sam提取unmapped seq

最新推荐文章于 2023-03-31 17:24:05 发布

wanguan2000

最新推荐文章于 2023-03-31 17:24:05 发布

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分类专栏： seq

本文链接：https://blog.csdn.net/wanguan2000/article/details/84077471

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__author__ = 'wanguan2000'
#coding=utf-8
import os.path
import os
import sys
import re

filename = '/home/wanguan2000/pg/myNGS/result_NGS/cui3132/s31_1_s31_2.sam'
n = 0
m = 0
mn = 0
mydict ={}

with open(filename,'rU') as f:
    for line in f:
        line = line.rstrip()
        if not line:
            break
        if not line.startswith('@'):

           spline = line.split('\t')
           if 'chr21' == spline[2]:
               mn+=1
               print line


'''
           if not spline[2].startswith('chr'): # or spline[10] == '*':

              # print line
               n +=1
               mydict[spline[2]] = mydict.get(spline[2],0)+1
           elif '*' in spline[10]:
               m +=1
           elif '0' == spline[4]:
'''
               #mydict[spline[2]] = mydict.get(spline[2],0)+1
        #else:
            #print line

print n
print m
print mn
'''
for mykey in mydict:
    print('%s\t%d' % (mykey,mydict[mykey]))


def readSam(filename,filehead='@HWI-ST499'):
    n = 0
    with open(filename,'rU') as f:
        while True:
            line = f.readline
            line = line.rstrip()
            if not line:
                break
            if line.startswith(filehead):
                print line


'''