/
parseHMM
executable file
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parseHMM
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#!/usr/bin/pypy
'''
Read the tabular output of nhmmer, and check which hits are in the upstream region
of a gene based on a GenBank file
'''
__author__ = "Marco Galardini"
from Bio import SeqIO
from regtools import *
################################################################################
# Read options
def getOptions():
import argparse
# create the top-level parser
description = ("Parse the tabular output of nhmmer, a GenBank file and a MEME motif file, "+
"providing the list of hits found in gene upstream regions")
parser = argparse.ArgumentParser(description = description)
parser.add_argument('nhmmer', action="store",
help='RSAT tabular file')
parser.add_argument('genome', action="store",
help='Genome GenBank file')
parser.add_argument('motif', action="store",
help='MEME motif file')
parser.add_argument('regulator', action="store",
help='Regulator name')
parser.add_argument('-m', '--maxup', action='store',
type=int,
default=600,
help='Max upstream location [Default: 600bp]')
parser.add_argument('-u', '--upstream', action='store',
type=int,
default=400,
help='Upstream region size [Default: 400bp]')
parser.add_argument('-d', '--downstream', action='store',
type=int,
default=100,
help='Upstream region size [Default: 100bp]')
parser.add_argument('-t', '--threshold', action='store',
type=float,
default=10,
help='p-value threshold [Default: 10]')
parser.add_argument('-o', '--order', action="store_true",
default=False,
dest='order',
help='The motif has to be found in forward with the gene (not for palindromic motifs)')
parser.add_argument('-f', '--fasta', action="store_true",
default=False,
dest='fasta',
help='Output in FASTA format')
parser.add_argument('-l', '--linear', action="store_true",
default=False,
help='Linear or draft genome')
parser.add_argument('-a', '--all', action="store_true",
dest='all',
default=False,
help='Save ALL upstream regions (not considering genes overlaps and -u option)')
parser.add_argument('-r', '--header', action="store_true",
dest='header',
default=False,
help='Print explanatory header (incompatible with -f)')
return parser.parse_args()
################################################################################
# Classes
class HMM(object):
def __init__(self, dna, strand, mname, start, stop, score, evalue):
self.dna = dna
self.strand = strand
self.mname = mname
self.start = int(start)
self.stop = int(stop)
self.score = float(score)
self.evalue = float(evalue)
################################################################################
# Functions
def parseHMM(fname, motifLen, threshold=10):
'''
Generator to relevant lines of a HMM tabular output
Returns HMM objects
'''
for l in open(fname):
if l.lstrip().startswith('#'):continue
l = l.strip()
while ' ' in l:
l=l.replace(' ', ' ')
s = l.split()
dna = s[0]
hmmfrom = s[4]
hmmto = s[5]
start = s[6]
stop = s[7]
strand = s[11]
evalue = s[12]
score = s[13]
start, stop = sorted([int(start), int(stop)])
if float(evalue) > threshold:continue
#if int(hmmto) - int(hmmfrom) + 1 != motifLen:continue
yield HMM(dna, strand, dna, start, stop, score, evalue)
def getUpstreams(record, b_up=400, b_down=100, is_circ=True, all_up=False):
genes=get_genes(record)
if len(genes)==0:
return []
whole_seq=get_whole_genome_seq(record)
if not all_up:
upstreams=get_all_upstreams(genes,whole_seq, b_up, b_down, is_circ)
else:
upstreams=get_all_upstreams_all(genes,whole_seq, b_up, b_down, is_circ)
return upstreams
################################################################################
# Main
if __name__ == "__main__":
options = getOptions()
# Read the input motif (we need to know its length)
for l in open(options.motif):
l=l.strip()
if 'LENG ' in l:
mLen=int(l.lstrip('LENG '))
hits = {}
for m in parseHMM(options.nhmmer, mLen, options.threshold):
if m.dna not in hits:
hits[m.dna] = set()
hits[m.dna].add(m)
i = 0
if options.header:
print '#' + '\t'.join([str(x) for x in ['locus_tag',
'dna_id', 'dna_strand',
'dna_start', 'dna_stop',
'motif_strand', 'motif_start',
'motif_stop',
'motif_seq', 'method',
'evalue', 'threshold',
'regulator_name']])
for s in SeqIO.parse(open(options.genome), 'genbank'):
if s.id not in hits:
continue
dups = {}
upstream = getUpstreams(s, options.upstream, options.downstream,
not options.linear, options.all)
for u in upstream:
dups[u.name] = u
hs = sorted(hits[s.id], key=lambda x: x.start)
for m in hs:
bFound = False
for f in filter(lambda x: x.type == 'CDS', s.features):
gname = f.qualifiers['locus_tag'][0]
if f.strand == 1:
if (m.start > (dups[gname].start) and
m.stop < (dups[gname].end)):
if options.order and m.strand == '-':continue
bFound = True
if m.strand == '-':
strand = '-'
else:
strand = '+'
start = m.start - f.location.start
stop = m.stop - f.location.start
# Discard those hits that are very far from the gene
if start < -(options.maxup):continue
if m.strand == '+':
seq = s[m.start -1:m.stop ].seq
else:
seq = s[m.start -1:m.stop ].seq.reverse_complement()
if options.fasta:
print '>%d'%i
print seq
i += 1
else:
print '\t'.join([str(x) for x in [gname,
s.id, m.strand,
m.start, m.stop,
strand, start, stop,
seq, 'nhmmer',
m.evalue, options.threshold,
options.regulator]])
else:
if (m.start > (dups[gname].start) and
m.stop < (dups[gname].end)):
if options.order and m.strand == '+':continue
bFound = True
if m.strand == '+':
strand = '-'
else:
strand = '+'
start = f.location.end - m.stop
stop = f.location.end - m.start
# Discard those hits that are very far from the gene
if start < -(options.maxup):continue
if m.strand == '+':
seq = s[m.start -1:m.stop ].seq
else:
seq = s[m.start -1:m.stop ].seq.reverse_complement()
if options.fasta:
print '>%d'%i
print seq
i += 1
else:
print '\t'.join([str(x) for x in [gname,
s.id, m.strand,
m.start, m.stop,
strand, start, stop,
seq, 'nhmmer',
m.evalue, options.threshold,
options.regulator]])
if not bFound:
# Not in front of a gene, print a "naked" record
if m.strand == '+':
seq = s[m.start -1:m.stop ].seq
else:
seq = s[m.start -1:m.stop ].seq.reverse_complement()
if options.fasta:
print '>%d'%i
print seq
i += 1
else:
print '\t'.join([str(x) for x in ['',
s.id, m.strand,
m.start, m.stop,
'', '', '',
seq, 'nhmmer',
m.evalue, options.threshold,
options.regulator]])