can't handle abi / ab1 files

[dbrami]

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