seqsero2: libs/BWA_analysis_O_new

annotate libs/BWA_analysis_O_new_dependent.py @ 3:38ad1130d077 draft

planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty

author	charles_s_test
date	Mon, 27 Nov 2017 11:21:07 -0500
parents	0d65b71ff8df
children	3d6680af0bec

rev	line source
0 6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	1 #!/usr/bin/env python
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	2 #tyr_of_O2_O9.fasta should be in the same directory, in it, O9 should be first then O2
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	3
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	4 import os
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	5 from Bio import SeqIO
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	6 import sys
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	7 from Initial_functions import Uniq
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	8 from Bio.Blast import NCBIXML
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	9
2 0d65b71ff8df planemo upload commit 464b391afaa5819bc681452e85bea9d882730eb6 charles_s_test parents: 0 diff changeset	10 BwaPath="bwa"
0d65b71ff8df planemo upload commit 464b391afaa5819bc681452e85bea9d882730eb6 charles_s_test parents: 0 diff changeset	11 SamTlsPth="samtools"
3 38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: 2 diff changeset	12 Makebltdb="makeblastdb"
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty charles_s_test parents: 2 diff changeset	13 Blastnpth="blastn"
0 6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	14
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	15 def BWA_O_analysis(sra_name,additional_file,database,mapping_mode,file_mode):
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	16 if file_mode=="1":#interleaved
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	17 if sra_name[-3:]=="sra":
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	18 os.system("fastq-dump --split-files "+sra_name)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	19 del_fastq=1
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	20 for_fq=sra_name.replace(".sra","_1.fastq")
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	21 rev_fq=sra_name.replace(".sra","_2.fastq")
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	22 for_sai=sra_name.replace(".sra","_1.sai")
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	23 rev_sai=sra_name.replace(".sra","_2.sai")
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	24 sam=sra_name.replace(".sra",".sam")
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	25 bam=sra_name.replace(".sra",".bam")
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	26 else:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	27 del_fastq=0
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	28 core_id=sra_name.split(".fastq")[0]
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	29 try:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	30 os.system("gunzip "+sra_name)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	31 except:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	32 pass
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	33 dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	34 os.system("perl "+dirpath+"/split_interleaved_fastq.pl --input "+core_id+".fastq --output "+core_id.replace(".","_")+".fastq")#######03152016
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	35 ori_size=os.path.getsize(core_id+".fastq")#######03152016
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	36 os.system("mv "+core_id.replace(".","_")+"-read1.fastq"+" "+core_id+"-read1.fastq")#######03152016
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	37 os.system("mv "+core_id.replace(".","_")+"-read2.fastq"+" "+core_id+"-read2.fastq")#######03152016
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	38 for_fq=core_id+"-read1.fastq"#######03152016
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	39 rev_fq=core_id+"-read2.fastq"#######03152016
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	40 if float(os.path.getsize(for_fq))/ori_size<=0.1 or float(os.path.getsize(rev_fq))/ori_size<=0.1:#09092015#12292015#######03152016
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	41 os.system("echo haha")#09092015
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	42 os.system("perl "+dirpath+"/splitPairedEndReads.pl "+core_id+".fastq")#09092015
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	43 os.system("mv "+core_id+".fastq_1 "+for_fq)##09092015
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	44 os.system("mv "+core_id+".fastq_2 "+rev_fq)##09092015
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	45 else:#09092015
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	46 os.system("echo hehe")#09092015
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	47 for_sai=core_id+"_1.sai"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	48 rev_sai=core_id+"_2.sai"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	49 sam=core_id+".sam"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	50 bam=core_id+".bam"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	51 elif file_mode=="2":#seperated
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	52 forword_seq=sra_name
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	53 reverse_seq=additional_file
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	54 try:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	55 os.system("gunzip "+forword_seq)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	56 except:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	57 pass
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	58 try:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	59 os.system("gunzip "+reverse_seq)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	60 except:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	61 pass
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	62 for_core_id=forword_seq.split(".fastq")[0]
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	63 re_core_id=reverse_seq.split(".fastq")[0]
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	64 for_fq=for_core_id+".fastq"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	65 rev_fq=re_core_id+".fastq"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	66 dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))#######03152016
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	67 print "check fastq id and make them in accordance with each other...please wait..."
