def write_fasta(loc, tmpdir=TMPDIR):
fasta = fastas[loc.org]
seq = fasta[loc.seqid]
fname = "%s/%s_%i_%i.fasta" % (tmpdir, loc.seqid, loc.start, loc.end)
if op.exists(fname):
return fname
start, end = sorted((loc.start, loc.end))
seq = seq[start - 1: end]
if loc.rc: seq = complement(seq)[::-1]
fh = open(fname, "w")
print >>fh, ">%s\n%s" % (fh.name, seq)
return fh.name
def main(reads, tags, fmt):
gen_record = gen_record_from_raw if fmt == "raw" else gen_record_from_fastq
for record in gen_record(reads):
# TODO: support case where there are no tags and just want to add both normal
# and rc read to new file.
if tags:
seq = record[1]
if seq.startswith(tags[0]):
seq = seq[len(tags[0]):]
elif seq.startswith(tags[1]):
seq = complement(seq[len(tags[1]):])[::-1]
else:
print >>sys.stderr, "warning:%s does not start with specified tags!"
record[1] = seq
if len(record) > 2:
record[3] = record[3][-len(seq):][::-1] # strip the stuff for tags.
print "\n".join(record)
"""
def calc_nuc_counts(pos_signal_bedtool, neg_signal_bedtool, fasta_filename,
revcomp_strand, min_counts,
offset_min, offset_max, region_size,
ignore_chroms, only_chroms, verbose):
''' main routine for calculating nuc_counts '''
if verbose:
msg = ">> analyzing sequences ...\n"
msg += ">> ignore:%s only:%s\n" % \
(str(ignore_chroms), str(only_chroms))
msg += ">> offset range: %d to %d\n" % (offset_min, offset_max)
msg += ">> region size: %d\n" % (region_size)
msg += ">> revcomp strand: %s\n" % str(revcomp_strand)
print >>sys.stderr, msg
seq_fasta = Fasta(fasta_filename)
nuc_counts = defaultdict(Counter)
bedtools = (pos_signal_bedtool, neg_signal_bedtool)
strands = ('+', '-')
# total number of sites examined
total_sites = 0
for bedtool, strand in izip(bedtools, strands):
for row in bedtool:
# skip data based on specified chromosomes
if row.chrom in ignore_chroms:
continue
if only_chroms and row.chrom not in only_chroms:
continue
# skip data if counts are too low
if row.count < min_counts: continue
# sites in bedgraph examined - must come after all checks
# above
total_sites += 1
for offset in range(offset_min, offset_max + 1):
# upstream offsets are negative values
if strand == '+':
start = row.start + offset
elif strand == '-':
start = row.start - offset
if region_size == 1:
# half open at the position of interest
end = start + region_size
else:
# make sure that the 3' most position in a region
# is the base of interest
if strand == '+':
end = start + 1 # include position with + 1
start = end - region_size
else:
# negative strand
end = start + region_size
# XXX: does this ever happen?
if start < 0: continue
nucs = seq_fasta[row.chrom][start:end]
# 1. libs where the captured strand is sequenced
# are the correct polarity as-is (i.e. Excision-seq
# libs)
# 2. libs where the *copy* of the captured strand
# is sequenced should be revcomplemented (i.e.
# circularization-based libs)
if (strand == '+' and revcomp_strand) or \
(strand == '-' and not revcomp_strand):
nucs = complement(nucs[::-1])
if len(nucs.strip()) != region_size: continue
nuc_counts[offset][nucs] += row.count
return total_sites, nuc_counts
def calc_nuc_counts(pos_signal_bedtool, neg_signal_bedtool, fasta_filename,
revcomp_strand, min_counts, offset_min, offset_max,
region_size, ignore_chroms, only_chroms, verbose):
''' main routine for calculating nuc_counts '''
if verbose:
msg = ">> analyzing sequences ...\n"
msg += ">> ignore:%s only:%s\n" % \
(str(ignore_chroms), str(only_chroms))
msg += ">> offset range: %d to %d\n" % (offset_min, offset_max)
msg += ">> region size: %d\n" % (region_size)
msg += ">> revcomp strand: %s\n" % str(revcomp_strand)
print >> sys.stderr, msg
seq_fasta = Fasta(fasta_filename)
nuc_counts = defaultdict(Counter)
bedtools = (pos_signal_bedtool, neg_signal_bedtool)
strands = ('+', '-')
# total number of sites examined
total_sites = 0
for bedtool, strand in izip(bedtools, strands):
for row in bedtool:
# skip data based on specified chromosomes
if row.chrom in ignore_chroms:
continue
if only_chroms and row.chrom not in only_chroms:
continue
# skip data if counts are too low
if row.count < min_counts: continue
# sites in bedgraph examined - must come after all checks
# above
total_sites += 1
for offset in range(offset_min, offset_max + 1):
# upstream offsets are negative values
if strand == '+':
start = row.start + offset
elif strand == '-':
start = row.start - offset
if region_size == 1:
# half open at the position of interest
end = start + region_size
else:
# make sure that the 3' most position in a region
# is the base of interest
if strand == '+':
end = start + 1 # include position with + 1
start = end - region_size
else:
# negative strand
end = start + region_size
# XXX: does this ever happen?
if start < 0: continue
nucs = seq_fasta[row.chrom][start:end]
# 1. libs where the captured strand is sequenced
# are the correct polarity as-is (i.e. Excision-seq
# libs)
# 2. libs where the *copy* of the captured strand
# is sequenced should be revcomplemented (i.e.
# circularization-based libs)
if (strand == '+' and revcomp_strand) or \
(strand == '-' and not revcomp_strand):
nucs = complement(nucs[::-1])
if len(nucs.strip()) != region_size: continue
nuc_counts[offset][nucs] += row.count
return total_sites, nuc_counts
