/usr/share/seqsero/libs/BWA_analysis_H_update_new_family_dependent.py is in seqsero 1.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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import os
from Bio import SeqIO
import sys
from Initial_functions import Uniq
from Bio.Blast import NCBIXML
def BWA_analysis(sra_name,additional_file,database,mapping_mode,file_mode,z):
global fliC_option
global fljB_option
global family_c_list
global family_b_list
global list_c_length
global list_b_length
family_c_list=[] #will catch families on the family test mapping
family_b_list=[]
if file_mode=="1":#interleaved
if sra_name[-3:]=="sra":
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]
for_fq=core_id+"-read1.fastq"
rev_fq=core_id+"-read2.fastq"
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
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"
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":
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]
for_fq=core_id+".fastq"
rev_fq=core_id+".fastq"
for_sai=core_id+"_1.sai"
rev_sai=core_id+"_2.sai"
sam=core_id+".sam"
bam=core_id+".bam"
database=database.split("/")[-1]##########1/27/2015
os.system("bwa index database/"+database)
if file_mode!="3":
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)
else:
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)
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(zip(a,b))
Sero_list_C=[]
Sero_list_B=[]
description=[] #for storage of whole desription to extract the multifasta file for second BWA mapping
fliC={}
fljB={}
for x in c:
if x[:4]=="fliC":
fliC[x]=c[x]
for x in c:
if x[:4]=="fljB":
fljB[x]=c[x]
final_fliC=sorted(fliC.iteritems(), key=lambda d:d[1], reverse = True) #order from frequency high to low, but tuple while not list
final_fljB=sorted(fljB.iteritems(), key=lambda d:d[1], reverse = True) #order from frequency high to low, but tuple while not list
print "Final_filC_list:"
print final_fliC
num_1=0#new inserted
num_2=0#new inserted
if len(final_fliC)>0: #new inserted
for x in final_fliC:#new inserted
num_1=num_1+x[1]#new inserted
print "Final_fliC_number_together: ",num_1#new inserted
print "Final_fljB_list:"
print final_fljB
if len(final_fljB)>0: #new inserted
for x in final_fljB: #new inserted
num_2=num_2+x[1] #new inserted
print "Final_fljB_number_together: ",num_2#new inserted
print "$$Genome:",sra_name
try:
fliC_option=final_fliC[0][0].split("_")[1]
except:
fliC_option="-"
try:
fljB_option=final_fljB[0][0].split("_")[1]
except:
fljB_option="-"
if z==0:
if len(final_fliC)==0 or num_1<=10:
print "$$$No fliC, due to no hit"
else:
if final_fliC[0][1]<=1 and z==1:
print "$$$No fliC, due to the hit reads number is small."
else:
try:
family=final_fliC[0][0].split("_")[-1]
Sero_list_C.append(family)
description.append(final_fliC[0][0])
print "$$Most possilble fliC family: ",Sero_list_C[0]," Number: ",final_fliC[0][1]
i=0
for x in final_fliC:
if x[0].split("_")[-1] not in Sero_list_C:
if i<=x[1]:
i=x[1]
sec_choice=x[0].split("_")[-1]
des=x[0]
number=x[1]
if locals().has_key('sec_choice'):
Sero_list_C.append(sec_choice)
description.append(des)
print "$$Sec possilble fliC family: ",sec_choice," Number: ",number
j=0
for x in final_fliC:
if x[0].split("_")[-1] not in Sero_list_C:
if j<=x[1]:
j=x[1]
third_choice=x[0].split("_")[-1]
des=x[0]
number=x[1]
if locals().has_key('third_choice'):
Sero_list_C.append(third_choice)
description.append(des)
print "$$Third possilble fliC family: ",third_choice," Number: ",number
except:
print "$$$No fliC, or failure of mapping"
try:
ratio=float(num_2)/float(num_1)
except:
ratio=0
if len(final_fljB)==0 or num_2<=5 or ratio<0.15:
print "$$$No fljB, due to no hit"
else:
if final_fljB[0][1]<=1 and z==1:
print "$$$No fljB, due to the hit reads number is small."
