# HG changeset patch # User public-health-bioinformatics # Date 1562283461 14400 # Node ID be856549e863bc72c68034c22c657494c39edc82 planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe diff -r 000000000000 -r be856549e863 data/FluA_H3_antigenic_aa_indices.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/FluA_H3_antigenic_aa_indices.csv Thu Jul 04 19:37:41 2019 -0400 @@ -0,0 +1,1 @@ +44,45,46,47,48,50,51,53,54,57,59,62,63,67,75,78,80,81,82,83,86,87,88,91,92,94,96,102,103,109,117,121,122,124,126,128,129,130,131,132,133,135,137,138,140,142,143,144,145,146,150,152,155,156,157,158,159,160,163,164,165,167,168,170,171,172,173,174,175,176,177,179,182,186,187,188,189,190,192,193,194,196,197,198,201,203,207,208,209,212,213,214,215,216,217,218,219,226,227,228,229,230,238,240,242,244,246,247,248,260,261,262,265,273,275,276,278,279,280,294,297,299,300,304,305,307,308,309,310,311,312 diff -r 000000000000 -r be856549e863 data/Flu_Clade_Definitions_H3_20171121.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/Flu_Clade_Definitions_H3_20171121.csv Thu Jul 04 19:37:41 2019 -0400 @@ -0,0 +1,12 @@ +3C.2a,1,3,I,144,S,145,S,159,Y,160,T,225,D,311,H,489,N,,,,,,,,,,,,,,,,,,,, +3C.2a_+_T131K_+_R142K_+_R261Q,2,3,I,131,K,142,K,144,S,145,S,159,Y,160,T,225,D,261,Q,311,H,489,N,,,,,,,,,,,,,, +3C.2a_+_N121K_+_S144K,2,3,I,121,K,144,K,145,S,159,Y,160,T,225,D,311,H,489,N,,,,,,,,,,,,,,,,,, +3C.2a_+_N31S_+_D53N_+_R142G_+_S144R_+_N171K_+_I192T_+_Q197H,2,3,I,31,S,53,N,142,G,144,R,145,S,159,Y,160,T,171,K,192,T,197,H,225,D,311,H,489,N,,,,,,,, +3C.2a1,2,3,I,144,S,145,S,159,Y,160,T,171,K,225,D,311,H,406,V,484,E,489,N,,,,,,,,,,,,,, +3C.2a1_+_N121K,3,3,I,121,K,144,S,145,S,159,Y,160,T,171,K,225,D,311,H,406,V,484,E,489,N,,,,,,,,,,,, +3C.2a1_+_N121K_+_K92R_+_H311Q,4,3,I,92,R,121,K,144,S,145,S,159,Y,160,T,171,K,225,D,311,Q,406,V,484,E,489,N,,,,,,,,,, +3C.2a1_+_N121K_+_T135K,4,3,I,121,K,135,K,144,S,145,S,159,Y,160,T,171,K,225,D,311,H,406,V,479,E,484,E,489,N,,,,,,,, +3C.2a1_+_N121K_+_I140M,4,3,I,121,K,140,M,144,S,145,S,159,Y,160,T,171,K,225,D,311,H,406,V,479,E,484,E,489,N,,,,,,,, +3C.2a1_+_N121K_+_R142G,4,3,I,121,K,142,G,144,S,145,S,159,Y,160,T,171,K,225,D,311,H,406,V,484,E,489,N,,,,,,,,,, +3C.2a1_+_N121K_+_R142G_+_I242V,5,3,I,121,K,142,G,144,S,145,S,159,Y,160,T,171,K,225,D,242,V,311,H,406,V,479,E,484,E,489,N,,,,,, +3C.3a,1,128,A,138,S,142,G,145,S,159,S,225,D,,,,,,,,,,,,,,,,,,,,,,,, diff -r 000000000000 -r be856549e863 data/MAP_3C.2a_A_Hong_Kong_4801_2014_X-263B_EGG.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data/MAP_3C.2a_A_Hong_Kong_4801_2014_X-263B_EGG.fasta Thu Jul 04 19:37:41 2019 -0400 @@ -0,0 +1,4 @@ +>Clade_3C.2a_A/Hong_Kong/4801/2014_X-263B_EGG +QNSSIEIDSQLENIQGQNKKLFVSKYSVPRTNNSNTGVTQNTSAIRSSSSRNTHLNYKAL +NTMNNEQFDKLIVGTDKDIFPAQSRXKRSAVIPNIGSIPSRIKGILNSTIRSSPGKKSEF +VRIACRYVKHS diff -r 000000000000 -r be856549e863 linelisting.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/linelisting.py Thu Jul 04 19:37:41 2019 -0400 @@ -0,0 +1,219 @@ +#!