python 中将fastq文件保存为字典

 

001、保存为字典

(base) root@PC1:/home/test2# ls
a.fastq  test.py
(base) root@PC1:/home/test2# cat a.fastq                        ## 测试fastq文件
@SRR1596091.1 HISEQ:62:C35RDACXX:2:1101:1546:1996/1
GGAAAATAAACATCAGTTTCTTCCAATGAAATGTCTCTCATTCTATCAAC
+
BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIFIIF
@SRR1596091.2 HISEQ:62:C35RDACXX:2:1101:1511:1997/1
CAAGCCACATCTAACAACAATATTAACTATCCAGAAAGGAGCCAGTTATC
+
BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@SRR1596091.3 HISEQ:62:C35RDACXX:2:1101:2357:1925/1
NACGGAGCTGAGCTGGATTTCAGGAGACCTCCTGCCCAGCAGTCAGGAAG
+
#0<FFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
(base) root@PC1:/home/test2# cat test.py                          ## 测试脚本
#!/usr/bin/python
in_file = open("a.fastq", "r")

dict1 = dict()
n  = 0
for i in in_file:
    n += 1
    i = i.strip()
    if n % 4 == 1:
        key = i
        dict1[key] = ""
    if n % 4 == 2:
        dict1[key] += i
print(dict1)

in_file.close()
(base) root@PC1:/home/test2# python test.py                        ## 程序执行结果
{'@SRR1596091.1 HISEQ:62:C35RDACXX:2:1101:1546:1996/1': 'GGAAAATAAACATCAGTTTCTTCCAATGAAATGTCTCTCATTCTATCAAC', '@SRR1596091.2 HISEQ:62:C35RDACXX:2:1101:1511:1997/1': 'CAAGCCACATCTAACAACAATATTAACTATCCAGAAAGGAGCCAGTTATC', '@SRR1596091.3 HISEQ:62:C35RDACXX:2:1101:2357:1925/1': 'NACGGAGCTGAGCTGGATTTCAGGAGACCTCCTGCCCAGCAGTCAGGAAG'}

 

002、保存为文件

(base) root@PC1:/home/test2# ls
a.fastq  test.py
(base) root@PC1:/home/test2# cat a.fastq             ## 测试fastq文件
@SRR1596091.1 HISEQ:62:C35RDACXX:2:1101:1546:1996/1
GGAAAATAAACATCAGTTTCTTCCAATGAAATGTCTCTCATTCTATCAAC
+
BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIFIIF
@SRR1596091.2 HISEQ:62:C35RDACXX:2:1101:1511:1997/1
CAAGCCACATCTAACAACAATATTAACTATCCAGAAAGGAGCCAGTTATC
+
BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@SRR1596091.3 HISEQ:62:C35RDACXX:2:1101:2357:1925/1
NACGGAGCTGAGCTGGATTTCAGGAGACCTCCTGCCCAGCAGTCAGGAAG
+
#0<FFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
(base) root@PC1:/home/test2# cat test.py            ## 测试程序
#!/usr/bin/python
in_file = open("a.fastq", "r")
out_file = open("result.txt", "w")
n = 0

for i in in_file:
    n += 1
    if n % 4 == 1:
        out_file.write(i)
    if n % 4 == 2:
        out_file.write(i)

in_file.close()
out_file.close()
(base) root@PC1:/home/test2# python test.py          ## 执行程序
(base) root@PC1:/home/test2# ls
a.fastq  result.txt  test.py
(base) root@PC1:/home/test2# cat result.txt          ## 程序运行结果
@SRR1596091.1 HISEQ:62:C35RDACXX:2:1101:1546:1996/1
GGAAAATAAACATCAGTTTCTTCCAATGAAATGTCTCTCATTCTATCAAC
@SRR1596091.2 HISEQ:62:C35RDACXX:2:1101:1511:1997/1
CAAGCCACATCTAACAACAATATTAACTATCCAGAAAGGAGCCAGTTATC
@SRR1596091.3 HISEQ:62:C35RDACXX:2:1101:2357:1925/1
NACGGAGCTGAGCTGGATTTCAGGAGACCTCCTGCCCAGCAGTCAGGAAG

 

参考：https://mp.weixin.qq.com/s?__biz=MzkyMTI1MTYxNA==&mid=2247493739&idx=1&sn=f690c93761307e6ec9bb77cca2eb4619&chksm=c184d21af6f35b0cda1d964ed896adee1091e1f615b7f6be0caf2508105275ca3ae66889c58e&mpshare=1&scene=23&srcid=0811LY0ghlyV0yNXki8WcW6m&sharer_sharetime=1660215059305&sharer_shareid=50b75c6a886e09824b582fb782a7678b#rd