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#!/usr/bin/python3
#tyr_of_O2_O9.fasta should be in the same directory, in it, O9 should be first then O2
import os
from Bio import SeqIO
import sys
from Initial_functions import Uniq
from Bio.Blast import NCBIXML
def BWA_O_analysis(sra_name,additional_file,database,mapping_mode,file_mode):
if file_mode=="1":#interleaved
if sra_name[-3:]=="sra":
os.system("fastq-dump --split-files "+sra_name)
del_fastq=1
for_fq=sra_name.replace(".sra","_1.fastq")
rev_fq=sra_name.replace(".sra","_2.fastq")
for_sai=sra_name.replace(".sra","_1.sai")
rev_sai=sra_name.replace(".sra","_2.sai")
sam=sra_name.replace(".sra",".sam")
bam=sra_name.replace(".sra",".bam")
else:
del_fastq=0
core_id=sra_name.split(".fastq")[0]
try:
os.system("gunzip "+sra_name)
except:
pass
dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
os.system("perl "+dirpath+"/split_interleaved_fastq.pl --input "+core_id+".fastq --output "+core_id.replace(".","_")+".fastq")#######03152016
ori_size=os.path.getsize(core_id+".fastq")#######03152016
os.system("mv "+core_id.replace(".","_")+"-read1.fastq"+" "+core_id+"-read1.fastq")#######03152016
os.system("mv "+core_id.replace(".","_")+"-read2.fastq"+" "+core_id+"-read2.fastq")#######03152016
for_fq=core_id+"-read1.fastq"#######03152016
rev_fq=core_id+"-read2.fastq"#######03152016
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
os.system("echo haha")#09092015
os.system("perl "+dirpath+"/splitPairedEndReads.pl "+core_id+".fastq")#09092015
os.system("mv "+core_id+".fastq_1 "+for_fq)##09092015
os.system("mv "+core_id+".fastq_2 "+rev_fq)##09092015
else:#09092015
os.system("echo hehe")#09092015
for_sai=core_id+"_1.sai"
rev_sai=core_id+"_2.sai"
sam=core_id+".sam"
bam=core_id+".bam"
elif file_mode=="2":#seperated
forword_seq=sra_name
reverse_seq=additional_file
try:
os.system("gunzip "+forword_seq)
except:
pass
try:
os.system("gunzip "+reverse_seq)
except:
pass
for_core_id=forword_seq.split(".fastq")[0]
re_core_id=reverse_seq.split(".fastq")[0]
for_fq=for_core_id+".fastq"
rev_fq=re_core_id+".fastq"
dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))#######03152016
print("check fastq id and make them in accordance with each other...please wait...")
os.system("python3 "+dirpath+"/compare_and_change_two_fastq_id.py "+for_fq+" "+rev_fq)#######03152016
for_sai=for_core_id+".sai"
rev_sai=re_core_id+".sai"
sam=for_core_id+".sam"
bam=sam.replace(".sam",".bam")
elif file_mode=="3":#single-end
if sra_name[-3:]=="sra":
os.system("fastq-dump --split-files "+sra_name)###01/28/2015
del_fastq=1
for_fq=sra_name.replace(".sra","_1.fastq")
for_sai=sra_name.replace(".sra","_1.sai")
sam=sra_name.replace(".sra",".sam")
bam=sra_name.replace(".sra",".bam")
else:
del_fastq=0
core_id=sra_name.split(".fastq")[0]
try:
os.system("gunzip "+sra_name)
except:
pass
for_fq=core_id+".fastq"
for_sai=core_id+"_1.sai"
sam=core_id+".sam"
bam=core_id+".bam"
os.system("bwa index "+database)
if file_mode!="3":
if mapping_mode=="sam":
os.system("bwa aln "+database+" "+for_fq+" > "+for_sai)
os.system("bwa aln "+database+" "+rev_fq+" > "+rev_sai)
