n_unmapped += 1
# Take only the first part of read1, to make sure quality is high
seq = reads[reads[1].is_read1].seq[:200]
seqb = Seq(seq, IUPAC.ambiguous_dna)
# Save to file, to test local blast
reads_unmapped.append(reads[reads[1].is_read1])
if len(reads_unmapped) >= 100:
break
continue
# BLAST it
blast_xml = NCBIWWW.qblast("blastn", "nr", seqb)
blast_record = NCBIXML.read(blast_xml)
ali = blast_record.alignments
if len(ali):
ali = ali[0]
print ali.title
else:
print 'No matches found'
seqs_unmapped = reads_to_seqrecord(reads_unmapped)
from Bio import SeqIO
SeqIO.write(seqs_unmapped, '/ebio/ag-neher/home/fzanini/tmp/seqs_for_blast.fastq', 'fastq')
SeqIO.write(seqs_unmapped, '/ebio/ag-neher/home/fzanini/tmp/seqs_for_blast.fasta', 'fasta')
def fish_distant_reads(bamfilename, ref,
min_mismatches=20, max_mismatches=30,
VERBOSE=0, maxseqs=-1):
'''Fish distant reads from the trash'''
import numpy as np
from hivwholeseq.utils.mapping import pair_generator, reads_to_seqrecord
from hivwholeseq.sequencing.filter_mapped_reads import check_overhanging_reads, \
get_distance_from_consensus
distances = []
seqs = []
edges = []
with pysam.Samfile(bamfilename, 'rb') as bamfile:
for irp, reads in enumerate(pair_generator(bamfile)):
if VERBOSE >= 2:
if not ((irp + 1) % 10000):
print irp + 1
(read1, read2) = reads
i_fwd = reads[0].is_reverse
# Check a few things to make sure we are looking at paired reads
if read1.qname != read2.qname:
raise ValueError('Read pair '+str(irp)+': reads have different names!')
# Ignore unmapped reads
if read1.is_unmapped or read2.is_unmapped:
continue
# Ignore not properly paired reads (this includes mates sitting on
# different fragments)
if (not read1.is_proper_pair) or (not read2.is_proper_pair):
continue
# Check for overhangs beyond the edge
skip = check_overhanging_reads(reads, len(ref))
if skip:
continue
# Fish out our reads
dc = get_distance_from_consensus(ref, reads, VERBOSE=VERBOSE)
if (min_mismatches <= dc.sum() <= max_mismatches):
if VERBOSE >= 3:
print 'Gotcha!', reads[0].qname
seqs.append(reads[0])
seqs.append(reads[1])
distances.append(dc)
edge = [(read.pos, read.pos + sum(bl for bt, bl in read.cigar if bt in (0, 2)))
for read in reads]
edges.append(edge)
if len(seqs) // 2 == maxseqs:
if VERBOSE >= 2:
print 'Max seqs reached:', maxseqs
break
seqs = list(pair_generator(reads_to_seqrecord(seqs)))
distances = np.array(distances, int)
return (distances, edges, seqs)
# Take only the first part of read1, to make sure quality is high
seq = reads[reads[1].is_read1].seq[:200]
seqb = Seq(seq, IUPAC.ambiguous_dna)
# Save to file, to test local blast
reads_unmapped.append(reads[reads[1].is_read1])
if len(reads_unmapped) >= 100:
break
continue
# BLAST it
blast_xml = NCBIWWW.qblast("blastn", "nr", seqb)
blast_record = NCBIXML.read(blast_xml)
ali = blast_record.alignments
if len(ali):
ali = ali[0]
print ali.title
else:
print 'No matches found'
seqs_unmapped = reads_to_seqrecord(reads_unmapped)
from Bio import SeqIO
SeqIO.write(seqs_unmapped,
'/ebio/ag-neher/home/fzanini/tmp/seqs_for_blast.fastq',
'fastq')
SeqIO.write(seqs_unmapped,
'/ebio/ag-neher/home/fzanini/tmp/seqs_for_blast.fasta',
'fasta')