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samJuncs.py
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samJuncs.py
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#!/usr/bin/env python3
########################################################################
# File: samJuncs.py
# executable: samJuncs.py
# Purpose:
#
#
# Author: Cameron M. Soulette
# History: cms 02/12/2018 Created
#
########################################################################
########################################################################
# Hot Imports & Global Variable
########################################################################
import os, sys
import numpy as np
from multiprocessing import Pool
import re
import pysam
########################################################################
# CommandLine
########################################################################
class CommandLine(object) :
'''
Handle the command line, usage and help requests.
CommandLine uses argparse, now standard in 2.7 and beyond.
it implements a standard command line argument parser with various argument options,
and a standard usage and help,
attributes:
myCommandLine.args is a dictionary which includes each of the available command line arguments as
myCommandLine.args['option']
methods:
'''
def __init__(self, inOpts=None) :
'''
CommandLine constructor.
Implements a parser to interpret the command line argv string using argparse.
'''
import argparse
self.parser = argparse.ArgumentParser(description = 'samJuncs.py - lorem ipsium.',
epilog = 'Please feel free to forward any questions or concerns to /dev/null',
add_help = True, #default is True
prefix_chars = '-',
usage = '%(prog)s -i input_sam ')
# Add args
self.parser.add_argument('-i', '--sam_file', type=str, action = 'store', required=True, help='Input SAM/BAM file.')
self.parser.add_argument('--isSam', action = 'store_true', default=False, help='File is sam')
if inOpts is None :
self.args = vars(self.parser.parse_args())
else :
self.args = vars(self.parser.parse_args(inOpts))
########################################################################
# Sequence Alignment File
########################################################################
class SAM(object):
'''
Handles sequence alignment format file input and output.
'''
def __init__(self, inFile=None, isBam=False):
# Attributes
self.isBam = isBam
self.inFile = inFile
self.juncCounts = dict()
# Start pysam object either as bam or sam object
if self.isBam == False:
readSam = "r"
else:
readSam = "rb"
try:
self.reader = pysam.AlignmentFile(self.inFile, readSam)
except:
#File does not exist.
print("ERROR: Cannot find file %s. Exiting!" % self.inFile, file=sys.stderr)
sys.exit(1)
self.strandInfo = {0:'+', 16:'-'}
#print(self.reader.find_introns((read for read in self.reader.fetch() if read.is_reverse)))
#sys.exit(1)
def countJuncs(self):
'''
Reads self.reader and reports junction counts for each junction.
Returns dictionary with junction counts per junction per chromosome.
'''
strandInfo = {0:'+', 16:'-'}
for read in self.reader.fetch():
try:
strand = strandInfo[read.flag]
except:
continue
qName = read.query_name
chromosome = read.reference_name
refPos = read.pos
refEnd = read.pos
startPos = read.pos
cigar = read.cigar
for num, flagTuple in enumerate(cigar,1):
flag, length = flagTuple
if flag not in [0,2,3,7,8]:
continue
if flag == 3:
if chromosome not in self.juncCounts:
self.juncCounts[chromosome] = dict()
if (refEnd, refEnd+length) not in self.juncCounts[chromosome]:
self.juncCounts[chromosome][(refEnd, refEnd+length)] = int()
self.juncCounts[chromosome][(refEnd, refEnd+length)] += 1
refPos = refEnd+length
refEnd = refPos
return self.juncCounts
def readJuncs(self):
'''
Returns start, end and junctions from a single read.
'''
for read in self.reader.fetch():
try:
# Skip unmapped or multimapped reads.
strand = self.strandInfo[read.flag]
except:
continue
qName = read.query_name
chromosome = read.reference_name
refPos = read.pos
refEnd = read.pos
startPos = read.pos
cigar = read.cigar
# Here is the read starts
rstart = int(read.pos)
# Next will be junctions
junctions = set()
orientation = read.flag
if orientation == 0:
orientation = "+"
elif orientation == 16:
orientation = "-"
else:
continue
tags = read.get_tags()
juncDir = [x[-1] for x in tags if x[0] == 'ts']
if not juncDir:
juncDir = 'nan'
else:
juncDir = juncDir[0]
if orientation == "+" and juncDir == "+":
juncDir = "+"
elif orientation == "+" and juncDir == "-":
juncDir = "-"
elif orientation == "-" and juncDir == "+":
juncDir = "-"
elif orientation == "-" and juncDir == "-":
juncDir = "+"
for num, flagTuple in enumerate(cigar,1):
flag, length = flagTuple
if flag not in [0,2,3,7,8]:
continue
if flag == 3:
junctions.add((refEnd, refEnd+length))
refPos = refEnd+length
refEnd = refPos
# Last is the end
rend = refEnd
yield (qName, chromosome, rstart, list(junctions), rend, orientation, juncDir)
def main():
'''
TDB
'''
myCommandLine = CommandLine()
alignmentFile = myCommandLine.args['sam_file']
isBam = myCommandLine.args['isSam']
sObj = SAM(alignmentFile, isBam)
d = sObj.countJuncs()
for c,j in d.items():
for i in j:
print(c,i[0]-1, i[1], d[c][i], sep="\t")
########################################################################
# Main
# Here is the main program
#
########################################################################
if __name__ == "__main__":
main();