", line 384, in write_seqs
seq = seqs2.next()
File "/sgi/asmopt/python27/lib/python2.7/site-packages/crumbs/seqio.py", line 102, in
seqs = (s for pair in chain.from_iterable(seq_packets) for s in pair)
File "/sgi/asmopt/python27/lib/python2.7/site-packages/crumbs/seqio.py", line 101, in
seq_packets = (p[SEQS_PASSED] for p in packets)
File "/sgi/asmopt/python27/lib/python2.7/site-packages/crumbs/trim.py", line 40, in seq_to_trim_packets
for packet in seq_packets:
File "/sgi/asmopt/python27/lib/python2.7/site-packages/crumbs/iterutils.py", line 93, in group_in_packets
chunk = tuple(islice(iterable, packet_size))
File "/sgi/asmopt/python27/lib/python2.7/site-packages/crumbs/seq.py", line 304, in
return (SeqWrapper(kind, seq, file_format) for seq in seqs)
File "/sgi/asmopt/python27/lib/python2.7/site-packages/Bio/SeqIO/init.py", line 537, in parse
for r in i:
File "/sgi/asmopt/python27/lib/python2.7/site-packages/Bio/SeqIO/AbiIO.py", line 94, in AbiIterator
raise ValueError("ABI files has to be opened in 'rb' mode.")
ValueError: ABI files has to be opened in 'rb' mode.

The command was:
/sgi/asmopt/python27/bin/trim_quality --in_format abi /bioscratch/data/jilian_automation/reads_ab1/corn_AP1/AP1-10-27_F_ref.ab1