os.system("bwa sampe "+database+" "+for_sai+" "+ rev_sai+" "+for_fq+" "+rev_fq+" > "+sam)
elif mapping_mode=="mem":
os.system("bwa mem "+database+" "+for_fq+" "+rev_fq+" > "+sam) #2014/12/23
elif mapping_mode=="nanopore": ##
os.system("bwa mem -x ont2d "+database+" "+for_fq+" "+rev_fq+" > "+sam)##
else:
if mapping_mode=="mem":
os.system("bwa mem "+database+" "+for_fq+" > "+sam) #2014/12/23
elif mapping_mode=="sam":
os.system("bwa aln "+database+" "+for_fq+" > "+for_sai)
os.system("bwa samse "+database+" "+for_sai+" "+for_fq+" > "+sam)
elif mapping_mode=="nanopore":##
os.system("bwa mem -x ont2d "+database+" "+for_fq+" > "+sam)##
os.system("samtools view -F 4 -Sbh "+sam+" > "+bam)
os.system("samtools view -h -o "+sam+" "+bam)
file=open(sam,"r")
handle=file.readlines()
name_list=[]
for line in handle:
if len(line)>300:
name_list.append(line.split("\t")[2])
a,b=Uniq(name_list)
c=dict(list(zip(a,b)))
final_O=sorted(iter(c.items()), key=lambda d:d[1], reverse = True) #order from frequency high to low, but tuple while not list
Sero_list_O=[]
print("Final_Otype_list:")
print(final_O)
num_1=0#new inserted
O9_wbav=0
O310_wzx=0
O946_wzy=0
if len(final_O)>0: #new inserted
for x in final_O:#new inserted
num_1=num_1+x[1]#new inserted
if "O-9,46_wbaV" in x[0]:
O9_wbaV=x[1]
if "O-3,10_wzx" in x[0]:
O310_wzx=x[1]
if "O-9,46_wzy" in x[0]:
O946_wzy=x[1]
if "O-3,10_not_in_1,3,19" in x[0]:
O310_no_1319=x[1]
if "O-9,46,27_partial_wzy" in x[0]:
O94627=x[1]
O_list=[]
O_choice=""
print("$$$Genome:",sra_name)
if len(final_O)==0:
print("$$$No Otype, due to no hit")
else:
if final_O[0][1]<8:
print("$$$No Otype, due to the hit reads number is small.")
else:
for x in final_O:
if x[1]>5:
O_list.append(x[0])
qq=1#
for x in final_O:#
if "sdf" in x[0] and x[1]>3:#
qq=0#
print("$$$",x[0],"got a hit, reads:",x[1])#
final_O.remove(x)
if qq!=0:#
print("$$$No sdf exists")#
if "O-9,46_wbaV" in O_list and float(O9_wbaV)/float(num_1) > 0.1:
if "O-9,46_wzy" in O_list and float(O946_wzy)/float(num_1) > 0.1:
O_choice="O-9,46"
print("$$$Most possilble Otype: O-9,46")
elif "O-9,46,27_partial_wzy" in O_list and float(O94627)/float(num_1) > 0.1:
O_choice="O-9,46,27"
print("$$$Most possilble Otype: O-9,46,27")
else:
O_choice="O-9"
if file_mode=="3":
rev_fq=""
rev_sai=""
assembly(sra_name,O_choice,for_fq,rev_fq,for_sai,rev_sai,sam,bam,mapping_mode)
else:
assembly(sra_name,O_choice,for_fq,rev_fq,for_sai,rev_sai,sam,bam,mapping_mode)
elif ("O-3,10_wzx" in O_list) and ("O-9,46_wzy" in O_list) and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1:
if "O-3,10_not_in_1,3,19" in O_list and float(O310_no_1319)/float(num_1) > 0.1:
O_choice="O-3,10"
print("$$$Most possilble Otype: O-3,10")
else:
O_choice="O-1,3,19"
print("$$$Most possilble Otype: O-1,3,19")
else:
try:
O_choice=final_O[0][0].split("_")[0]
if O_choice=="O-1,3,19":
O_choice=final_O[1][0].split("_")[0]
print("$$$Most possilble Otype: ",O_choice)
except:
print("$$$No suitable Otype, or failure of mapping (please check the quality of raw reads)")
def assembly(sra_name,potential_choice,for_fq,rev_fq,for_sai,rev_sai,sam,bam,mapping_mode):
