Mercurial > repos > estrain > seqsero_v1

comparison SeqSero/libs/BWA_analysis_O_new_dependent.py @ 0:c577b57b7c74 draft

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author estrain
date Wed, 06 Dec 2017 15:59:29 -0500
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1 #!/usr/bin/env python
2 #tyr_of_O2_O9.fasta should be in the same directory, in it, O9 should be first then O2
3
4 import os
5 from Bio import SeqIO
6 import sys
7 from Initial_functions import Uniq
8 from Bio.Blast import NCBIXML
9
10 def BWA_O_analysis(sra_name,additional_file,database,mapping_mode,file_mode):
11 if file_mode=="1":#interleaved
12 if sra_name[-3:]=="sra":
13 os.system("fastq-dump --split-files "+sra_name)
14 del_fastq=1
15 for_fq=sra_name.replace(".sra","_1.fastq")
16 rev_fq=sra_name.replace(".sra","_2.fastq")
17 for_sai=sra_name.replace(".sra","_1.sai")
18 rev_sai=sra_name.replace(".sra","_2.sai")
19 sam=sra_name.replace(".sra",".sam")
20 bam=sra_name.replace(".sra",".bam")
21 else:
22 del_fastq=0
23 core_id=sra_name.split(".fastq")[0]
24 try:
25 os.system("gunzip "+sra_name)
26 except:
27 pass
28 dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
29 os.system("perl "+dirpath+"/split_interleaved_fastq.pl --input "+core_id+".fastq --output "+core_id.replace(".","_")+".fastq")#######03152016
30 ori_size=os.path.getsize(core_id+".fastq")#######03152016
31 os.system("mv "+core_id.replace(".","_")+"-read1.fastq"+" "+core_id+"-read1.fastq")#######03152016
32 os.system("mv "+core_id.replace(".","_")+"-read2.fastq"+" "+core_id+"-read2.fastq")#######03152016
33 for_fq=core_id+"-read1.fastq"#######03152016
34 rev_fq=core_id+"-read2.fastq"#######03152016
35 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
36 os.system("echo haha")#09092015
37 os.system("perl "+dirpath+"/splitPairedEndReads.pl "+core_id+".fastq")#09092015
38 os.system("mv "+core_id+".fastq_1 "+for_fq)##09092015
39 os.system("mv "+core_id+".fastq_2 "+rev_fq)##09092015
40 else:#09092015
41 os.system("echo hehe")#09092015
42 for_sai=core_id+"_1.sai"
43 rev_sai=core_id+"_2.sai"
44 sam=core_id+".sam"
45 bam=core_id+".bam"
46 elif file_mode=="2":#seperated
47 forword_seq=sra_name
48 reverse_seq=additional_file
49 try:
50 os.system("gunzip "+forword_seq)
51 except:
52 pass
53 try:
54 os.system("gunzip "+reverse_seq)
55 except:
56 pass
57 for_core_id=forword_seq.split(".fastq")[0]
58 re_core_id=reverse_seq.split(".fastq")[0]
59 for_fq=for_core_id+".fastq"
60 rev_fq=re_core_id+".fastq"
61 dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))#######03152016
62 print "check fastq id and make them in accordance with each other...please wait..."
63 os.system("python "+dirpath+"/compare_and_change_two_fastq_id.py "+for_fq+" "+rev_fq)#######03152016
64 for_sai=for_core_id+".sai"
65 rev_sai=re_core_id+".sai"
66 sam=for_core_id+".sam"
67 bam=sam.replace(".sam",".bam")
68 elif file_mode=="3":#single-end
69 if sra_name[-3:]=="sra":
70 os.system("fastq-dump --split-files "+sra_name)###01/28/2015
71 del_fastq=1
72 for_fq=sra_name.replace(".sra","_1.fastq")
73 for_sai=sra_name.replace(".sra","_1.sai")
74 sam=sra_name.replace(".sra",".sam")
75 bam=sra_name.replace(".sra",".bam")
76 else:
77 del_fastq=0
78 core_id=sra_name.split(".fastq")[0]
79 try:
80 os.system("gunzip "+sra_name)
81 except:
82 pass
83 for_fq=core_id+".fastq"
84 for_sai=core_id+"_1.sai"
85 sam=core_id+".sam"
86 bam=core_id+".bam"
87
88 os.system("bwa index "+database)
89 if file_mode!="3":
90 if mapping_mode=="sam":