/usr/bin/env python +'''Reads in a fasta file of extracted antigenic sites and one containing a +reference flu antigenic map, reading them in as protein SeqRecords. Compares each amino +acid of each sample antigenic map to corresponding sites in the reference and replaces +identical amino acids with dots. Writes headers (including amino acid position numbers +read in from the respective index array), the reference amino acid sequence and column +headings required for non-aggregated line lists. Outputs headers and modified (i.e. dotted) +sequences to a csv file.''' + +'''Author: Diane Eisler, Molecular Microbiology & Genomics, BCCDC Public Health Laboratory, Nov 2017''' + +import sys,string,os, time, Bio, re, argparse +from Bio import Seq, SeqIO, SeqUtils, Alphabet, SeqRecord +from Bio.SeqRecord import SeqRecord +from Bio.Alphabet import IUPAC +from Bio.Seq import Seq + +inputAntigenicMaps = sys.argv[1] #batch fasta file with antigenic map sequences +refAntigenicMap = sys.argv[2] #fasta file of reference antigenic map sequence +antigenicSiteIndexArray = sys.argv[3] #antigenic site index array csv file +cladeDefinitionFile = sys.argv[4] #clade definition csv file +outFileHandle = sys.argv[5] #user-specifed output filename + +lineListFile = open(outFileHandle,'w') #open a writable output file + +indicesLine = "" #comma-separated antigenic site positions +cladeList = [] #list of clade names read from clade definition file +ref_seq = "" #reference antigenic map (protein sequence) +seqList = [] #list of aa sequences to compare to reference + +BC_list = [] #empty list for BC samples +AB_list = [] #empty list for AB samples +ON_list = [] #empty list for ON samples +QC_list = [] #empty list for QC samples +nonprov_list = [] #empty list for samples not in above 4 provinces +#dictionary for location-separated sequence lists +segregated_lists = {'1_BC':BC_list,'2_AB':AB_list,'3_ON':ON_list,'4_QC': QC_list, '5_nonprov': nonprov_list} +uniqueSeqs = {} #empty dict with unique seqs as keys and lists of SeqRecords as values + +def replace_matching_aa_with_dot(record): + """Compare amino acids in record to reference sequence, replace matching symbols + with dots, and return record with modified amino acid sequence.""" + orig_seq = str(record.seq) #get sequence string from SeqRecord + mod_seq = "" + #replace only those aa's matching the reference with dots + for i in range(0, len(orig_seq)): + if (orig_seq[i] == ref_seq[i]): + mod_seq = mod_seq + '.' + else: + mod_seq = mod_seq + orig_seq[i] + #assign modified sequence to new SeqRecord and return it + rec = SeqRecord(Seq(mod_seq,IUPAC.protein), id = record.id, name = "", description = "") + return rec + +def extract_clade(record): + """Extract clade name (or 'No_Match') from sequence name and return as clade name. """ + if record.id.endswith('No_Match'): + clade_name = 'No_Match' + end_index = record.id.index(clade_name) + record.id = record.id[:end_index -1] + return clade_name + else: # + for clade in cladeList: + if record.id.endswith(clade): + clade_name = clade + end_index = record.id.index(clade) + record.id = record.id[:end_index -1] + return clade_name + +def sort_by_location(record): + """Search sequence name for province name or 2 letter province code and add SeqRecord to + province-specific dictionary.""" + seq_name = record.id + if ('-BC-' in seq_name) or ('/British_Columbia/' in seq_name): + BC_list.append(record) #add Sequence record to BC_list + elif ('-AB-' in