Python初体验

今天开始所有的工作脚本全都从perl转变到python，开发速度明显降低了不少，相信以后随着熟练度提升会好起来。贴一下今天一个工作代码，由于之前去一家小公司测序时，序列长度竟然都没有达到要求，为了之后的索赔事宜，写了个脚本统计所有序列的结果，主要包括总的reads数，bases数，和达到测序策略要求长度的reads数（双端），bases数，高质量（Q30）bases数，高质量reads数（双端）等等......多个文件的统计工作一般会写一个单独处理一个文件的脚本，然后再写一个脚本用来生成多个文件的处理的shell脚本，然后想办法并行处理这个shell就可以，效率会快很多。由于测序数据往往比较大，IO操作时，逐行读取是上策。

统计单个文件测序数据情况脚本：

 1 from __future__ import division

 2 from Bio import SeqIO as fq

 3 import os

 4 import sys

 5 import re

 6 read1_gzfile = sys.argv[1]

 7 read2_gzfile = sys.argv[2]

 8 gz_handle1 = os.popen( 'gunzip -cd %s' % read1_gzfile )

 9 gz_handle2 = os.popen( 'gunzip -cd %s' % read2_gzfile )

10 basename1 = os.path.basename(read1_gzfile)

11 basename1 = re.match('(\S+)_R1_001\.fastq\.gz',basename1).group(1)

12 basename2 = os.path.basename(read2_gzfile)

13 basename2 = re.match('(\S+)_R2_001\.fastq\.gz',basename2).group(1)

14 if basename1 != basename2:

15     raise 'Two Read are not mapped!'

16 cwd = os.getcwd()

17 out_handle = open('%s/%s.stat'%(cwd,basename1),'w')

18 out_handle.write('AllReadsNum\tRead1_PE300_ReadsNum\tRead2_PE300_ReadsNum\tUseful_ReadsNum(Read1>=300 and Read2>=300)\tAll_Bases\tRead1_Q30_Bases(PE300)\tRead2_Q30_Bases(PE300)\tQ30_PE_Reads(Q30>50%)\tUseful_Bases(All)\tUseful_Ratio\n')

19 

20 AllReadsNum = 0

21 AllBases = 0

22 Read1_PE300_ReadsNum = 0

23 Read2_PE300_ReadsNum = 0

24 Useful_ReadsNum = 0

25 Read1_Q30_Bases = 0

26 Read2_Q30_Bases = 0

27 Q30_PE_Reads = 0

28 Useful_Bases = 0

29 

30 def PE300(seq):

31     if len(seq) >= 300:

32         return True

33     else:

34         return False

35 

36 def Q30(qual_list):

37     num = 0

38     for qual in qual_list:

39         if qual >= 30:

40             num += 1

41     return num

42 

43 reads2 = fq.parse(gz_handle2,'fastq')

44 for read1 in fq.parse(gz_handle1,'fastq'):

45     read2 = reads2.next()

46     seq1 = read1.seq

47     qual1 = read1.letter_annotations['phred_quality']

48     seq2 = read2.seq

49     qual2 = read2.letter_annotations['phred_quality']

50     AllReadsNum += 1

51     AllBases += len(seq1)

52     AllBases += len(seq2)

53     R1_300 = PE300(seq1)

54     R2_300 = PE300(seq2)

55     if R1_300 and R2_300:

56         Useful_ReadsNum +=1

57         R1_Q30 = Q30(qual1)

58         R2_Q30 = Q30(qual2)

59         Read1_Q30_Bases += R1_Q30

60         Read2_Q30_Bases += R2_Q30

61         if ( R1_Q30 / len(seq1) >= 0.5 ) and ( R2_Q30 / len(seq2) >= 0.5 ):

62             Q30_PE_Reads += 1

63             Useful_Bases += R1_Q30

64             Useful_Bases += R2_Q30

65     elif R1_300:

66         Read1_PE300_ReadsNum += 1

67     elif R2_300:

68         Read2_PE300_ReadsNum += 1

69 

70 Useful_Ratio = Useful_Bases / AllBases

71 out_handle.write('%i\t%i\t%i\t%i\t%i\t%i\t%i\t%i\t%i\t%f\n'%(AllReadsNum,Read1_PE300_ReadsNum,Read2_PE300_ReadsNum,Useful_ReadsNum,AllBases,Read1_Q30_Bases,Read2_Q30_Bases,Q30_PE_Reads,Useful_Bases,Useful_Ratio))

summary.py

 生成脚本：

1 import os

2 out = open('summary.sh','w')

3 cwd = os.getcwd()

4 with open('templist') as gzfiles:

5     for gzfile1 in gzfiles:

6         gzfile2 = gzfiles.next()

7         out.write('python %s/summary.py %s %s\n'%(cwd,gzfile1.strip(),gzfile2.strip()))

run_summary.py

使用qsub_sge方法，并行投递生成的summary.sh就完成了