else:
try:
family=final_fljB[0][0].split("_")[-1]
Sero_list_B.append(family)
description.append(final_fljB[0][0])
print "$$Most possilble fljB family: ",Sero_list_B[0]," Number: ",final_fljB[0][1]
i=0
for x in final_fljB:
if x[0].split("_")[-1] not in Sero_list_B:
if i<=x[1]:
i=x[1]
B_sec_choice=x[0].split("_")[-1]
des=x[0]
number=x[1]
if locals().has_key('B_sec_choice'):
Sero_list_B.append(B_sec_choice)
description.append(des)
print "$$Sec possilble fljB: ",B_sec_choice," Number: ",number
j=0
for x in final_fljB:
if x[0].split("_")[-1] not in Sero_list_B:
if j<=x[1]:
j=x[1]
B_third_choice=x[0].split("_")[-1]
des=x[0]
number=x[1]
if locals().has_key('B_third_choice'):
Sero_list_B.append(B_third_choice)
description.append(des)
print "$$Third possilble fljB: ",B_third_choice," Number: ",number
except:
print "$$$No fljB, or failure of mapping"
if len(description)==0: #used for the case which fljB and fliC both has no hit, it will directly cease the function
return
handle=SeqIO.parse("database/"+database,"fasta")########1/27/2015
handle=list(handle)
file1=open("temp"+sra_name+".fasta","w")
for x in handle:
for y in description:
if x.description==y:
title=">"+x.description
seq=str(x.seq)
file1.write(title+"\n")
file1.write(seq+"\n")
file1.close()
data_base2="temp"+sra_name+".fasta"
os.system("mv "+data_base2+" database")######1/27/2015
z=1
BWA_analysis(sra_name,additional_file,data_base2,mapping_mode,file_mode,z) #z=1 this time, z is the pointer for the seqeunce of run
return
if z==1:
list_c_length=len(final_fliC)
list_b_length=len(final_fljB)
family_test(final_fliC,"fliC",type,sra_name,for_fq,rev_fq,for_sai,rev_sai,sam,bam)
family_test(final_fljB,"fljB",type,sra_name,for_fq,rev_fq,for_sai,rev_sai,sam,bam)
#os.system("rm "+for_fq)###01/28/2015#$$$$$$$
#os.system("rm "+rev_fq)###01/28/2015
#os.system("rm "+for_sai)
#os.system("rm "+rev_sai)
#os.system("rm "+bam)
#os.system("rm "+sam)###01/28/2015
#os.system("rm temp.txt")###01/28/2015
#os.system("rm "+sam+".fasta"+"_db.*")###01/28/2015
#os.system("rm temp"+sra_name+".fasta")###01/28/2015
def family_test(fliC_fljB_list,listtype,type,sra_name,for_fq,rev_fq,for_sai,rev_sai,sam,bam):
Sero_list_C=[]
Sero_list_B=[]
if listtype=="fliC":
if len(fliC_fljB_list)==0:
print "$$No fliC, due to no hit" #because the only possible situation for len(final_fliC)==0 is above (z=0) len(final_fliC)==0, so there is no need to use "$$$" here
else:
if fliC_fljB_list[0][1]<=1:
print "$$No fliC, due to the hit reads number is small." #similiar with above, no "$$$"
else:
if fliC_fljB_list[0][0].split("_")[-1]=="g,m":
type="fliC"
database="FliC_f_g_s_whole.fasta"
database2="FliC_Family_g_special_genes.fasta"
assembly(type,sra_name,for_fq,rev_fq,for_sai,rev_sai,sam,bam,database,database2,list_c_length,mapping_mode)
elif fliC_fljB_list[0][0].split("_")[-1]=="l,v":
type="fliC"
database="fliC_l_z13_whole.fasta"
database2="FliC_Family_l,v_special_genes.fasta"
assembly(type,sra_name,for_fq,rev_fq,for_sai,rev_sai,sam,bam,database,database2,list_c_length,mapping_mode)
elif fliC_fljB_list[0][0].split("_")[-1]=="r,i":
type="fliC"
database="fliC_r_whole.fasta"
database2="FliC_Family_r,i_special_genes_short.fasta"
assembly(type,sra_name,for_fq,rev_fq,for_sai,rev_sai,sam,bam,database,database2,list_c_length,mapping_mode)