91 os.system("bwa aln "+database+" "+for_fq+" > "+for_sai)
92 os.system("bwa aln "+database+" "+rev_fq+" > "+rev_sai)
93 os.system("bwa sampe "+database+" "+for_sai+" "+ rev_sai+" "+for_fq+" "+rev_fq+" > "+sam)
94 elif mapping_mode=="mem":
95 os.system("bwa mem "+database+" "+for_fq+" "+rev_fq+" > "+sam) #2014/12/23
96 elif mapping_mode=="nanopore": ##
97 os.system("bwa mem -x ont2d "+database+" "+for_fq+" "+rev_fq+" > "+sam)##
98 else:
99 if mapping_mode=="mem":
100 os.system("bwa mem "+database+" "+for_fq+" > "+sam) #2014/12/23
101 elif mapping_mode=="sam":
102 os.system("bwa aln "+database+" "+for_fq+" > "+for_sai)
103 os.system("bwa samse "+database+" "+for_sai+" "+for_fq+" > "+sam)
104 elif mapping_mode=="nanopore":##
105 os.system("bwa mem -x ont2d "+database+" "+for_fq+" > "+sam)##
106 os.system("samtools view -F 4 -Sbh "+sam+" > "+bam)
107 os.system("samtools view -h -o "+sam+" "+bam)
108
109 file=open(sam,"r")
110 handle=file.readlines()
111 name_list=[]
112 for line in handle:
113 if len(line)>300:
114 name_list.append(line.split("\t")[2])
115 a,b=Uniq(name_list)
116 c=dict(zip(a,b))
117 final_O=sorted(c.iteritems(), key=lambda d:d[1], reverse = True) #order from frequency high to low, but tuple while not list
118 Sero_list_O=[]
119 print "Final_Otype_list:"
120 print final_O
121 num_1=0#new inserted
122 O9_wbav=0
123 O310_wzx=0
124 O946_wzy=0
125 if len(final_O)>0: #new inserted
126 for x in final_O:#new inserted
127 num_1=num_1+x[1]#new inserted
128 if "O-9,46_wbaV" in x[0]:
129 O9_wbaV=x[1]
130 if "O-3,10_wzx" in x[0]:
131 O310_wzx=x[1]
132 if "O-9,46_wzy" in x[0]:
133 O946_wzy=x[1]
134 if "O-3,10_not_in_1,3,19" in x[0]:
135 O310_no_1319=x[1]
136 if "O-9,46,27_partial_wzy" in x[0]:
137 O94627=x[1]
138 O_list=[]
139 O_choice=""
140
141
142 print "$$$Genome:",sra_name
143 if len(final_O)==0:
144 print "$$$No Otype, due to no hit"
145 else:
146 if final_O[0][1]<8:
147 print "$$$No Otype, due to the hit reads number is small."
148 else:
149 for x in final_O:
150 if x[1]>5:
151 O_list.append(x[0])
152 qq=1#
153 for x in final_O:#
154 if "sdf" in x[0] and x[1]>3:#
155 qq=0#
156 print "$$$",x[0],"got a hit, reads:",x[1]#
157 final_O.remove(x)
158 if qq!=0:#
159 print "$$$No sdf exists"#
160
161 if "O-9,46_wbaV" in O_list and float(O9_wbaV)/float(num_1) > 0.1:
162 if "O-9,46_wzy" in O_list and float(O946_wzy)/float(num_1) > 0.1:
163 O_choice="O-9,46"
164 print "$$$Most possilble Otype: O-9,46"
165 elif "O-9,46,27_partial_wzy" in O_list and float(O94627)/float(num_1) > 0.1:
166 O_choice="O-9,46,27"
167 print "$$$Most possilble Otype: O-9,46,27"
168 else:
169 O_choice="O-9"
170 if file_mode=="3":
171 rev_fq=""
172 rev_sai=""
173 assembly(sra_name,O_choice,for_fq,rev_fq,for_sai,rev_sai,sam,bam,mapping_mode)
174 else:
175 assembly(sra_name,O_choice,for_fq,rev_fq,for_sai,rev_sai,sam,bam,mapping_mode)
176 elif ("O-3,10_wzx" in O_list) and ("O-9,46_wzy" in O_list) and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1:
177 if "O-3,10_not_in_1,3,19" in O_list and float(O310_no_1319)/float(num_1) > 0.1:
178 O_choice="O-3,10"
179 print "$$$Most possilble Otype: O-3,10"
180 else:
181 O_choice="O-1,3,19"
182 print "$$$Most possilble Otype: O-1,3,19"
183 else:
184 try:
185 O_choice=final_O[0][0].split("_")[0]
186 if O_choice=="O-1,3,19":
187 O_choice=final_O[1][0].split("_")[0]
188 print "$$$Most possilble Otype: ",O_choice
189 except:
190 print "$$$No suitable Otype, or failure of mapping (please check the quality of raw reads)"
191
192
