Mercurial > repos > public-health-bioinformatics > antigenic_site_extraction

annotate antigenic_site_extraction.py @ 0:a1b46e339580 draft default tip

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planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
author public-health-bioinformatics
date Thu, 04 Jul 2019 19:36:38 -0400
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a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
public-health-bioinformatics
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1 #!/usr/bin/env python
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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3 '''Accepts fasta files of amino acid sequence, extracts specific amino acids (defined in a csv index array),
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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4 and outputs extracted sequences - representing flu antigenic sites - to fasta (default) or csv.'''
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a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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6 '''Author: Diane Eisler, Molecular Microbiology & Genomics, BCCDC Public Health Laboratory,Sept 2017'''
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a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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8 import sys,string,os, time, Bio, argparse
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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9 from Bio import Seq, SeqIO, SeqUtils, Alphabet, SeqRecord
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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10 from Bio.SeqRecord import SeqRecord
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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11 from Bio.Alphabet import IUPAC
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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12 from Bio.Seq import Seq
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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14 #parse command line arguments
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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15 parser = argparse.ArgumentParser()
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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16 parser.add_argument("-c","--csv",help="export extracted antigenic sites to csv file",action="store_true")
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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17 parser.add_argument("inFileHandle1") #batch fasta file with sequences to be parsed
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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18 parser.add_argument("inFileHandle2") # .csv file containing positions of aa's to extract
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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19 parser.add_argument("outFileHandle") #user-specified name for output file of extracted aa seq's
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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20 args = parser.parse_args()
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22 #inFileHandle1 = sys.argv[1] #batch fasta file with sequences to be parsed
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23 #inFileHandle2 = sys.argv[2] # .csv file containing positions of aa's to extract
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24 #outFileHandle = sys.argv[3] #user-specified name for output file of extracted aa seq's
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26 outFile= open(args.outFileHandle,'w') #open a writable, appendable output file
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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27 localtime = time.asctime(time.localtime(time.time())) #date and time of analysis
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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28 seqList = [] #list of aa sequence objects to parse for oligo sequences
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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29 indexArray = [] # .csv list of aa's corresponding to antigenic site positions
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30 extractedSeqList = [] #list of extracted antigenic sites extracted from seqList
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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32 def extract_aa_from_sequence(record):
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33 """Extract specific amino acids from SeqRecord, create new SeqRecord and append to list."""
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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34 original_sequence = str(record.seq) #pull out the SeqRecord's Seq object and ToString it
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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35 new_sequence = "" #set variable to empty
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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36 new_id = record.id #store the same sequence id as the original sequence
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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37 #iterate over each position in index array, extract corresponding aa and add to string
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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38 for pos in indexArray:
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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39 char = original_sequence[pos-1] #aa positions must be zero indexed
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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40 new_sequence = new_sequence + char
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41 rec = SeqRecord(Seq(new_sequence,IUPAC.protein), id = record.id, name = "", description = "")
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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42 extractedSeqList.append(rec) #add new SeqRecord object to the list
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43
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44 with open (args.inFileHandle2,'r') as inFile2:
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45 '''Open csv file containing amino acid positions to extract and add to list.'''
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46 #read items separated by comma's to position list
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47 positionList = ""
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48 for line in inFile2:
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49 #remove whitespace from the end of each line
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50 strippedLine = line.rstrip()
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51 #split the line at commas and assigned the returned list as indexArray
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52 positionList = strippedLine.split(',')
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53 #Convert string items in positionList from strings to int and add to indexArray
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54 for item in positionList:
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55 indexArray.append(int(item))
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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56 #print number of amino acids to extract and array to console as user check
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57 print("Amino Acid positions to extract: %i " %(len(indexArray)))
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58 print(indexArray)
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59
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60 with open(args.inFileHandle1,'r') as inFile:
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61 '''Open fasta of amino acid sequences to parse, uppercase and add to protein Sequence list.'''
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62 #read in Sequences from fasta file, uppercase and add to seqList
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63 for record in SeqIO.parse(inFile, "fasta", alphabet=IUPAC.protein):
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64 record = record.upper()
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65 seqList.append(record) #add Seq to list of Sequences
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66 #print number of sequences to be process as user check
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67 print("\n%i flu sequences will be extracted for antigenic sites..." % len(seqList))
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68 #parse each target sequence object
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69 for record in seqList:
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70 extract_aa_from_sequence(record)
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71
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72 #print original and extracted sequence
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73 for x in range(0, len(seqList)):
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74 print("Original %s: %i amino acids,\tExtracted: %i" % (seqList[x].id,len(seqList[x]),len(extractedSeqList[x])))
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75
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76 #determine if output format is fasta (default) or csv
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77 if args.csv:
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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78 #write csv file of extracted antigenic sits
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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79 for record in extractedSeqList:
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80 #outFile.write(record.id),","
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81 name_part = (record.id).rstrip() + ','
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82 sequence = str(record.seq).strip()
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83 csv_seq = ",".join(sequence)
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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84 comma_separated_sequence = name_part + csv_seq + "\n"
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
public-health-bioinformatics
parents:
diff changeset
85 print(comma_separated_sequence)
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
public-health-bioinformatics
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diff changeset
86 outFile.write(comma_separated_sequence)
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
public-health-bioinformatics
parents:
diff changeset
87 else:
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
public-health-bioinformatics
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88 #write fasta file of extracted antigenic sites
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
public-health-bioinformatics
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diff changeset
89 SeqIO.write(extractedSeqList,outFile,"fasta")
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
public-health-bioinformatics
parents:
diff changeset
90
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
public-health-bioinformatics
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91 print("\n%i Sequences Extracted to Output file: %s" % ((len(extractedSeqList),args.outFileHandle)))
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
public-health-bioinformatics
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92 inFile.close()
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
public-health-bioinformatics
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diff changeset
93 inFile2.close()
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
public-health-bioinformatics
parents:
diff changeset
94 outFile.close()
a1b46e339580 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
public-health-bioinformatics
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diff changeset
95