elif fliC_fljB_list[0][0].split("_")[-1]=="k,z":
type="fliC"
database="fliC_k,z_whole.fasta"
database2="FliC_Family_k,z_special_genes.fasta"
assembly(type,sra_name,for_fq,rev_fq,for_sai,rev_sai,sam,bam,database,database2,list_c_length,mapping_mode)
elif fliC_fljB_list[0][0].split("_")[-1]=="b,d,j":
type="fliC"
database="fliC_b_whole.fasta"
database2="FliC_Family_b,d,j_special_genes.fasta"
assembly(type,sra_name,for_fq,rev_fq,for_sai,rev_sai,sam,bam,database,database2,list_c_length,mapping_mode)
elif fliC_fljB_list[0][0].split("_")[-1]=="z4,z23":
type="fliC"
database="fliC_z4z23_whole.fasta"
database2="fliC_z4,z23_family.fasta" #"FliC_Family_z4z23_special_genes.fasta"
assembly(type,sra_name,for_fq,rev_fq,for_sai,rev_sai,sam,bam,database,database2,list_c_length,mapping_mode)
elif fliC_fljB_list[0][0].split("_")[-1]=="z36,z38":
type="fliC"
database="fliC_z36,z38_whole.fasta"
database2="FliC_Family_z36z38_special_genes.fasta"
assembly(type,sra_name,for_fq,rev_fq,for_sai,rev_sai,sam,bam,database,database2,list_c_length,mapping_mode)
else:
try:
Sero_list_C.append(fliC_fljB_list[0][0].split("_")[1])
print "$$$Most possilble fliC: ",Sero_list_C[0]," Number: ",fliC_fljB_list[0][1]
i=0
for x in fliC_fljB_list:
if x[0].split("_")[1] not in Sero_list_C:
if i<=x[1]:
i=x[1]
sec_choice=x[0].split("_")[1]
number=x[1]
if locals().has_key('sec_choice'):
Sero_list_C.append(sec_choice)
print "$$$Sec possilble fliC: ",sec_choice," Number: ",number
j=0
for x in fliC_fljB_list:
if x[0].split("_")[1] not in Sero_list_C:
if j<=x[1]:
j=x[1]
third_choice=x[0].split("_")[1]
number=x[1]
if locals().has_key('third_choice'):
Sero_list_C.append(third_choice)
print "$$$Third possilble fliC: ",third_choice," Number: ",number
except:
print "$$$No fliC, or failure of mapping (second run)"
if listtype=="fljB":
if len(fliC_fljB_list)==0:
print "$$No fljB, due to no hit" #similiar with above, no "$$$"
else:
if fliC_fljB_list[0][1]<=1:
print "$$No fljB, due to the hit reads number is small." #similiar with above, no "$$$"
else:
if fliC_fljB_list[0][0].split("_")[-1]=="1":
type="fljB"
database="FljB_1_2_7_whole.fasta"
database2="FljB_Family_1_special_genes_all.fasta"
assembly(type,sra_name,for_fq,rev_fq,for_sai,rev_sai,sam,bam,database,database2,list_b_length,mapping_mode)
elif fliC_fljB_list[0][0].split("_")[-1]=="e":
type="fljB"
database="fljB_e,n,z15_whole.fasta"
database2="FljB_Family_e_special_genes.fasta"
assembly(type,sra_name,for_fq,rev_fq,for_sai,rev_sai,sam,bam,database,database2,list_b_length,mapping_mode)
elif fliC_fljB_list[0][0].split("_")[-1]=="l,v":
type="fljB"
database="FljB_l,z13,z28_whole.fasta"
database2="FljB_Family_l,v_special_genes.fasta"
assembly(type,sra_name,for_fq,rev_fq,for_sai,rev_sai,sam,bam,database,database2,list_b_length,mapping_mode)
elif fliC_fljB_list[0][0].split("_")[-1]=="k,z":
type="fljB"
database="FljB_z6_whole.fasta"
database2="FljB_Family_k,z_special_genes.fasta"
assembly(type,sra_name,for_fq,rev_fq,for_sai,rev_sai,sam,bam,database,database2,list_b_length,mapping_mode)
else:
try:
Sero_list_B.append(fliC_fljB_list[0][0].split("_")[1])
print "$$$Most possilble fljB: ",Sero_list_B[0]," Number: ",fliC_fljB_list[0][1]
i=0
for x in fliC_fljB_list:
if x[0].split("_")[1] not in Sero_list_B:
if i<=x[1]:
i=x[1]
