# HG changeset patch # User public-health-bioinformatics # Date 1547770170 18000 # Node ID 0d3dad15541307fb79a7a2c988c15fab6cbbdf9e # Parent 1dc65ec11a40d3ed1f2e46ee2fdadfd6f766d4ea planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit e6d31e4b3666b5e1d322e22f44526f23c66692fb diff -r 1dc65ec11a40 -r 0d3dad155413 README.md --- a/README.md Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ -# Flu Classification Suite -Influenza viruses continually evolve to evade population immunity. We have developed a publicly-available Galaxy workflow Flu Analysis Suite, for rapid clade-mapping of sequenced influenza viruses. This suite provides rapid, high-resolution understanding of circulating influenza strain evolution to inform influenza vaccine effectiveness and the need for potential vaccine reformulation. - -# Installation - -# Tools - -## Aggregate Line List -Transforms fasta files of flu antigenic site amino acids into aggregated line lists, comparing antigenic maps to that of a reference sequence and collapsing and enumerating identical sequences. - -## Antigenic Site Extraction -Extracts antigenic amino acids from flu sequence, using a specific index array (i.e. for H3, H1 etc.). - -## Assign Clades -Assign clade designations to influenza amino acid fasta files. - -## Change Fasta Deflines -Renames definition lines in fasta files. Requires a fasta file requiring sequence name changes and a 2-column renaming file (either tab-delimited text or csv). Searches for fasta definition lines matching column 1 and, if found, replaces fasta definition line with string specified in column 2 of the renaming file. - -## Line List -Transforms fasta files of flu antigenic site amino acids into line lists, comparing antigenic maps to that of a reference sequence. - -## Reformat USearch-Collapsed Fasta -Parses format of USearch-collapsed fasta output files and outputs fasta with customized definition line formatting. diff -r 1dc65ec11a40 -r 0d3dad155413 assign_clades.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/assign_clades.py Thu Jan 17 19:09:30 2019 -0500 @@ -0,0 +1,133 @@ +#!/usr/bin/env python + +'''Accepts fasta files containing amino acid sequence, reading them in as +amino acid sequence objects. Reads influenza clade defintions (i.e. amino +acids at certain positions) from .csv file into dictionary structure. Searches +each of the amino acid sequence objects for a list of matching clades, assigns +the most 'evolved' (i.e. child as opposed to parent clade) to the sequence. Appends +"_cladename" to the Sequence name and generates a fasta file of original sequences with +modified names.''' + +'''Author: Diane Eisler, Molecular Microbiology & Genomics, BCCDC Public Health Laboratory, Oct 2017''' + +import sys,string,os, time, Bio +from Bio import Seq, SeqIO, SeqUtils, Alphabet, SeqRecord +from Bio.SeqRecord import SeqRecord +from Bio.Alphabet import IUPAC +from Bio.Seq import Seq + +localtime = time.asctime(time.localtime(time.time())) #date and time of analysis +inFileHandle1 = sys.argv[1] #batch fasta file with sequences to be parsed +inFileHandle2 = sys.argv[2] # .csv file containing clade definitions and "depth" +outFileHandle = sys.argv[3] #user-specified name for output file of aa seq's with clade suffixes +outFile= open(outFileHandle,'w') #open a writable, appendable output file +seqList = [] #list of aa sequence objects to parse for clade definitions +cladeList = [] #empty list to hold clade tuples i.e. ("3C.3a", 1 ,{"3":"I", "9":"V"..