database="ParaA_rfb.fasta"
os.system("bwa index database/"+database)###01/28/2015
if rev_fq=="":#2015/09/09
if mapping_mode=="mem":
os.system("bwa mem database/"+database+" "+for_fq+" > "+sam) #2014/12/23
elif mapping_mode=="sam":
os.system("bwa aln database/"+database+" "+for_fq+" > "+for_sai)
os.system("bwa samse database/"+database+" "+for_sai+" "+for_fq+" > "+sam)
elif mapping_mode=="nanopore":##
os.system("bwa mem -x ont2d database/"+database+" "+for_fq+" > "+sam)##
else:
if mapping_mode=="mem":
os.system("bwa mem database/"+database+" "+for_fq+" "+rev_fq+" > "+sam) #2014/12/23
elif mapping_mode=="sam":
os.system("bwa aln database/"+database+" "+for_fq+" > "+for_sai)
os.system("bwa aln database/"+database+" "+rev_fq+" > "+rev_sai)
os.system("bwa sampe database/"+database+" "+for_sai+" "+ rev_sai+" "+for_fq+" "+rev_fq+" > "+sam)
elif mapping_mode=="nanopore":
os.system("bwa mem -x ont2d database/"+database+" "+for_fq+" "+rev_fq+" > "+sam)
os.system("samtools view -F 4 -Sbh "+sam+" > "+bam)
os.system("samtools view -h -o "+sam+" "+bam)
os.system("cat "+sam+"|awk '{if ($5>0) {print $10}}'>"+sam+"_seq.txt")
os.system("cat "+sam+"|awk '{if ($5>0) {print $1}}'>"+sam+"_title.txt")
file1=open(sam+"_title.txt","r")
file2=open(sam+"_seq.txt","r")
file1=file1.readlines()
file2=file2.readlines()
file=open(sam+".fasta","w")
for i in range(len(file1)):
title=">"+file1[i]
seq=file2[i]
if len(seq)>=50 and len(title)>6:#generally,can be adjusted
file.write(title)
file.write(seq)
file.close()
database2="tyr_of_O2_O9.fasta"
os.system('makeblastdb -in database/'+database2+' -out '+database2+'_db '+'-dbtype nucl')
os.system("blastn -query "+sam+".fasta"+" -db "+database2+"_db -out "+sam+"_vs_O29.xml -outfmt 5")
handle=open(sam+"_vs_O29.xml")
handle=NCBIXML.parse(handle)
handle=list(handle)
O9_bigger=0
O2_bigger=0
for x in handle:
O9_score=0
O2_score=0
try:
if 'O-9' in x.alignments[0].hit_def:
O9_score=x.alignments[0].hsps[0].bits
O2_score=x.alignments[1].hsps[0].bits
elif 'O-2' in x.alignments[0].hit_def:
O9_score=x.alignments[1].hsps[0].bits
O2_score=x.alignments[0].hsps[0].bits
if O9_score>O2_score:
O9_bigger+=1
if O9_score<O2_score:
O2_bigger+=1
except:
continue
print("$$$Genome:",sra_name)
if O9_bigger>O2_bigger:
print("$$$Most possible Otype is O-9")
elif O9_bigger<O2_bigger:
print("$$$Most possible Otype is O-2")
else:
print("$$$No suitable one, because can't distinct it's O-9 or O-2, but ",potential_choice," has a more possibility.")
print("O-9 number is:",O9_bigger)
print("O-2 number is:",O2_bigger)
os.system("rm "+sam+"_title.txt")###01/28/2015
os.system("rm "+sam+"_seq.txt")###01/28/2015
os.system("rm "+sam+".fasta")###01/28/2015
os.system("rm "+database2+"_db.*")###01/28/2015
os.system("rm "+sam+"_vs_O29.xml")###01/28/2015
target=sys.argv[1] #should be sra format
data_base=sys.argv[2]
mapping_mode=sys.argv[3]
if sys.argv[4] not in ("1","2","3"):
additional_file=sys.argv[4]
file_mode=sys.argv[5]
else:
additional_file=""
file_mode=sys.argv[4]
BWA_O_analysis(target,additional_file,data_base,mapping_mode,file_mode)
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