seq_name) or ('/Alberta/' in seq_name): + AB_list.append(record) #add Sequence record to AB_list + elif ('-ON-' in seq_name) or ('/Ontario/' in seq_name): + ON_list.append(record) #add Sequence record to ON_list + elif ('-QC-' in seq_name) or ('/Quebec/' in seq_name): + QC_list.append(record) #add Sequence record to QC_list + else: + nonprov_list.append(record) #add Sequence record to nonprov_list + return + +def extract_province(record): + """Search sequence name for province name or 2 letter province code and return province.""" + seq_name = record.id + if ('-BC-' in seq_name) or ('/British_Columbia/' in seq_name): + province = 'British Columbia' + elif ('-AB-' in seq_name) or ('Alberta' in seq_name): + province = '/Alberta/' + elif ('-ON-' in seq_name) or ('/Ontario/' in seq_name): + province = 'Ontario' + elif ('-QC-' in seq_name) or ('/Quebec/' in seq_name): + province = 'Quebec' + else: + province = "other" + return province + +def get_sequence_length(record): + """Return the length of a sequence in a Sequence record.""" + sequenceLength = len(str((record.seq))) + return sequenceLength + +def get_antigenic_site_substitutions(record): + """Count number of non-dotted amino acids in SeqRecord sequence and return as substitutions.""" + sequenceLength = get_sequence_length(record) + seqString = str(record.seq) + matches = seqString.count('.') + substitutions = sequenceLength - matches + return substitutions + +def calculate_percent_id(record, substitutions): + """Calculate sequence identity to a reference (based on substitutions and sequence length) and return percent id.""" + sequenceLength = get_sequence_length(record) + percentID = (1.00 - (float(substitutions)/float(sequenceLength))) + return percentID + +def output_linelist(sequenceList): + """Output a list of SeqRecords to a non-aggregated line list in csv format.""" + for record in sequenceList: + #get province, clade from sequence record + province = extract_province(record) + clade = extract_clade(record) + #calculate number of substitutions and % id to reference + substitutions = get_antigenic_site_substitutions(record) + percentID = calculate_percent_id(record,substitutions) + name_part = (record.id).rstrip() + ',' + clade_part = clade + ',' + substitutions_part = str(substitutions) + ',' + percID_part = str(percentID) + ',' + col = " ," #empty column + sequence = str(record.seq).strip() + csv_seq = ",".join(sequence) +"," + #write linelisted antigenic maps to csv file + comma_sep_line = name_part + col + clade_part + col + csv_seq + substitutions_part + percID_part + "\n" + lineListFile.write(comma_sep_line) + return + +with open (antigenicSiteIndexArray,'r') as siteIndices: + """Read amino acid positions from antigenic site index array and print as header after one empty row.""" + col = "," #empty column + #read items separated by comma's to position list + for line in siteIndices: + #remove whitespace from the end of each line + indicesLine = line.rstrip() + row1 = "\n" + #add comma-separated AA positions to header line + row2 = col + col + col + col + indicesLine + "\n" + #write first (empty) and 2nd (amino acid position) lines to linelist output file + lineListFile.write(row1) + lineListFile.write(row2) + +with