Removal of connectors in sequencing reads: adaptor

Prior to write a program in C, find whether the reads contains adaptor, if detected to filter out the reads containing adaptor, this time after filtering data found that the connector sequence is more, in order to improve the assembly effect, can not greatly affect the amount of data, Need to truncate the connector, and filter the short reads, with Python wrote a short program, specify more than 3 mismatch within the match is considered to match, and the length of less than 50bp reads filter, in the following program based on the addition of incoming parameters, can be applied to more cases (single-ended, Double-ended, containing single, etc.):

1 ImportSYS2 ImportRe3  fromBioImportSeqio4 5 defRmpe (read1,read2,adaptor1,adaptor2,min_length):6Res_1 =RmSE (read1,adaptor1,min_length)7Res_2 =RmSE (read2,adaptor2,min_length)8     ifRes_1 andres_2:9         returnres_1,res_2Ten     Else: One         returnFalse A  - defRmSE (read,adaptor,min_length): -Seq =Read.seq theSeed_len = 6 -A_len =len (adaptor) -Seq_len =len (seq) -      forIinchRange (A_len-Seed_len): +Seed = adaptor[i:i+Seed_len] -pos =0 +          while(Pos <Seq_len): AFind_pos =Seq.find (Seed,pos) at             ifFind_pos >0: -Mistaken_count =0 -_b =Find_pos -_e = Find_pos +Seed_len -                  while(_b >= 0 andI >= Find_pos-_b): -                     ifAdaptor[i-find_pos + _b]! =Seq[_b]: inMistaken_count + = 1 -                     ifMistaken_count > 3: to                          Break +_b-= 1 -                 Else : the                      while(_e < Seq_len andI-find_pos + _e <A_len): *                         ifadaptor[I-find_pos + _e]! =Seq[_e]: $Mistaken_count + = 1Panax Notoginseng                         ifMistaken_count > 3: -                              Break the_e + = 1 +                     Else: A                         ifFind_pos-i >min_length: the                             returnread[:find_pos-i] +                         Else : -                             returnFalse $pos = Find_pos + 1 $             Else: -                  Break -     returnRead the  - defRmadaptor (argv):Wuyi argv.pop (0) theRead1_file,read2_file,reads_file,adaptor1,adaptor2,out_prefix,min_length =argv -Reads_records = Seqio.parse (open (Reads_file),'FASTQ') WuRead2_records = Seqio.parse (open (Read2_file),'FASTQ') -Read1_out = open ('%S.1.FQ'%out_prefix,'W' ) AboutRead2_out = open ('%S.2.FQ'%out_prefix,'W' ) $Reads_out = open ('%S.SINGLE.FQ'%out_prefix,'W' ) -      forRead1inchSeqio.parse (Open (Read1_file),'FASTQ'): -Read2 =Read2_records.next () -Reads =Reads_records.next () ARmpe_res =Rmpe (read1,read2,adaptor1,adaptor2,min_length) +         ifRmpe_res: theRead1_out.write (Rmpe_res[0].format ('FASTQ')) -Read2_out.write (Rmpe_res[1].format ('FASTQ')) $Rmse_res =False the         ifRe.search ('[\s\/] (\d)', reads.id) = ='1': theRmse_res =RmSE (reads,adaptor1,min_length) the         elifRe.search ('[\s\/] (\d)', reads.id) = ='2': theRmse_res =RmSE (reads,adaptor2,min_length) -         ifRmse_res: inReads_out.write (Rmse_res.format ('FASTQ')) the  the if __name__=='__main__': AboutRmadaptor (SYS.ARGV)

Removal of connectors in sequencing reads: adaptor