}) + +'''Searches record for required amino acids at defined positions. If found, assigns +clade name to sequence name by appending underscore and clade name to record id.''' +def call_clade(record): + print "---------------------------------------------------------------------" + print "Parsing %s for matching flu clade definitions..." % (record.id) + matchList = [] #empty list to hold clades that match 100% + #iterate over each tuple in the clade list + for clade in cladeList: + cladeName = clade[0] #temp variable for name + depth = clade[1] #temp variable for depth + sites = clade[2] #temp variable for aa def dictionary + shouldFind = len(sites) #number of sites that should match + found = 0 #a counter to hold matches to antigenic sites + #iterate over each position in sites dictionary + for pos, aa in sites.iteritems(): + #translate pos to corresponding index in target sequence + index = int(pos) - 1 + #if record at index has same amino acid as 'aa', increment 'found' + if record[index] == aa: + found += 1 + if (found == shouldFind): + #add the matching clade tuple to the list of matches + matchList.append(clade) + return matchList + +'''Compares depth level of clades in a list and returns the most granular one''' +def decide_clade_by_depth(matchList): + #empty variable for maximum depth encountered + max_depth = 0 + best_match_name = '' #variable to hold most granular clade + #for each matching clade, check depth of the corresponding tuple + for clade in matchList: + #if the current clade is 'deeper' than the one before it + if clade[1] > max_depth: + #store this depth + max_depth = clade[1] + #store name of the clade + best_match_name = clade[0] + return best_match_name + +'''opens the .csv file of clade definitions and clade "depth" ''' +with open (inFileHandle2, 'r') as clade_file: + #remove whitespace from the end of each line and split elements at commas + for line in clade_file: + #print "Current Line in File:" + line + sites={} #initialize a dictionary for clade + elementList = line.rstrip().split(',') + new_list = [] #start a new list to put non-empty strings into + #remove empty stings in list + for item in elementList: + if item != '': + new_list.append(item) + name = new_list.pop(0) #move 1st element to name field + depth = int(new_list.pop(0)) #move 2nd element to depth field + #read remaining pairs of non-null elements into clade def dictionary + for i in range(0, len(new_list), 2): + #move next 2 items from the list into the dict + pos = new_list[i] + aa = new_list[i + 1] + sites[pos] = aa + #add the clade info as a tuple to the cladeList[] + oneClade =(name, depth, sites) + cladeList.append(oneClade) + print "The List of Clades:" + for clade in cladeList: + print "Clade Name: %s Depth: %i Antigenic Sites: %i" % (clade[0], clade[1], len(clade[2])) + for pos, aa in clade[2].iteritems(): + print "Pos: %s\tAA: %s" % (pos,aa) + +'''opens readable input file of sequences to parse using filename from cmd line, + instantiates as AA Sequence objects, with ppercase sequences''' +with open(inFileHandle1,'r') as inFile: + #read in Sequences from fasta file, uppercase and add to seqList + for record in SeqIO.parse(inFile, "fasta", alphabet=IUPAC.protein): + record = record.upper() + seqList.append(record) #add Seq to list of Sequences + print "\n%i flu HA sequences will be compared to current clade definitions..." % len(seqList) + #parse each target sequence object + for record in seqList: + clade_call = '' #empty variale for final clade call on sequence + matchingCladeList = call_clade(record) #holds matching clade tuples + #if there is more than one clade match + if len(matchingCladeList) > 1: + #choose