193 def assembly(sra_name,potential_choice,for_fq,rev_fq,for_sai,rev_sai,sam,bam,mapping_mode):
194 database="ParaA_rfb.fasta"
195 os.system("bwa index database/"+database)###01/28/2015
196 if rev_fq=="":#2015/09/09
197 if mapping_mode=="mem":
198 os.system("bwa mem database/"+database+" "+for_fq+" > "+sam) #2014/12/23
199 elif mapping_mode=="sam":
200 os.system("bwa aln database/"+database+" "+for_fq+" > "+for_sai)
201 os.system("bwa samse database/"+database+" "+for_sai+" "+for_fq+" > "+sam)
202 elif mapping_mode=="nanopore":##
203 os.system("bwa mem -x ont2d database/"+database+" "+for_fq+" > "+sam)##
204 else:
205 if mapping_mode=="mem":
206 os.system("bwa mem database/"+database+" "+for_fq+" "+rev_fq+" > "+sam) #2014/12/23
207 elif mapping_mode=="sam":
208 os.system("bwa aln database/"+database+" "+for_fq+" > "+for_sai)
209 os.system("bwa aln database/"+database+" "+rev_fq+" > "+rev_sai)
210 os.system("bwa sampe database/"+database+" "+for_sai+" "+ rev_sai+" "+for_fq+" "+rev_fq+" > "+sam)
211 elif mapping_mode=="nanopore":
212 os.system("bwa mem -x ont2d database/"+database+" "+for_fq+" "+rev_fq+" > "+sam)
213 os.system("samtools view -F 4 -Sbh "+sam+" > "+bam)
214 os.system("samtools view -h -o "+sam+" "+bam)
215 os.system("cat "+sam+"|awk '{if ($5>0) {print $10}}'>"+sam+"_seq.txt")
216 os.system("cat "+sam+"|awk '{if ($5>0) {print $1}}'>"+sam+"_title.txt")
217 file1=open(sam+"_title.txt","r")
218 file2=open(sam+"_seq.txt","r")
219 file1=file1.readlines()
220 file2=file2.readlines()
221 file=open(sam+".fasta","w")
222 for i in range(len(file1)):
223 title=">"+file1[i]
224 seq=file2[i]
225 if len(seq)>=50 and len(title)>6:#generally,can be adjusted
226 file.write(title)
227 file.write(seq)
228 file.close()
229 database2="tyr_of_O2_O9.fasta"
230 os.system('makeblastdb -in database/'+database2+' -out '+database2+'_db '+'-dbtype nucl')
231 os.system("blastn -query "+sam+".fasta"+" -db "+database2+"_db -out "+sam+"_vs_O29.xml -outfmt 5")
232 handle=open(sam+"_vs_O29.xml")
233 handle=NCBIXML.parse(handle)
234 handle=list(handle)
235 O9_bigger=0
236 O2_bigger=0
237 for x in handle:
238 O9_score=0
239 O2_score=0
240 try:
241 if 'O-9' in x.alignments[0].hit_def:
242 O9_score=x.alignments[0].hsps[0].bits
243 O2_score=x.alignments[1].hsps[0].bits
244 elif 'O-2' in x.alignments[0].hit_def:
245 O9_score=x.alignments[1].hsps[0].bits
246 O2_score=x.alignments[0].hsps[0].bits
247 if O9_score>O2_score:
248 O9_bigger+=1
249 if O9_score<O2_score:
250 O2_bigger+=1
251 except:
252 continue
253 print "$$$Genome:",sra_name
254 if O9_bigger>O2_bigger:
255 print "$$$Most possible Otype is O-9"
256 elif O9_bigger<O2_bigger:
257 print "$$$Most possible Otype is O-2"
258 else:
259 print "$$$No suitable one, because can't distinct it's O-9 or O-2, but ",potential_choice," has a more possibility."
260 print "O-9 number is:",O9_bigger
261 print "O-2 number is:",O2_bigger
262
263 os.system("rm "+sam+"_title.txt")###01/28/2015
264 os.system("rm "+sam+"_seq.txt")###01/28/2015
265 os.system("rm "+sam+".fasta")###01/28/2015
266 os.system("rm "+database2+"_db.*")###01/28/2015
267 os.system("rm "+sam+"_vs_O29.xml")###01/28/2015
268
269
270 target=sys.argv[1] #should be sra format
271 data_base=sys.argv[2]
272 mapping_mode=sys.argv[3]
273 if sys.argv[4] not in ("1","2","3"):
274 additional_file=sys.argv[4]
275 file_mode=sys.argv[5]
276 else:
277 additional_file=""
278 file_mode=sys.argv[4]
279
280 BWA_O_analysis(target,additional_file,data_base,mapping_mode,file_mode)