open (refAntigenicMap,'r') as refMapFile: + """Read reference antigenic map from fasta and output amino acids, followed by column headers.""" + #read sequences from fasta to SeqRecord, uppercase, and store sequence string to ref_seq + record = SeqIO.read(refMapFile,"fasta",alphabet=IUPAC.protein) + record = record.upper() + ref_seq = str(record.seq).strip() #store sequence in variable for comparison to sample seqs + col = "," #empty column + name_part = (record.id).rstrip() + ',' + sequence = str(record.seq).strip() + csv_seq = ",".join(sequence) + #output row with reference sequence displayed above sample sequences + row3 = name_part + col + col + col + csv_seq + "\n" + lineListFile.write(row3) + #replaces digits in the indicesLine with empty strings + positions = indicesLine.split(',') + numPos = len(positions) + empty_indicesLine = ',' * numPos + #print column headers for sample sequences + row4 = "Sequence Name,N,Clade,Extra Substitutions," + empty_indicesLine + "Number of Amino Acid Substitutions in Antigenic Sites,% Identity of Antigenic Site Residues\n" + lineListFile.write(row4) + print("\nREFERENCE ANTIGENIC MAP: '%s' (%i amino acids)" % (record.id, len(record))) + +with open(cladeDefinitionFile,'r') as cladeFile: + """Read clade definition file and store clade names in a list.""" + #remove whitespace from the end of each line and split elements at commas + for line in cladeFile: + elementList = line.rstrip().split(',') + name = elementList[0] #move 1st element to name field + cladeList.append(name) + +with open(inputAntigenicMaps,'r') as extrAntigMapFile: + """Read antigenic maps as protein SeqRecords and add to list.""" + #read Sequences from fasta file, uppercase and add to seqList + for record in SeqIO.parse(extrAntigMapFile, "fasta", alphabet=IUPAC.protein): + record = record.upper() + seqList.append(record) #add Seq to list of Sequences + +#print number of sequences to be process as user check +print("\nCOMPARING %i flu antigenic map sequences to the reference..." % len(seqList)) +#parse each antigenic map sequence object +for record in seqList: + #assign Sequence to dictionaries according to location in name + sort_by_location(record) +#sort dictionary keys that access province-segregated lists +sorted_segregated_list_keys = sorted(segregated_lists.keys()) +print("\nSequence Lists Sorted by Province: ") +#process each province-segregated SeqRecord list +for listname in sorted_segregated_list_keys: + #acesss list of sequences by the listname key + a_list = segregated_lists[listname] + # sort original SeqRecords by record id (i.e. name) + a_list = [f for f in sorted(a_list, key = lambda x : x.id)] + mod_list = [] # empty temporary list + for record in a_list: + #replace matching amino acid symbols with dots + rec = replace_matching_aa_with_dot(record) + mod_list.append(rec) #populate a list of modified records + segregated_lists[listname] = mod_list + print("\n'%s' List (Amino Acids identical to Reference Masked): " % (listname)) + #output the list to csv as non-aggregated linelist + output_linelist(segregated_lists[listname]) + +extrAntigMapFile.close() +refMapFile.close() +lineListFile.close() \ No newline at end of file diff -r 000000000000 -r be856549e863 linelisting.