B_sec_choice=x[0].split("_")[1]
number=x[1]
if locals().has_key('B_sec_choice'):
Sero_list_B.append(B_sec_choice)
print "$$$Sec possilble fljB: ",B_sec_choice," Number: ",number
j=0
for x in fliC_fljB_list:
if x[0].split("_")[1] not in Sero_list_B:
if j<=x[1]:
j=x[1]
B_third_choice=x[0].split("_")[1]
number=x[1]
if locals().has_key('B_third_choice'):
Sero_list_B.append(B_third_choice)
print "$$$Third possilble fljB: ",B_third_choice," Number: ",number
except:
print "$$$No fljB, or failure of mapping (second run)"
def assembly(type,sra_name,for_fq,rev_fq,for_sai,rev_sai,sam,bam,database,database2,list_length,mapping_mode):
os.system("bwa index database/"+database)
if file_mode!="3":
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)
else:
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)
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}}'>"+database+sam+"_seq.txt")
os.system("cat "+sam+"|awk '{if ($5>=0) {print $1}}'>"+database+sam+"_title.txt")
file1=open(database+sam+"_title.txt","r")
file2=open(database+sam+"_seq.txt","r")
file1=file1.readlines()
file2=file2.readlines()
file=open(database+"_"+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 with different situations
file.write(title)
file.write(seq)
file.close()
os.system("mv "+database+"_"+sam+".fasta"+" database")######1/27/2015
os.system('makeblastdb -in database/'+database+"_"+sam+".fasta"+' -out '+sam+".fasta"+'_db '+'-dbtype nucl >temp.txt') #temp.txt is to forbid the blast result interrupt the output of our program###1/27/2015
os.system("blastn -query database/"+database2+" -db "+sam+".fasta"+"_db -out "+database2+"_vs_"+sam+".xml -outfmt 5 >temp.txt")###1/27/2015
handle=open(database2+"_vs_"+sam+".xml")
handle=NCBIXML.parse(handle)
handle=list(handle)
List=[]
List_score=[]
for i in range(len(handle)):
if len(handle[i].alignments)>0:
List.append(handle[i].query)
score=0
for j in range(len(handle[i].alignments)):
for z in range(len(handle[i].alignments[j].hsps)):
score+=handle[i].alignments[j].hsps[z].bits
List_score.append(score)
temp=dict(zip(List,List_score))
Final_list=sorted(temp.iteritems(), key=lambda d:d[1], reverse = True)
family=database2.split("_")[2]
try:
Final_list[0][0].split("_")[1] # or it will always print "$$$Genome...."(next line)
print "$$$Genome:",sra_name
print "$$$Most possilble "+type+": ",Final_list[0][0].split("_")[1]," Score(due_to_special_test, number changed to score): ",Final_list[0][1]
print Final_list
except:
if type=="fliC":
print "$$$There may be no hit for "+type+"_"+family+" family due to the reads not covering core seqeunce, but just based on reads hit number, the most possible one is: ",fliC_option
if type=="fljB":
print "$$$There may be no hit for "+type+"_"+family+" family due to the reads not covering core seqeunce, but just based on reads hit number, the most possible one is: ",fljB_option
os.system("rm "+database2+"_vs_"+sam+".xml")###01/28/2015
os.system("rm "+database+sam+"_seq.txt")###01/28/2015
os.system("rm "+database+sam+"_title.txt")###01/28/2015
os.system("rm temp.txt")###01/28/2015
os.system("rm "+sam+".fasta"+"_db.*")###01/28/2015
z=0
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_analysis(target,additional_file,data_base,mapping_mode,file_mode,z)
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