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	68 os.system("python "+dirpath+"/compare_and_change_two_fastq_id.py "+for_fq+" "+rev_fq)#######03152016
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	69 for_sai=for_core_id+".sai"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	70 rev_sai=re_core_id+".sai"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	71 sam=for_core_id+".sam"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	72 bam=sam.replace(".sam",".bam")
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	73 elif file_mode=="3":#single-end
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	74 if sra_name[-3:]=="sra":
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	75 os.system("fastq-dump --split-files "+sra_name)###01/28/2015
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	76 del_fastq=1
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	77 for_fq=sra_name.replace(".sra","_1.fastq")
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	78 for_sai=sra_name.replace(".sra","_1.sai")
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	79 sam=sra_name.replace(".sra",".sam")
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	80 bam=sra_name.replace(".sra",".bam")
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	81 else:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	82 del_fastq=0
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	83 core_id=sra_name.split(".fastq")[0]
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	84 try:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	85 os.system("gunzip "+sra_name)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	86 except:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	87 pass
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	88 for_fq=core_id+".fastq"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	89 for_sai=core_id+"_1.sai"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	90 sam=core_id+".sam"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	91 bam=core_id+".bam"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	92
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	93 os.system(BwaPath+" index "+database)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	94 if file_mode!="3":
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	95 if mapping_mode=="sam":
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	96 os.system(BwaPath+" aln "+database+" "+for_fq+" > "+for_sai)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	97 os.system(BwaPath+" aln "+database+" "+rev_fq+" > "+rev_sai)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	98 os.system(BwaPath+" sampe "+database+" "+for_sai+" "+ rev_sai+" "+for_fq+" "+rev_fq+" > "+sam)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	99 elif mapping_mode=="mem":
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	100 os.system(BwaPath+" mem "+database+" "+for_fq+" "+rev_fq+" > "+sam) #2014/12/23
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	101 else:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	102 if mapping_mode=="mem":
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	103 os.system(BwaPath+" mem "+database+" "+for_fq+" > "+sam) #2014/12/23
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	104 elif mapping_mode=="sam":
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	105 os.system(BwaPath+" aln "+database+" "+for_fq+" > "+for_sai)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	106 os.system(BwaPath+" samse "+database+" "+for_sai+" "+for_fq+" > "+sam)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	107 os.system(SamTlsPth+" view -F 4 -Sbh "+sam+" > "+bam)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	108 os.system(SamTlsPth+" view -h -o "+sam+" "+bam)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	109
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	110 file=open(sam,"r")
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	111 handle=file.readlines()
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	112 name_list=[]
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	113 for line in handle:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	114 if len(line)>300:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	115 name_list.append(line.split("\t")[2])
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	116 a,b=Uniq(name_list)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	117 c=dict(zip(a,b))
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	118 final_O=sorted(c.iteritems(), key=lambda d:d[1], reverse = True) #order from frequency high to low, but tuple while not list
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	119 Sero_list_O=[]
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	120 print "Final_Otype_list:"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	121 print final_O
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	122 num_1=0#new inserted
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	123 O9_wbav=0
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	124 O310_wzx=0
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	125 O946_wzy=0
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	126 if len(final_O)>0: #new inserted
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	127 for x in final_O:#new inserted
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	128 num_1=num_1+x[1]#new inserted
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	129 if "O-9,46_wbaV" in x[0]:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	130 O9_wbaV=x[1]
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	131 if "O-3,10_wzx" in x[0]:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	132 O310_wzx=x[1]
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	133 if "O-9,46_wzy" in x[0]:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	134 O946_wzy=x[1]
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	135 if "O-3,10_not_in_1,3,19" in x[0]:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	136 O310_no_1319=x[1]
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	137 if "O-9,46,27_partial_wzy" in x[0]:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	138 O94627=x[1]
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	139 O_list=[]
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	140 O_choice=""
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	141
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	142
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	143 print "$$$Genome:",sra_name
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	144 if len(final_O)==0:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	145 print "$$$No Otype, due to no hit"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	146 else:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	147 if final_O[0][1]<8:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	148 print "$$$No Otype, due to the hit reads number is small."