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/linelisting.xml Thu Jul 04 19:37:41 2019 -0400 @@ -0,0 +1,35 @@ + + + biopython + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r be856549e863 test-data/FluA_H3_antigenic_aa_indices.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/FluA_H3_antigenic_aa_indices.csv Thu Jul 04 19:37:41 2019 -0400 @@ -0,0 +1,1 @@ +44,45,46,47,48,50,51,53,54,57,59,62,63,67,75,78,80,81,82,83,86,87,88,91,92,94,96,102,103,109,117,121,122,124,126,128,129,130,131,132,133,135,137,138,140,142,143,144,145,146,150,152,155,156,157,158,159,160,163,164,165,167,168,170,171,172,173,174,175,176,177,179,182,186,187,188,189,190,192,193,194,196,197,198,201,203,207,208,209,212,213,214,215,216,217,218,219,226,227,228,229,230,238,240,242,244,246,247,248,260,261,262,265,273,275,276,278,279,280,294,297,299,300,304,305,307,308,309,310,311,312 diff -r 000000000000 -r be856549e863 test-data/Flu_Clade_Definitions_H3_20171121.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Flu_Clade_Definitions_H3_20171121.csv Thu Jul 04 19:37:41 2019 -0400 @@ -0,0 +1,12 @@ +3C.2a,1,3,I,144,S,145,S,159,Y,160,T,225,D,311,H,489,N,,,,,,,,,,,,,,,,,,,, +3C.2a_+_T131K_+_R142K_+_R261Q,2,3,I,131,K,142,K,144,S,145,S,159,Y,160,T,225,D,261,Q,311,H,489,N,,,,,,,,,,,,,, +3C.2a_+_N121K_+_S144K,2,3,I,121,K,144,K,145,S,159,Y,160,T,225,D,311,H,489,N,,,,,,,,,,,,,,,,,, +3C.2a_+_N31S_+_D53N_+_R142G_+_S144R_+_N171K_+_I192T_+_Q197H,2,3,I,31,S,53,N,142,G,144,R,145,S,159,Y,160,T,171,K,192,T,197,H,225,D,311,H,489,N,,,,,,,, +3C.2a1,2,3,I,144,S,145,S,159,Y,160,T,171,K,225,D,311,H,406,V,484,E,489,N,,,,,,,,,,,,,, +3C.2a1_+_N121K,3,3,I,121,K,144,S,145,S,159,Y,160,T,171,K,225,D,311,H,406,V,484,E,489,N,,,,,,,,,,,, +3C.2a1_+_N121K_+_K92R_+_H311Q,4,3,I,92,R,121,K,144,S,145,S,159,Y,160,T,171,K,225,D,311,Q,406,V,484,E,489,N,,,,,,,,,, +3C.2a1_+_N121K_+_T135K,4,3,I,121,K,135,K,144,S,145,S,159,Y,160,T,171,K,225,D,311,H,406,V,479,E,484,E,489,N,,,,,,,, +3C.2a1_+_N121K_+_I140M,4,3,I,121,K,140,M,144,S,145,S,159,Y,160,T,171,K,225,D,311,H,406,V,479,E,484,E,489,N,,,,,,,, +3C.2a1_+_N121K_+_R142G,4,3,I,121,K,142,G,144,S,145,S,159,Y,160,T,171,K,225,D,311,H,406,V,484,E,489,N,,,,,,,,,, +3C.2a1_+_N121K_+_R142G_+_I242V,5,3,I,121,K,142,G,144,S,145,S,159,Y,160,T,171,K,225,D,242,V,311,H,406,V,479,E,484,E,489,N,,,,,, +3C.3a,1,128,A,138,S,142,G,145,S,159,S,225,D,,,,,,,,,,,,,,,,,,,,,,,, diff -r 000000000000 -r be856549e863 test-data/MAP_3C.2a_A_Hong_Kong_4801_2014_X-263B_EGG.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MAP_3C.2a_A_Hong_Kong_4801_2014_X-263B_EGG.fasta Thu Jul 04 19:37:41 2019 -0400 @@ -0,0 +1,4 @@ +>Clade_3C.2a_A/Hong_Kong/4801/2014_X-263B_EGG +QNSSIEIDSQLENIQGQNKKLFVSKYSVPRTNNSNTGVTQNTSAIRSSSSRNTHLNYKAL +NTMNNEQFDKLIVGTDKDIFPAQSRXKRSAVIPNIGSIPSRIKGILNSTIRSSPGKKSEF +VRIACRYVKHS diff -r 000000000000 -r be856549e863 test-data/fluA_H3_clade_assigned_antigenic_sites_extracted.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fluA_H3_clade_assigned_antigenic_sites_extracted.fasta Thu Jul 04 19:37:41 2019 -0400 @@ -0,0 +1,94 @@ +>A-ON-314-2017_3C.3a +QNSSIEIDSQLENIQGQNKKLFVNKYNVPRTNNSNAGVTQNTSSIGSKSSRNTHLNSKAL 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