def record_iterator(string_iterable):
"""@param string_iterable iterable containing
string versions of records
@return iterator over the records
"""
filter_func = lambda l: not l.startswith("#")
return line_record_iterator(GFFRecord_t, GFFRecord_types, ifilter(filter_func, string_iterable))
def record_iterator(string_iterable):
'''
@param string_iterable iterable containing string versions of records
@return iterator over records
'''
try:
first_record = string_iterable.next()
except StopIteration:
return []
nfields = len(first_record.split())
h = { len(Blast6Types): (Blast6Record, Blast6Types),
len(Blast6SeqTypes): (Blast6SeqRecord, Blast6SeqTypes)}
btypes = h.get(nfields)
if not btypes:
raise Exception, "Not a valid blast string iterable"
return line_record_iterator(btypes[0],btypes[1], chain([first_record],
string_iterable))
def correct_oxford(reads_fn=None, alignments_fn=None):
'''Corrects oxford reads'''
log = logger(sys.stderr)
if not reads_fn or not alignments_blast6_fn:
if not len(sys.argv) == 3:
sys.exit("correct.py raw_reads.fa alignments.blast6")
(reads_fn,alignments_fn) = sys.argv[1:3]
log("Reading raw reads into memory")
#just put all reads in memory
fastas = compose(fasta_iterator, iterator_over_file)(reads_fn)
raw_reads = dict(map(attrgetter("name","seq"), fastas))
log("Reading raw reads DONE :)")
#The alignments need to be sorted by the long read name (second column)
alignment_it = line_record_iterator(Blast6SeqRecord, Blast6SeqTypes,
iterator_over_file(alignments_fn))
important_field_getter = attrgetter("qname","sname","qstart","qend",
"sstart","send", "qseq", "sseq")
for readname, alignments in groupby(alignment_it, attrgetter("sname")):
log("Working on %s" % readname)
raw_read_seq = raw_reads.get(readname)
if not raw_read_seq:
log("Can not find sequence for %s" % readname)
continue
log("Raw Read Length: %d" % len(raw_read_seq))
g = AlnGraph(raw_read_seq)
alignments = imap(important_field_getter, alignments)
num_alignments = 0
for qname,sname,qstart,qend,sstart,send,qseq,sseq in alignments:
#blast alignments are one based, convert to 0 based
(qstart, qend) = (qstart-1, qend-1)
(sstart, send) = (sstart-1, send-1)
#reverse complement, must switch the alignment strings
if send < sstart:
(qseq, sseq) = tuple(map(reverse_complement, [qseq,sseq]))
send, sstart = sstart,send
(qseq, sseq) = convert_mismatches(qseq,sseq)
try:
alignment_tuple =((qstart, qend, qseq),
(sstart, send, sseq), qname)
g.add_alignment( alignment_tuple)
except Exception as e:
log("Add Alignmented Error: %s" % e)
continue
if num_alignments > TOO_MANY_ALIGNMENTS:
break
num_alignments += 1
log("Processed Alignments: %d" % num_alignments)
if num_alignments > TOO_MANY_ALIGNMENTS:
log("Too Many Alignments, Skipping")
continue
log("Generating Consensus")
consensus = g.generate_all_consensus(min_cov=0)[0]
log("Consensus Length %d" % len(consensus[0]))
log("%s Done\n\n" % readname)
#log("Output dag info")
#output_dag_info(g, "g.info")
print ">"+readname+"_consensus"
print consensus[0]
def record_iterator(stream):
return line_record_iterator(NucRecord, NucRecordTypes, stream)