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	149 else:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	150 for x in final_O:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	151 if x[1]>5:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	152 O_list.append(x[0])
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	153 qq=1#
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	154 for x in final_O:#
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	155 if "sdf" in x[0] and x[1]>3:#
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	156 qq=0#
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	157 print "$$$",x[0],"got a hit, reads:",x[1]#
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	158 if qq!=0:#
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	159 print "$$$No sdf exists"#
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	160
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	161 if "O-9,46_wbaV" in O_list and float(O9_wbaV)/float(num_1) > 0.1:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	162 if "O-9,46_wzy" in O_list and float(O946_wzy)/float(num_1) > 0.1:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	163 O_choice="O-9,46"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	164 print "$$$Most possilble Otype: O-9,46"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	165 elif "O-9,46,27_partial_wzy" in O_list and float(O94627)/float(num_1) > 0.1:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	166 O_choice="O-9,46,27"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	167 print "$$$Most possilble Otype: O-9,46,27"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	168 else:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	169 O_choice="O-9"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	170 if file_mode=="3":
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	171 rev_fq=""
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	172 rev_sai=""
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	173 assembly(sra_name,O_choice,for_fq,rev_fq,for_sai,rev_sai,sam,bam,mapping_mode)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	174 else:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	175 assembly(sra_name,O_choice,for_fq,rev_fq,for_sai,rev_sai,sam,bam,mapping_mode)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	176 elif ("O-3,10_wzx" in O_list) and ("O-9,46_wzy" in O_list) and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	177 if "O-3,10_not_in_1,3,19" in O_list and float(O310_no_1319)/float(num_1) > 0.1:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	178 O_choice="O-3,10"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	179 print "$$$Most possilble Otype: O-3,10"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	180 else:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	181 O_choice="O-1,3,19"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	182 print "$$$Most possilble Otype: O-1,3,19"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	183 else:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	184 try:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	185 O_choice=final_O[0][0].split("_")[0]
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	186 if O_choice=="O-1,3,19":
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	187 O_choice=final_O[1][0].split("_")[0]
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	188 print "$$$Most possilble Otype: ",O_choice
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	189 except:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	190 print "$$$No suitable Otype, or failure of mapping (please check the quality of raw reads)"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	191
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	192
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	193 def assembly(sra_name,potential_choice,for_fq,rev_fq,for_sai,rev_sai,sam,bam,mapping_mode):
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	194 database="ParaA_rfb.fasta"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	195 os.system(BwaPath+" index database/"+database)###01/28/2015
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	196 if rev_fq=="":#2015/09/09
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	197 if mapping_mode=="mem":
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	198 os.system(BwaPath+" mem database/"+database+" "+for_fq+" > "+sam) #2014/12/23
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	199 elif mapping_mode=="sam":
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	200 os.system(BwaPath+" aln database/"+database+" "+for_fq+" > "+for_sai)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	201 os.system(BwaPath+" samse database/"+database+" "+for_sai+" "+for_fq+" > "+sam)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	202 else:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	203 if mapping_mode=="mem":
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	204 os.system(BwaPath+" mem database/"+database+" "+for_fq+" "+rev_fq+" > "+sam) #2014/12/23
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	205 elif mapping_mode=="sam":
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	206 os.system(BwaPath+" aln database/"+database+" "+for_fq+" > "+for_sai)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	207 os.system(BwaPath+" aln database/"+database+" "+rev_fq+" > "+rev_sai)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	208 os.system(BwaPath+" sampe database/"+database+" "+for_sai+" "+ rev_sai+" "+for_fq+" "+rev_fq+" > "+sam)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	209 os.system(SamTlsPth+" view -F 4 -Sbh "+sam+" > "+bam)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	210 os.system(SamTlsPth+" view -h -o "+sam+" "+bam)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	211 os.system("cat "+sam+"\|awk '{if ($5>0) {print $10}}'>"+sam+"_seq.txt")
