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bam_cov.py
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#!/usr/bin/env python
import os, sys, argparse
import pysam
from collections import defaultdict
parser = argparse.ArgumentParser(description="Coverage")
parser.add_argument("f1", help="Input BAM file")
parser.add_argument("--start", default=332500, type=int, help="Start")
parser.add_argument("--end", default=348000, type=int, help="End")
parser.add_argument("--print_cov", default=False, action="store_true", help="End")
parser.add_argument("--print_regions", default=False, action="store_true", help="End")
parser.add_argument("--print_genes", default=False, action="store_true", help="End")
parser.add_argument("--print_reads", default=False, action="store_true", help="End")
parser.add_argument("--forward", default=False, action="store_true", help="End")
parser.add_argument("--f2r1", default=False, action="store_true", help="End")
args = parser.parse_args()
bamf = pysam.AlignmentFile(args.f1, "rb")
#CVER
#seq = "NODE_5_length_936291_cov_13.3144_ID_5280"
#regions = []
#genes = [["entB",345938,346780,0]]
#CVER
#~ seq = "NODE_5_length_936291_cov_13.3144_ID_5280"
#~ regions = [["entH_entA",336789,336815,0,0],["entA_entE",337573,337693,0,0],["entE_entC",339306,339502,0,0],["entC_entF",340689,340877,0,0],["entF_entD",344800,344983,0,0],["entD_entB",345702,345938,0,0]]
#~ genes = [["entH",336382,336789,0],["entA",336815,337573,0],["entE",337693,339306,0],["entC",339502,340689,0],["entF",340877,344800,0],["entD",344983,345702,0],["entB",345938,346780,0]]
#SBOM
#~ seq = "NODE_25_length_94690_cov_24.2565_ID_3467"
#~ regions = [["entB_TM",33138,34080,0,0],["TM_Fre",35543,35607,0,0],["Fre_entA",37559,37823,0,0],["entA_entE",38575,38812,0,0],["entE_entC",40401,40877,0,0],["entC_entF",42022,42979,0,0],["entF_entD",46899,47350,0,0]]
#~ regions = [["entB_Fre",33138,35607,0,0],["Fre_entA",37559,37823,0,0],["entA_entE",38575,38812,0,0],["entE_entC",40401,40877,0,0],["entC_entF",42022,42979,0,0],["entF_entD",46899,47350,0,0]]
#~ genes = [["entB",32302,33138,0],["TM",34080,35543,0],["Fre",35607,37559,0],["entA",37823,38575,0],["entE",38812,40401,0],["entC",40877,42022,0],["entF",42979,46899,0],["entD",47350,48084,0]]
#CAPI
#~ seq = "LBNK01000008.1"
#~ regions = [["entD_entF",512488,512836,0,0],["entF_entC",516879,519352,0,0],["entC_entE",520467,521051,0,0]]
#~ regions = [["entD_entF",512488,512836,0,0],["entF_SNZ",516879,517227,0,0],["SNZ_SNO",518081,518177,0,0],["SNO_entC",518806,519352,0,0],["entC_entE",520467,521051,0,0]]
#~ genes = [["entD",511757,512488,0],["entF",512836,516879,0],["SNZ",517227,518081,0],["SNO",518177,518806,0],["entC",519352,520467,0],["entE",521051,522658,0]]
#~ seq = "LBNK01000003.1"
#~ regions = [["entA_Fre",943019,943463,0,0],["Fre_TM",945457,945509,0,0],["TM_entB",947014,947614,0,0]]
#~ genes = [["entA",942270,943019,0],["Fre",943463,945457,0],["TM",945509,947014,0],["entB",947614,948474,0]]
#COLI
seq = "NC_000913.3"
#regions = [["entD_fepA",610079,610257,0,0],["fepA_fes",612494,612737,0,0],["fes_entF",613936,614157,0,0],["entF_fepE",618035,618254,0,0],["fepE_fepC",619384,619387,0,0],["fepC_fepG",620199,620199,0,0],["fepG_fepD",621188,621188,0,0],["fepD_entS",622189,622300,0,0],["entS_fepB",623547,623557,0,0],["fepB_entC",624510,624885,0,0],["entC_entE",626057,626070,0,0],["entE_entB",627677,627694,0,0],["entB_entA",628548,628551,0,0],["entA_entH",629294,629300,0,0]]
regions = [["entD_fepA",610079,610257,0,0],["fepA_fes",612494,612737,0,0],["fes_ybdZ",613936,613942,0,0],["ybdZ_entF",614157,614157,0,0],["entF_fepE",618035,618254,0,0],["fepE_fepC",619384,619387,0,0],["fepC_fepG",620199,620199,0,0],["fepG_fepD",621188,621188,0,0],["fepD_entS",622189,622300,0,0],["entS_fepB",623547,623557,0,0],["fepB_entC",624510,624885,0,0],["entC_entE",626057,626070,0,0],["entE_entB",627677,627694,0,0],["entB_entA",628548,628551,0,0],["entA_entH",629294,629300,0,0]]
