Mercurial > repos > public-health-bioinformatics > antigenic_site_extraction

annotate antigenic_site_extraction.py @ 2:f879bf22aa12 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit e6d31e4b3666b5e1d322e22f44526f23c66692fb
author public-health-bioinformatics
date Thu, 17 Jan 2019 19:08:56 -0500
parents 89deee583d6d
children f5522fa90c03
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
1 #!/usr/bin/env python
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
2
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
3 '''Accepts fasta files of amino acid sequence, extracts specific amino acids (defined in a csv index array),
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
4 and outputs extracted sequences - representing flu antigenic sites - to fasta (default) or csv.'''
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
5
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
6 '''Author: Diane Eisler, Molecular Microbiology & Genomics, BCCDC Public Health Laboratory,Sept 2017'''
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
7
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
8 import sys,string,os, time, Bio, argparse
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
9 from Bio import Seq, SeqIO, SeqUtils, Alphabet, SeqRecord
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
10 from Bio.SeqRecord import SeqRecord
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
11 from Bio.Alphabet import IUPAC
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
12 from Bio.Seq import Seq
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
13
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
14 #parse command line arguments
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
15 parser = argparse.ArgumentParser()
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
16 parser.add_argument("-c","--csv",help="export extracted antigenic sites to csv file",action="store_true")
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
17 parser.add_argument("inFileHandle1") #batch fasta file with sequences to be parsed
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
18 parser.add_argument("inFileHandle2") # .csv file containing positions of aa's to extract
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
19 parser.add_argument("outFileHandle") #user-specified name for output file of extracted aa seq's
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
20 args = parser.parse_args()
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
21
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
22 #inFileHandle1 = sys.argv[1] #batch fasta file with sequences to be parsed
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
23 #inFileHandle2 = sys.argv[2] # .csv file containing positions of aa's to extract
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
24 #outFileHandle = sys.argv[3] #user-specified name for output file of extracted aa seq's
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
25
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
26 outFile= open(args.outFileHandle,'w') #open a writable, appendable output file
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
27 localtime = time.asctime(time.localtime(time.time())) #date and time of analysis
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
28 seqList = [] #list of aa sequence objects to parse for oligo sequences
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
29 indexArray = [] # .csv list of aa's corresponding to antigenic site positions
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
30 extractedSeqList = [] #list of extracted antigenic sites extracted from seqList
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
31
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
32 def extract_aa_from_sequence(record):
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
33 """Extract specific amino acids from SeqRecord, create new SeqRecord and append to list."""
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
34 original_sequence = str(record.seq) #pull out the SeqRecord's Seq object and ToString it
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
35 new_sequence = "" #set variable to empty
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
36 new_id = record.id #store the same sequence id as the original sequence
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
37 #iterate over each position in index array, extract corresponding aa and add to string
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
38 for pos in indexArray:
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
39 char = original_sequence[pos-1] #aa positions must be zero indexed
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
40 new_sequence = new_sequence + char
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
41 rec = SeqRecord(Seq(new_sequence,IUPAC.protein), id = record.id, name = "", description = "")
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
42 extractedSeqList.append(rec) #add new SeqRecord object to the list
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
43
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
44 with open (args.inFileHandle2,'r') as inFile2:
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
45 '''Open csv file containing amino acid positions to extract and add to list.'''
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
46 #read items separated by comma's to position list
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
47 positionList = ""
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
48 for line in inFile2:
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
49 #remove whitespace from the end of each line
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
50 strippedLine = line.rstrip()
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
51 #split the line at commas and assigned the returned list as indexArray
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
52 positionList = strippedLine.split(',')
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
53 #Convert string items in positionList from strings to int and add to indexArray
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
54 for item in positionList:
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
55 indexArray.append(int(item))
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
56 #print number of amino acids to extract and array to console as user check
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
57 print "Amino Acid positions to extract: %i " %(len(indexArray))
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
58 print indexArray
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
59
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
60 with open(args.inFileHandle1,'r') as inFile:
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
61 '''Open fasta of amino acid sequences to parse, uppercase and add to protein Sequence list.'''
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
62 #read in Sequences from fasta file, uppercase and add to seqList
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
63 for record in SeqIO.parse(inFile, "fasta", alphabet=IUPAC.protein):
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
64 record = record.upper()
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
65 seqList.append(record) #add Seq to list of Sequences
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
66 #print number of sequences to be process as user check
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
67 print "\n%i flu sequences will be extracted for antigenic sites..." % len(seqList)
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
68 #parse each target sequence object
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
69 for record in seqList:
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
70 extract_aa_from_sequence(record)
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
71
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
72 #print original and extracted sequence
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
73 for x in range(0, len(seqList)):
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
74 print "Original %s: %i amino acids,\tExtracted: %i" % (seqList[x].id,len(seqList[x]),len(extractedSeqList[x]))
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
75
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
76 #determine if output format is fasta (default) or csv
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
77 if args.csv:
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
78 #write csv file of extracted antigenic sits
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
79 for record in extractedSeqList:
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
80 #outFile.write(record.id),","
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
81 name_part = (record.id).rstrip() + ','
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
82 sequence = str(record.seq).strip()
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
83 csv_seq = ",".join(sequence)
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
84 comma_separated_sequence = name_part + csv_seq + "\n"
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
85 print comma_separated_sequence
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
86 outFile.write(comma_separated_sequence)
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
87 else:
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
88 #write fasta file of extracted antigenic sites
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
89 SeqIO.write(extractedSeqList,outFile,"fasta")
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
90
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
91 print("\n%i Sequences Extracted to Output file: %s" % ((len(extractedSeqList),args.outFileHandle)))
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
92 inFile.close()
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
93 inFile2.close()
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
94 outFile.close()
89deee583d6d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 561cde8c8bd4a6164b1bef19ecff9809ac3340e0
public-health-bioinformatics
parents:
diff changeset
95