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FastQEncoding.py
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FastQEncoding.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
########################################################################################
#################################################
## File: FastQEncoding
#################################################
import sys
import argparse
_author="Sebastian Szpakowski"
_date="Oct 12, 2012"
_version="Version 1"
#################################################
## Classes
##
#################################################
### Iterator over input fastq file.
### Only reading when requested
### Useful for very large files
### with many sequences
class FastqParser:
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("+") or 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__(self):
return ("reading file: %s" % self.filename)
# SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS.....................................................
# ..........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......................
# ...............................IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII......................
# .................................JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ......................
# LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL....................................................
# !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
# | | | | | |
# 33 59 64 73 104 126
#
# S - Sanger Phred+33, raw reads typically (0, 40)
# X - Solexa Solexa+64, raw reads typically (-5, 40)
# I - Illumina 1.3+ Phred+64, raw reads typically (0, 40)
# J - Illumina 1.5+ Phred+64, raw reads typically (3, 40)
# with 0=unused, 1=unused, 2=Read Segment Quality Control Indicator (bold)
# (Note: See discussion above).
# L - Illumina 1.8+ Phred+33, raw reads typically (0, 41)
class FastQDecoder:
def __init__(self):
self.encodings = {
"64" : set(list("""@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~""" )),
"33" : set(list("""!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJ""" ))
}
def guessEncoding(self, input):
guesses = set()
#print ""
#print "\t", self.format(input)
for name, quals in self.encodings.items():
tmp = input.difference(quals)
# print name, "\t", self.format(quals)
# print "\t", self.format(tmp)
#print name, "\t", self.format(tmp)
if len(tmp)==0:
guesses.add(name)
return guesses
def format(self, input):
tmp = list(input)
tmp.sort
return "".join(tmp)
#################################################
## Functions
##
#################################################
## Arguments
##
#import argparse
#parser = argparse.ArgumentParser(description='Process some integers.')
#parser.add_argument('integers', metavar='N', type=int, nargs='+',
# help='an integer for the accumulator')
#parser.add_argument('--sum', dest='accumulate', action='store_const',
# const=sum, default=max,
# help='sum the integers (default: find the max)')
#args = parser.parse_args()
#print args.accumulate(args.integers)
#################################################
## Begin
##
observedQs = set()
decoder = FastQDecoder()
encodings = set(["64", "33"])
count = 0
guessing = True
for head, seq in FastqParser(sys.argv[-1]):
if head.startswith("+"):
observedQs = observedQs.union(list(seq))
encodings = decoder.guessEncoding(observedQs)
if len(encodings)==1:
count+=1
if count >100 and len(encodings)==1:
print list(encodings)[0]
guessing = False
break;
if guessing:
print "33\n"
#################################################
## Finish
#################################################