the most granular clade based on depth + clade_call = decide_clade_by_depth(matchingCladeList) + #if there is only one clade call + elif len(matchingCladeList) > 0: + clade = matchingCladeList[0] #take the first tuple in the list + clade_call = clade[0] #clade name is the first item in the tuple + #empty list return, no matches + else: + clade_call = "No_Match" + print clade_call + seq_name = record.id + mod_name = seq_name + "_" + clade_call + print "New Sequence Name: " + mod_name + record.id = mod_name + + +#output fasta file with clade calls appended to sequence names +SeqIO.write(seqList,outFile,"fasta") + +#print("\n%i Sequences Extracted to Output file: %s" % ((len(extractedSeqList),outFileHandle))) +inFile.close() +clade_file.close() +outFile.close() + diff -r 1dc65ec11a40 -r 0d3dad155413 assign_clades.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/assign_clades.xml Thu Jan 17 19:09:30 2019 -0500 @@ -0,0 +1,29 @@ + + + biopython + + + + + + + + + + + + + + + + + + + + diff -r 1dc65ec11a40 -r 0d3dad155413 test-data/clades.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clades.csv Thu Jan 17 19:09:30 2019 -0500 @@ -0,0 +1,15 @@ +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_+_Q197K_+_R261Q,2,3,I,144,S,145,S,159,Y,160,T,197,K,225,D,261,Q,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_(w/o_N121K),3,3,I,144,S,145,S,159,Y,160,T,171,K,225,D,311,H,406,V,484,E,489,N,,,,,,,, +3C.2a1_+_N121K,4,3,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_+_R142G_+_I242V,4,3,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.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_+_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_+_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_+_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_+_R142G,4,3,I,142,G,144,S,145,S,159,Y,160,T,171,K,225,D,311,H,406,V,484,E,489,N,,,,,, +3C.2a1_+_S47T_+_G78S,4,3,I,47,T,78,S,144,S,145,S,159,Y,160,T,171,K,225,D,311,H,406,V,484,E,489,N,,,, +3C.3a,1,128,A,138,S,142,G,145,S,159,S,225,D,,,,,,,,,,,,,,,,,, diff -r 1dc65ec11a40 -r 0d3dad155413 test-data/output.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.fa Thu Jan 17 19:09:30 2019 -0500 @@ -0,0 +1,10 @@ +>test_3C.3a test +QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILD +GENCTLIDALLGDPQCDGFQNKKWDLFVERNKAYSSCYPYDVPDYASLRSLVASSGTLEF +NNESFNWAGVTQNGTSSSCIRGSKSSFFSRLNWLTHLNSKYPALNVTMPNNEQFDKLYIW +GVHHPGTDKDQISLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPG +DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRI +TYGACPRYVKQSTLKLATGMRNVPERQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEG +RGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDL +WSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGS +IRNGTYDHNVYRDEALNNRFQIKGVELKSGYKDW diff -r 1dc65ec11a40 -r 0d3dad155413 test-data/test_input.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_input.fasta Thu Jan 17 19:09:30 2019 -0500 @@ -0,0 +1,2 @@ +>test +QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERNKAYSSCYPYDVPDYASLRSLVASSGTLEFNNESFNWAGVTQNGTSSSCIRGSKSSFFSRLNWLTHLNSKYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQISLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKQSTLKLATGMRNVPERQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHNVYRDEALNNRFQIKGVELKSGYKDW diff -r 1dc65ec11a40 -r 0d3dad155413 tools/aggregate_linelisting/aggregate_linelisting.py --- a/tools/aggregate_linelisting/aggregate_linelisting.py Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,279 +0,0 @@ -#!