错误地删除了过度代表的序列。TypeError: coercing to Unicode: need string or buffer, NoneType found.

Question

嗨，我正在运行这个python脚本，以删除我的fastq文件中的过度代表序列，但我一直得到的错误。我是生物信息组学的新手，一直按照一套固定的流水线进行序列组装。我想用这个脚本来删除过度代表性的序列。

python homeTranscriptomeAssemblyToolsRemoveFastqcOverrepSequenceReads.py -1 R1_1.fq -2 R1_2.fq**这里是错误的Traceback（最近一次调用最后一次）。

File "TranscriptomeAssemblyToolsRemoveFastqcOverrepSequenceReads.py", line 46, inleftseqs=ParseFastqcLog(opts.l_fastqc)File "TranscriptomeAssemblyToolsRemoveFastqcOverrepSequenceReads. py"，第33行，在ParseFastqcLogwith open(fastqclog) as fp:TypeError: coercing to Unicode: need string or buffer, NoneType found**。

• 以下是脚本 :

                import sys
                import gzip
                from os.path import basename
                import argparse
                import re
                from itertools import izip,izip_longest

                def seqsmatch(overreplist,read):
                    flag=False
                    if overreplist!=[]:
                        for seq in overreplist:
                            if seq in read:
                                flag=True
                                break
                    return flag

                def get_input_streams(r1file,r2file):
                    if  r1file[-2:]=='gz':
                        r1handle=gzip.open(r1file,'rb')
                        r2handle=gzip.open(r2file,'rb')
                    else:
                        r1handle=open(r1file,'r')
                        r2handle=open(r2file,'r')

                    return r1handle,r2handle

                def FastqIterate(iterable,fillvalue=None):
                    "Grab one 4-line fastq read at a time"
                    args = [iter(iterable)] * 4
                    return izip_longest(fillvalue=fillvalue, *args) 

                def ParseFastqcLog(fastqclog):    
                    with open(fastqclog) as fp:
                        for result in re.findall('Overrepresented sequences(.*?)END_MODULE', fp.read(), re.S):
                            seqs=([i.split('\t')[0] for i in result.split('\n')[2:-1]])
                    return seqs     

                if __name__=="__main__": 
                    parser = argparse.ArgumentParser(description="options for removing reads with over-represented sequences")
                    parser.add_argument('-1','--left_reads',dest='leftreads',type=str,help='R1 fastq file')
                    parser.add_argument('-2','--right_reads',dest='rightreads',type=str,help='R2 fastq file')
                    parser.add_argument('-fql','--fastqc_left',dest='l_fastqc',type=str,help='fastqc text file for R1')
                    parser.add_argument('-fqr','--fastqc_right',dest='r_fastqc',type=str,help='fastqc text file for R2')
                    opts = parser.parse_args()

                    leftseqs=ParseFastqcLog(opts.l_fastqc)
                    rightseqs=ParseFastqcLog(opts.r_fastqc)

                    r1_out=open('rmoverrep_'+basename(opts.leftreads).replace('.gz',''),'w')
                    r2_out=open('rmoverrep_'+basename(opts.rightreads).replace('.gz',''),'w')

                    r1_stream,r2_stream=get_input_streams(opts.leftreads,opts.rightreads)

                    counter=0
                    failcounter=0

                    with r1_stream as f1, r2_stream as f2:
                        R1=FastqIterate(f1)
                        R2=FastqIterate(f2)
                        for entry in R1:
                            counter+=1
                            if counter%100000==0:
                                print "%s reads processed" % counter

                            head1,seq1,placeholder1,qual1=[i.strip() for i in entry]
                            head2,seq2,placeholder2,qual2=[j.strip() for j in R2.next()]

                            flagleft,flagright=seqsmatch(leftseqs,seq1),seqsmatch(rightseqs,seq2)

                            if True not in (flagleft,flagright):
                                r1_out.write('%s\n' % '\n'.join([head1,seq1,'+',qual1]))
                                r2_out.write('%s\n' % '\n'.join([head2,seq2,'+',qual2]))
                            else:
                                failcounter+=1


                        print 'total # of reads evaluated = %s' % counter
                        print 'number of reads retained = %s' % (counter-failcounter)
                        print 'number of PE reads filtered = %s' % failcounter


                r1_out.close()
                r2_out.close()

Answer 1

也许你已经解决了，我有同样的错误，但现在运行良好。希望这个帮助

(1)我们需要的文件:用法.删除FastqcOverrepSequenceReads.py RemoveFastqcOverrepSequenceReads.py [-h] [-1 LEFTREADS] [-2 RIGHTREADS] [-fql L_FASTQC] [-fqr R_FASTQC

(2)指定fastqc输出中的fastqc_data.text文件，解压到输出目录下

'-fql','-fastqc_left',dest='l_fastqc',type=str,help='fastqc text file for R1'。

'-fqr','-fastqc_right',dest='r_fastqc',type=str,help='fastqc文本文件R2'。

(3)将读取的数据和fastqc_data文本保存在同一个目录下。

(4) 在每个文件前指定路径位置 python RemoveFastqcOverrepSequenceReads.py -1 .bicho.fq.1.gz -2.bicho.fq.2.gz -fql .fastqc_data_bicho_1.txt -fqr .fastqc_data_bicho_2.txt.

(5)跑! :)