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interweaveMates.py
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interweaveMates.py
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########################################################################################
## This file is a part of YAP package of scripts. https://github.com/shpakoo/YAP
## Distributed under the MIT license: http://www.opensource.org/licenses/mit-license.php
## Copyright (c) 2011-2013 Sebastian Szpakowski
########################################################################################
#################################################
## Interwaeve two mates
#################################################
import sys
from optparse import OptionParser
from collections import defaultdict
_author="Sebastian Szpakowski"
_date="2011/01/01"
_version="Version 1"
#################################################
## Classes
##
#################################################
### Iterator over input fasta file.
### Only reading when requested
### Useful for very large FASTA files
### with many sequences
class FastaParser:
def __init__ (self, x, quals=False):
self.filename = x
self.fp = open(x, "r")
self.currline = ""
self.currentFastaName = ""
self.currentFastaSequence = ""
self.lastitem=False
if quals:
self.linesep=" "
else:
self.linesep=""
def __iter__(self):
return(self)
#####
def next(self):
for self.currline in self.fp:
if self.currline.startswith(">"):
self.currline = self.currline[1:]
if self.currentFastaName == "":
self.currentFastaName = self.currline
else:
otpt = (self.currentFastaName.strip(), self.currentFastaSequence.strip())
self.currentFastaName = self.currline
self.currentFastaSequence = ""
self.previoustell = self.fp.tell()
return (otpt)
else:
self.addSequence(self.currline)
if not self.lastitem:
self.lastitem=True
return (self.currentFastaName.strip(), self.currentFastaSequence.strip())
else:
raise StopIteration
def addSequence(self, x):
self.currentFastaSequence = "%s%s%s" % (self.currentFastaSequence,self.linesep, x.strip())
def __str__():
return ("reading file: %s" %self.filename)
class FastaLikeParser:
def __init__ (self, x):
self.filename = x
self.fp = open(x, "r")
self.currline = ""
self.currentFastaName = ""
self.currentFastaSequence = ""
self.lastitem=False
def __iter__(self):
return(self)
#####
def next(self):
for self.currline in self.fp:
if self.currline.startswith(">"):
self.currline = self.currline[1:]
if self.currentFastaName == "":
self.currentFastaName = self.currline
else:
otpt = (self.currentFastaName.strip(), self.currentFastaSequence.strip())
self.currentFastaName = self.currline
self.currentFastaSequence = ""
self.previoustell = self.fp.tell()
return (otpt)
else:
self.addSequence(self.currline)
if not self.lastitem:
self.lastitem=True
return (self.currentFastaName.strip(), self.currentFastaSequence.strip())
else:
raise StopIteration
def addSequence(self, x):
self.currentFastaSequence = "%s\n%s" % (self.currentFastaSequence, x.strip())
def __str__():
return ("reading file: %s" %self.filename)
#################################################
## Functions
##
def parseMate(infile):
seqs = dict()
for head, seq in FastaParser(infile):
id = head.strip().split("/")[0].strip().split()[0]
seqs[id]= seq
print "loaded %s reads" % (len(seqs.keys()))
return seqs
def parseCluster(infile):
repr = defaultdict(set)
for clusterid, contents in FastaLikeParser(infile):
representative= ""
descendants = set()
for line in contents.strip().split("\n"):
id = line.split(">")[1].split("...")[0].split()[0]
id = id.strip().split("/")[0]
if line.endswith("*"):
representative = id
### self is always a descendant of itself!
descendants.add(id)
for k in descendants:
repr[k]=descendants
return (repr)
def mergeClusters(c1, c2):
unique = set()
all = set(c1.keys()) | set(c2.keys())
for id in all:
A1 = c1[id]
A2 = c2[id]
representative = A1 & A2
representative = list(representative)
representative.sort()
if len(representative)>0:
representative = representative[0]
unique.add(representative)
else:
representative = ""
nondups = A1 ^ A2
unique = unique | nondups
#
# if representative !="":
# print id, c1[id], c2[id],
# print representative, nondups
# print
return (unique)
#################################################
## Arguments
##
parser = OptionParser()
parser.add_option("-f", "--fasta", dest="fn_fasta",
help="write report to FILE", metavar="FILE")
parser.add_option("-c", "--clusters", dest="fn_cluster", default="",
help="write report to FILE", metavar="FILE")
#parser.add_option("-q", "--quiet",
# action="store_false", dest="verbose", default=True,
# help="don't print status messages to stdout")
(options, args) = parser.parse_args()
#################################################
## Begin
##
file1, file2 = options.fn_fasta.strip().split(",")
seq1 = parseMate(file1)
seq2 = parseMate(file2)
A = set(seq1.keys()).intersection(set(seq2.keys()))
print "\t%s sequences mated." % (len(A))
clusters = options.fn_cluster.strip().split(",")
if len(clusters)==2:
c1, c2 = clusters
c1 = parseCluster(c1)
c2 = parseCluster(c2)
unique = mergeClusters(c1, c2)
print "\t%s unique mates." % (len(unique))
A = A & unique
otptfilename = "%s.weave.fasta" % ".".join(file1.strip().split(".")[:-1])
otpt = open(otptfilename, "w")
for id in A:
line = ">%s/1\n%s\n>%s/2\n%s\n" % (id.strip().split()[0], seq1[id], id.strip().split()[0], seq2[id])
otpt.write(line)
otpt.close()
#################################################
## Finish
#################################################