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HmmPy.py
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HmmPy.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
from re import split
from itertools import groupby
from operator import itemgetter
__author__ = 'Enzo Guerrero-Araya (biologoenzo@gmail.com)'
__version__ = '0.1'
__date__ = 'July 13, 2016'
class HMMparser(object):
"""Parser of --domtblout of HMMER
Default values of Evalue and coverage was taken from dbCAN.
http://csbl.bmb.uga.edu/dbCAN/download/readme.txt
** About what E-value and Coverage cutoff thresholds you should use, we
have done some evaluation analyses using arabidopsis, rice, Aspergillus
nidulans FGSC A4, Saccharomyces cerevisiae S288c and Escherichia
coli K-12 MG1655, Clostridium thermocellum ATCC 27405 and
Anaerocellum thermophilum DSM 6725. Our suggestion is that
for plants, use E-value < 1e-23 and coverage > 0.2;
for bacteria, use E-value < 1e-18 and coverage > 0.35;
and for fungi, use E-value < 1e-17 and coverage > 0.45."""
def __init__(self, HMMfile):
self.HMMfile = HMMfile
try:
self.data_HMMfile = open(self.HMMfile).read()
except FileNotFoundError as e:
print("The name file or folder is incorrect.\
An error has occurred.")
raise e
self.parameters = {} # dict_keys(["Target file", "Option settings", "Program", "Version", "Date", "Current dir", "Pipeline mode", "Query file"])
for i, line in enumerate(self.data_HMMfile.split("\n")[-10:-2]):
line = line.split(":")
key = line[0][2:]
value = line[1].strip()
self.parameters[key] = value
if self.parameters["Program"] == "hmmscan":
self.matrix = self.hmmscanParser()
elif self.parameters["Program"] == "hmmsearch":
self.matrix = self.hmmsearchParser()
def filterByEvalue(self, evalue=1e-18):
if self.parameters["Program"] == "hmmscan":
for i, row in enumerate(self.matrix):
if float(row[12]) > evalue: # domain[11] -> i-Evalue (whole database)
self.matrix.pop(i)
elif self.parameters["Program"] == "hmmsearch":
for i, row in enumerate(self.matrix):
if float(row[7]) > evalue: # domain[11] -> Evalue of domine
self.matrix.pop(i)
def filterByBitscore(self, bits=50):
if self.parameters["Program"] == "hmmscan":
for i, row in enumerate(self.matrix):
if float(row[13]) < bits: # domain[13] -> Bitscore
self.matrix.pop(i)
elif self.parameters["Program"] == "hmmsearch":
for i, row in enumerate(self.matrix):
if float(row[8]) < bits: # domain[8] -> Bitscore
self.matrix.pop(i)
def filterByCoverage(self, cov=0.35): # covered fraction of HMM
if self.parameters["Program"] == "hmmscan":
for i, row in enumerate(self.matrix):
coverage = (float(row[16]) - float(row[15])) / float(row[2])
if coverage < cov: # domain[13] -> Bitscore
self.matrix.pop(i)
elif self.parameters["Program"] == "hmmsearch":
print("This type of filter due to technical stuff is only \
available for hmmscan program, please rerun your hmmsearch \
as hmmscan if you need this filter")
def uniqueByBestBitscore(self,): # by domain
if self.parameters["Program"] == "hmmscan":
matrix = sorted(self.matrix, key=itemgetter(3), reverse=True)
for query, group in groupby(matrix, itemgetter(3)):
group = list(group)
if len(group) == 1:
continue
group = sorted(group, key=itemgetter(13), reverse=True)
for dom in group[1:]:
index = self.matrix.index(dom)
self.matrix.pop(index)
elif self.parameters["Program"] == "hmmsearch":
print("This type of filter due to technical stuff is only \
available for hmmscan program, please rerun your hmmsearch \
as hmmscan if you need this filter")
def hmmscanParser(self, ):
matrix = []
# header = ["target name", "accession", "tlen", "query name",
# "accession", "qlen", "E-value", "score", "bias", "#", "of",
# "c-Evalue", "i-Evalue", "score", "bias", "from", "to",
# "from", "to", "from", "to", "acc", "description of target"]
# matrix.append(header)
for line in self.data_HMMfile.split("\n"):
if line.startswith("#") or line is "":
continue
line = split("\s+", line, 22) # just 22 because the last can contain \s+ characters
matrix.append(line)
return matrix
def hmmsearchParser(self, ):
matrix = []
# header = ["target name", "accession", "query name", "accession",
# "E-value", "score", "bias", "E-value", "score", "bias",
# "exp", "reg", "clu", "ov", "env", "dom", "rep", "inc",
# "description of target"]
# matrix.append(header)
for line in self.data_HMMfile.split("\n"):
if line.startswith("#") or line is "":
continue
line = split("\s+", line, 18) # just 18 because the last can contain \s+ characters
matrix.append(line)
return matrix
# Module test
if __name__ == "__main__":
import argparse
import sys
usage = """%(prog)s reads .domtblout file and returns a custom filtred \
result (by Evalue, Bitscore, Coverage of HMM model) or it can \
show only the Best Bitscore domain for each query on hmmscan \
program output"""
parser = argparse.ArgumentParser(description=usage)
parser.add_argument("-b", "--bits", dest="bits",
help="The minimum Bitscore threshold to considerate a \
domain as a truly hits [be careful with false \
positives] (recomended: 50)", type=float)
parser.add_argument("-e", "--evalue", dest="evalue",
help="The maximun E-value threshold to considerate a \
domain as a truly hits [be careful with false \
positives] (recomended: 1e-18)", type=float)
parser.add_argument("-c", "--cov", dest="cov",
help="The minimum coverage threshold to considerate a \
domain as a truly hits [be careful with false \
positives] (recomended: 0.35)", type=float)
parser.add_argument("-u", "--unique", dest="unique", action="store_true",
help="show only the Best Bitscore domain for each \
query on hmmscan program output", default=False)
parser.add_argument("-s", "--spacer", dest="spacer", help="Select the \
spacer for the program output", default="\t")
parser.add_argument("-o", "--outfile", nargs="?", help="(default: stdout)",
type=argparse.FileType("w"), default=sys.stdout)
parser.add_argument("-v", "--version", action="version", version="%(prog)s v{} ({}) By: {}".format(__version__, __date__, __author__))
parser.add_argument("domtblout", type=str)
args = parser.parse_args()
bits = args.bits
evalue = args.evalue
cov = args.cov
outfile = args.outfile
domtblout = args.domtblout
spacer = args.spacer
hmm = HMMparser(domtblout)
if args.bits:
hmm.filterByBitscore(bits)
if args.evalue:
hmm.filterByEvalue(evalue)
if args.cov:
hmm.filterByCoverage(cov)
if args.unique:
hmm.uniqueByBestBitscore()
if hmm.parameters["Program"] == "hmmscan":
header = ["target name", "accession", "tlen", "query name",
"accession", "qlen", "E-value", "score", "bias", "#", "of",
"c-Evalue", "i-Evalue", "score", "bias", "from", "to",
"from", "to", "from", "to", "acc", "description of target"]
else:
header = ["target name", "accession", "query name", "accession",
"E-value", "score", "bias", "E-value", "score", "bias",
"exp", "reg", "clu", "ov", "env", "dom", "rep", "inc",
"description of target"]
print(spacer.join(header), file=outfile)
for row in hmm.matrix:
row = spacer.join(row)
print(row, file=outfile)