genes = [["entD",609462,610079,0],["fepA",610257,612494,0],["fes",612737,613936,0],["ybdZ",613942,614157,0],["entF",614157,618035,0],["fepE",618254,619384,0],["fepC",619387,620199,0],["fepG",620199,621188,0],["fepD",621188,622189,0],["entS",622300,623547,0],["fepB",623557,624510,0],["entC",624885,626057,0],["entE",626070,627677,0],["entB",627694,628548,0],["entA",628551,629294,0],["entH",629300,629710,0],["fur",710203,710646,0]]
fr_flag = 64
rw_flag = 128
if args.f2r1 == True:
fr_flag = 128
rw_flag = 64
reads = bamf.fetch(seq, args.start, args.end)
read_cov = defaultdict(int)
span_cov = defaultdict(int)
read_names = defaultdict(list)
read_names2 = defaultdict(list)
passed_reads = defaultdict(int)
insert_limit = 1000
i = 1
for read in reads:
read_data = str(read).split()
name = read_data[0]
flags = int(read_data[1])
pos1 = int(read_data[3])
pos2 = int(read_data[7])
len1 = int(read_data[8])
if pos2-pos1 > insert_limit:
continue
#f1r2
if args.forward == False:
#if (flags & 64) != 0 and name not in passed_reads:
if (flags & fr_flag) != 0 and name not in passed_reads:
for p in range(pos1,pos1+len1):
read_cov[p] += 1
for p in range(pos1+len1,pos2):
span_cov[p] += 1
for r in regions:
if pos1 < r[1] and pos2 > r[2]:
r[3] += 1
read_names[r[0]].append(name)
#read_names[r[0]].append(read)
if (pos1 < r[1] and pos2 > r[1]) or (pos1 < r[2] and pos2 > r[2]):
r[4] += 1
for g in genes:
if pos1+len1 > g[1] and pos2 < g[2]:
g[3] += 1
#read_names2[g[0]].append(name)
#elif (flags & 128) != 0 and name in passed_reads:
elif (flags & rw_flag) != 0 and name in passed_reads:
for p in range(pos1,pos1+len1):
read_cov[p] += 1
#if pos1 < r[2] and pos2 > r[1]:
# r[4] += 1
for r in regions:
if name not in read_names[r[0]]:
if passed_reads[name] < r[1] and pos1+len1 > r[2]:
r[3] += 1
read_names[r[0]].append(name)
#read_names[r[0]].append(read)
#for g in genes:
# if name not in read_names2[g[0]]:
# if passed_reads[name] < g[1] and pos1+len1 > g[2]:
# r[3] += 1
# read_names[r[0]].append(name)
# #read_names[r[0]].append(read)
elif args.forward == True:
#if (flags & 128) != 0 and name not in passed_reads:
if (flags & rw_flag) != 0 and name not in passed_reads:
for p in range(pos1,pos1+len1):
read_cov[p] += 1
for p in range(pos1+len1,pos2):
span_cov[p] += 1
for r in regions:
if pos1 < r[1] and pos2 > r[2]:
r[3] += 1
read_names[r[0]].append(name)
#read_names[r[0]].append(read)
if (pos1 < r[1] and pos2 > r[1]) or (pos1 < r[2] and pos2 > r[2]):
r[4] += 1
for g in genes:
if pos1+len1 > g[1] and pos2 < g[2]:
g[3] += 1
#read_names2[g[0]].append(name)
#elif (flags & 64) != 0 and name in passed_reads:
elif (flags & fr_flag) != 0 and name in passed_reads:
for p in range(pos1,pos1+len1):
read_cov[p] += 1
#if pos1 < r[2] and pos2 > r[1]:
# r[4] += 1
for r in regions:
if name not in read_names[r[0]]:
if passed_reads[name] < r[1] and pos1+len1 > r[2]:
r[3] += 1
read_names[r[0]].append(name)
#read_names[r[0]].append(read)
#for g in genes:
# if name not in read_names2[g[0]]:
# if passed_reads[name] < g[1] and pos1+len1 > g[2]:
# r[3] += 1
# read_names[r[0]].append(name)
# #read_names[r[0]].append(read)
passed_reads[name] = pos1
if args.print_regions == True:
print "REGIONS COV"
for r in regions:
print r[0],r[3],r[4]
print
if args.print_genes == True:
print "GENES COV"
for g in genes:
print g[0],g[1],g[2],g[2]-g[1],g[3]
print
if args.print_reads == True:
print "REGIONS READS"
for r in regions:
print "\n"+r[0]
for read in read_names[r[0]]:
print read
print
if args.print_cov == True:
print "POS READ SPAN SUM PROP"
for pos in range(min(min(read_cov.keys(),span_cov.keys())),max(max(read_cov.keys(),span_cov.keys()))):
prop = ""
if read_cov[pos] > 0 or span_cov[pos] > 0:
prop = "{0:.2f}".format(float(read_cov[pos])/(float(read_cov[pos])+float(span_cov[pos])))
print pos,read_cov[pos],span_cov[pos],read_cov[pos]+span_cov[pos],prop