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	212 os.system("cat "+sam+"\|awk '{if ($5>0) {print $1}}'>"+sam+"_title.txt")
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	213 file1=open(sam+"_title.txt","r")
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	214 file2=open(sam+"_seq.txt","r")
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	215 file1=file1.readlines()
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	216 file2=file2.readlines()
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	217 file=open(sam+".fasta","w")
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	218 for i in range(len(file1)):
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	219 title=">"+file1[i]
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	220 seq=file2[i]
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	221 if len(seq)>=50 and len(title)>6:#generally,can be adjusted
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	222 file.write(title)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	223 file.write(seq)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	224 file.close()
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	225 database2="tyr_of_O2_O9.fasta"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	226 os.system(Makebltdb+' -in database/'+database2+' -out '+database2+'_db '+'-dbtype nucl')
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	227 os.system(Blastnpth+" -query "+sam+".fasta"+" -db "+database2+"_db -out "+sam+"_vs_O29.xml -outfmt 5")
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	228 handle=open(sam+"_vs_O29.xml")
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	229 handle=NCBIXML.parse(handle)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	230 handle=list(handle)
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	231 O9_bigger=0
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	232 O2_bigger=0
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	233 for x in handle:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	234 O9_score=0
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	235 O2_score=0
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	236 try:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	237 if 'O-9' in x.alignments[0].hit_def:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	238 O9_score=x.alignments[0].hsps[0].bits
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	239 O2_score=x.alignments[1].hsps[0].bits
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	240 elif 'O-2' in x.alignments[0].hit_def:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	241 O9_score=x.alignments[1].hsps[0].bits
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	242 O2_score=x.alignments[0].hsps[0].bits
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	243 if O9_score>O2_score:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	244 O9_bigger+=1
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	245 if O9_score<O2_score:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	246 O2_bigger+=1
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	247 except:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	248 continue
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	249 print "$$$Genome:",sra_name
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	250 if O9_bigger>O2_bigger:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	251 print "$$$Most possible Otype is O-9"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	252 elif O9_bigger<O2_bigger:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	253 print "$$$Most possible Otype is O-2"
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	254 else:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	255 print "$$$No suitable one, because can't distinct it's O-9 or O-2, but ",potential_choice," has a more possibility."
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	256 print "O-9 number is:",O9_bigger
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	257 print "O-2 number is:",O2_bigger
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	258
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	259 os.system("rm "+sam+"_title.txt")###01/28/2015
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	260 os.system("rm "+sam+"_seq.txt")###01/28/2015
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	261 os.system("rm "+sam+".fasta")###01/28/2015
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	262 os.system("rm "+database2+"_db.*")###01/28/2015
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	263 os.system("rm "+sam+"_vs_O29.xml")###01/28/2015
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	264
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	265
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	266 target=sys.argv[1] #should be sra format
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	267 data_base=sys.argv[2]
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	268 mapping_mode=sys.argv[3]
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	269 if sys.argv[4] not in ("1","2","3"):
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	270 additional_file=sys.argv[4]
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	271 file_mode=sys.argv[5]
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	272 else:
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	273 additional_file=""
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	274 file_mode=sys.argv[4]
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	275
6895de35a263 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty charles_s_test parents: diff changeset	276 BWA_O_analysis(target,additional_file,data_base,mapping_mode,file_mode)

Mercurial > repos > charles_s_test > seqsero2

annotate libs/BWA_analysis_O_new_dependent.py @ 3:38ad1130d077 draft