python向服务器上传fq文件,利用biopython给fastq文件添加标签基因并合并fastq文件

#!/usr/bin/python

# -*- coding: utf-8 -*-

# @Date : 2017-03-06 22:46:45

# @Author : XYZ (superxyz@vip.qq.com)

# @Link : www.bubblefertilizer.com

# @Version : 1.0

from Bio import SeqIO

from Bio.Seq import Seq

from Bio.Alphabet import generic_dna

from Bio.SeqRecord import SeqRecord

def add_barcode(path,barcode_seq): #定义一个加标签基因的函数

reads=SeqIO.parse(path,'fastq')

barcode=Seq(barcode_seq,generic_dna)

records_with_barcode=[]

for record in reads: #fastq用的文件格式

seq_with_barcode=barcode+record.seq #序列

record_with_barcode=SeqRecord(seq_with_barcode,id=record.id,description=record.description) #id，注释

record_with_barcode.letter_annotations['phred_quality']=[39,39,39,39,39,39]+record.letter_annotations["phred_quality"] #碱基质量

records_with_barcode.append(record_with_barcode)

return records_with_barcode

file_and_barcode=[] #填写要合并并添加标签的fastq文件路径，以及标签序列

file_and_barcode.append(('D:/Shared_Folder/P101SC16122213-01-B1-3/result/00.RawData/CK1/CK1.extendedFrags.fastq','ACTTGA'))

file_and_barcode.append(('D:/Shared_Folder/P101SC16122213-01-B1-3/result/00.RawData/CK2/CK2.extendedFrags.fastq','GGCTAC'))

file_and_barcode.append(('D:/Shared_Folder/P101SC16122213-01-B1-3/result/00.RawData/CK3/CK3.extendedFrags.fastq','GATCAG'))

file_and_barcode.append(('D:/Shared_Folder/P101SC16122213-01-B1-3/result/00.RawData/OM1/OM1.extendedFrags.fastq','CAGATC'))

file_and_barcode.append(('D:/Shared_Folder/P101SC16122213-01-B1-3/result/00.RawData/OM2/OM2.extendedFrags.fastq','GCCAAT'))

file_and_barcode.append(('D:/Shared_Folder/P101SC16122213-01-B1-3/result/00.RawData/OM3/OM3.extendedFrags.fastq','TAGCTT'))

allrecords=[] #合并文件

for content in file_and_barcode:

print('file_path:',content[0],'barcode_sequnce:',content[1])

allrecords=allrecords+(add_barcode(content[0],content[1])) #这里不能用append

count=SeqIO.write(allrecords,"allrecords_with_barcode.fastq","fastq")

print("Saved %i reads" % count)

#参考网址：http://biopython.org/DIST/docs/api/Bio.SeqIO-module.html