/usr/bin/env python -'''Reads in a fasta file of antigenic maps and one with the reference antigenic map as -protein SeqRecords. Compares amino acids of sample antigenic maps to corresponding sites -in the reference and masks identical amino acids with dots. Writes headers (including -amino acid position numbers read from the respective index array), the reference amino -acid sequence and column headings required for both non-aggregated and aggregated line lists. -Outputs all headers and modified (i.e. dotted) sample sequences to a csv file.''' - -'''Author: Diane Eisler, Molecular Microbiology & Genomics, BCCDC Public Health Laboratory, Jan 2018''' - -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 - -agg_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 -prov_lists = {'1_BC':BC_list,'2_AB':AB_list,'3_ON':ON_list,'4_QC': QC_list, '5_nonprov': nonprov_list} - -def replace_matching_aa_with_dot(record): - """Compare amino acids in record to reference, mask identical symbols with dots, and return modified record.""" - orig_seq = str(record.seq) #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' - else: # - for clade in cladeList: - if record.id.endswith(clade): - clade_name = clade - return clade_name - -def extract_sample_name(record, clade): - """Extract sample name from sequence name and return sample name. """ - end_index = record.id.index(clade) - sample_name = record.id[:end_index -1] - #return sample name as sequence name minus underscore and clade name - return sample_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 length of sequence in a SeqRecord.""" - 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 percent sequence identity to reference sequence, based on substitutions -and sequence length and return percent id as a ratio (i.e. 0.90 no 90%).""" - sequenceLength = get_sequence_length(record) - percentID = (1.00 - (float(substitutions)/float(sequenceLength))) - return percentID - -def output_aggregated_linelist(a_list): - """Output aggregated line list of SeqRecords in csv format.""" - sequevars = {} #dict of sequevar: SeqRecord list - firstRecordID = None - #examine dotted/masked sequences in list and assign unique ones as dict keys - for rec in a_list: - rec = replace_matching_aa_with_dot(rec) - sequence =str(rec.seq) - #if the sequence is a key in the dict, add SeqRecord to list - if sequence in sequevars: - #if sequence already in dict as a key, increment the value - sequevars[sequence].append(rec) - else: - #if sequence not in dict, add is as new key with list of 1 SeqRecord - sequevars[sequence] = [rec] - #get list of sorted unique sequence keys - sorted_unique_seq_keys = sorted(sequevars.keys()) - #process each list of SeqRecords sharing a unique sequence - for u in sorted_unique_seq_keys: - #access list of sequences by unique sequence - listOfSeqs = sequevars[u] - #sort this list of SeqRecords by record.id (i.e. name) - listOfSeqs = [f for f in sorted(listOfSeqs, key = lambda x : x.id)] - N = len(listOfSeqs) - #output details of first SeqRecord to csv - firstRecord = listOfSeqs[0] - province = extract_province(firstRecord) - clade = extract_clade(firstRecord) - substitutions = get_antigenic_site_substitutions(firstRecord) - percentID = calculate_percent_id(firstRecord,substitutions) - name = extract_sample_name(firstRecord, clade) - name_part = name.rstrip() + ',' - N_part = str(N) + ',' - clade_part = clade + ',' - substitutions_part = str(substitutions) + ',' - percID_part = str(percentID) + ',' - col = " ," #empty column - sequence = str(firstRecord.seq).strip() - csv_seq = ",".join(sequence) +"," - comma_sep_output = name_part + N_part + clade_part + col + csv_seq + substitutions_part + percID_part + "\n" - #write first member of unique sequence list to csv - agg_lineListFile.write(comma_sep_output) - #print sequence records in sequevar to console - print "\n\t\t%i SeqRecords matching Sequevar: %s" % (len(listOfSeqs), u) - - #to uncollapse sequevar group, print each member of the sequevar list to csv output - '''for i in range(1,len(listOfSeqs)): - currentRec = listOfSeqs[i] - province = extract_province(currentRec) - clade = extract_clade(currentRec) - substitutions = get_antigenic_site_substitutions(currentRec) - percentID = calculate_percent_id(currentRec,substitutions) - name_part = (currentRec.id).rstrip() + ',' - N_part = "n/a" + ',' - clade_part = clade + ',' - substitutions_part = str(substitutions) + ',' - percID_part = str(percentID) + ',' - col = " ," #empty column - sequence = str(currentRec.seq).strip() - csv_seq = ",".join(sequence) +"," - comma_sep_output = name_part + N_part + clade_part + col + csv_seq + substitutions_part + percID_part + "\n" - agg_lineListFile.write(comma_sep_output) ''' - 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 amino acid positions and remove trailing whitespace - 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 output file - agg_lineListFile.write(row1) - agg_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" - agg_lineListFile.write(row3) - 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" - agg_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 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 processed as user check -print "\nCOMPARING %i flu antigenic map sequences to the reference..." % len(seqList) -for record in seqList: - #assign SeqRecords to province-specific dictionaries - sort_by_location(record) - -#access prov segregated lists in order -sorted_prov_keys = sorted(prov_lists.keys()) -print "\nSequence Lists Sorted by Province: " -for prov in sorted_prov_keys: - current_list = prov_lists[prov] - #mask AA's identical to reference sequence with dot - masked_list = [] # empty temporary list to park masked sequences - for record in current_list: - masked_rec = replace_matching_aa_with_dot(record) - masked_list.append(masked_rec) - prov_lists[prov] = masked_list #replace original SeqRecord list with masked list - -#group sequences in province-sorted list into clades -for prov in sorted_prov_keys: - prov_list = prov_lists[prov] - by_clades_dict = {} #empty dict for clade:seqRecord list groups - print "\n'%s' List (Amino Acids identical to Reference are Masked): " % (prov) - for rec in prov_list: - clade = extract_clade(rec) - if clade in by_clades_dict: - #if clade already in dict as key, append record to list (value) - by_clades_dict[clade].append(rec) - else: #add clade as key to dict, value is list of 1 SeqRecord - by_clades_dict[clade] = [rec] - #get list of alphabetically sorted clade keys - sorted_clade_keys = sorted(by_clades_dict.keys()) - print "\tNumber of clades: ", len(by_clades_dict) - #group each list of sequences in clade by sequevars - for key in sorted_clade_keys: - print "\n\tCLADE: %s Number of Members: %i" % (key, len(by_clades_dict[key])) - a_list = by_clades_dict[key] - for seqrec in a_list: - print "\t %s: %s" %(seqrec.id,str(seqrec.seq)) - #output the list to csv as aggregated linelist - output_aggregated_linelist(a_list) - -print("Aggregated Linelist written to file: '%s\n'" % (outFileHandle)) -extrAntigMapFile.close() -refMapFile.close() -agg_lineListFile.close() diff -r 1dc65ec11a40 -r 0d3dad155413 tools/aggregate_linelisting/aggregate_linelisting.xml --- a/tools/aggregate_linelisting/aggregate_linelisting.xml Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,35 +0,0 @@ - - - biopython - - - - - - - - - - - - - - - - - - - - - - - - diff -r 1dc65ec11a40 -r 0d3dad155413 tools/aggregate_linelisting/test-data/FluA_H3_antigenic_aa_indices.csv --- a/tools/aggregate_linelisting/test-data/FluA_H3_antigenic_aa_indices.csv Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -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 1dc65ec11a40 -r 0d3dad155413 tools/aggregate_linelisting/test-data/Flu_Clade_Definitions_H3_20171121.csv --- a/tools/aggregate_linelisting/test-data/Flu_Clade_Definitions_H3_20171121.csv Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -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 1dc65ec11a40 -r 0d3dad155413 tools/aggregate_linelisting/test-data/MAP_3C.2a_A_Hong_Kong_4801_2014_X-263B_EGG.fasta --- a/tools/aggregate_linelisting/test-data/MAP_3C.2a_A_Hong_Kong_4801_2014_X-263B_EGG.fasta Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->Clade_3C.2a_A/Hong_Kong/4801/2014_X-263B_EGG -QNSSIEIDSQLENIQGQNKKLFVSKYSVPRTNNSNTGVTQNTSAIRSSSSRNTHLNYKAL -NTMNNEQFDKLIVGTDKDIFPAQSRXKRSAVIPNIGSIPSRIKGILNSTIRSSPGKKSEF -VRIACRYVKHS diff -r 1dc65ec11a40 -r 0d3dad155413 tools/aggregate_linelisting/test-data/fluA_H3_clade_assigned_antigenic_sites_extracted.fasta --- a/tools/aggregate_linelisting/test-data/fluA_H3_clade_assigned_antigenic_sites_extracted.fasta Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,94 +0,0 @@ ->A-ON-314-2017_3C.3a -QNSSIEIDSQLENIQGQNKKLFVNKYNVPRTNNSNAGVTQNTSSIGSKSSRNTHLNSKAL -NTMNNEQFDKLIVGTDKDISLAQSRTKRSAVIPNIGSIPSRIKGILNSTIRSSPGKKSEF -VRIACRYVKQS - ->A-AB-399-2017_3C.2a_+_N31S_+_D53N_+_R142G_+_S144R_+_N171K_+_I192T_+_Q197H -QNSSIEINSQLENIQGQNKKLFVSKYNVPRTNNSNTGVTQNTSAIGSRSSRNTHLNYTAL -NTMNKEQFDKLIVGTDKDTFLAHSRTKRSAVIPNIGSIPSRIKGLLNSTIRSSPGKKSEF -VRIACRYVKHS - ->A-QC-303-2017_3C.2a_+_N31S_+_D53N_+_R142G_+_S144R_+_N171K_+_I192T_+_Q197H -QNSSIEINSQLENIQGQNKKLFVSKYNVPRTNNSNTGVTQNTSAIGSRSSRNTHLNYTAL -NTMNKEQFDKLIVGTDKDTFLAHSRTKRSAVIPNIGSIPSRIKGLLNSTIRSSPGKKSEF -VRIACRYVKHS - ->A-AB-319-2017_3C.2a_+_N31S_+_D53N_+_R142G_+_S144R_+_N171K_+_I192T_+_Q197H -QNSSIEINSQLENIQGQNKKLFVSKYNVPRTNNSNTGVTQNTSAIGSRSSRNTHLNYTAL -NTMNKEQFDKLIVGTDKDTFLAHSRTKRSAVIPNIGSIPSRIKGLLNSTIRSSPGKKSEF -VRIACRYVKHS - ->A-AB-308-2017_3C.2a1_+_N121K_+_T135K -QNSSIEIDSQLENIQDQNKKLFVSKHNVPRTKDSNTGVTQNKSAIRSSSSRNTHLNYTAL -NTMNKEQFDKLIIGTDKDIFLAQSRTKRSAVIPNIGSIPSRIKGILNSTIRSSPGKKSEF -VRIACRYVKHS - ->A-AB-341-2017_3C.2a1_+_N121K_+_T135K -QNSSIEIDSQLENIQDQNKKLFVSKHNVPRTKDSNTGVTQNKSAIRSSSSRNTHLNYTAL -NTMNKEQFDKLIIGTDKDIFLAQSRTKRSAVIPNIGSIPSRIKGILNSTIRSSPGKKSEF -VRIACRYVKHS - ->A-BC-024-2018_3C.2a1_+_N121K_+_T135K -QNSSIEIDSQLENIQDQNKKLFVSKHNVPRTKNSNTGVTQNKSAIRSSSSRNTHLNYTAL -NTMNKEQFDKLIIGTDKDIFLAQSRTKRSAVIPNIGSIPSRIKGILNSTIRSSPGKKSEF -VRIACRYVKHS - ->A-QC-309-2017_3C.2a1_+_N121K_+_K92R_+_H311Q -QNSSIEIDSQLGNIQDQNKKLFVSRYNVPRTKDSNTGVTQNKSAIGSSSSRNTHLNYTAL -NTMNKEQFDKLIVGTDKDIFLAQSRTKRSAVIPNIGSIPSRIKGILNSTIRSSPGKKSEF -VRIACRYVKQS - ->A-BC-324-2017_3C.2a1_+_N121K_+_K92R_+_H311Q -QNSSMEIDSQLGNIQGQNKKLFVSRYNVPRTKNSNTGVTQNKSAIGSSSSRNTHLNYTAL -NTMNKEQFDKLIVGTDKDIFLAQSRTKRSAVIPNIGSIPSRIKGILNSTIRSSPGKKSEF -VRIACRYVKQS - ->A-QC-315-2017_3C.2a1_+_N121K_+_K92R_+_H311Q -QNSSIEIDSQLGNIQGQNKKLFVSRYNVPRTKNSNAGVTQNKSAIGSSSSRNTHLNYTAL -NTMNKEQFDKLIVGTDKDIFLAQSRTKRSAVIPNIGSIPSRIKGILNSTIRSSPGKKSEF -VRIACRYVKQS - ->A-ON-016-2018_3C.2a_+_N121K_+_S144K -QNSSIEIDSQLENIQGQNKKLFVSKYNVPRTKNSNTGVTQNKSAIRSKSSKNTHLNYTAL -NTMNNEQFDKLIVGTDKDIFLAQSRTKRSAVIPNIGSIPSRIKGILNSTIQSSPGKKSEF -VRIACRYVKHS - ->A-BC-325-2017_3C.2a_+_N121K_+_S144K -QNSSIEIDSQLENIQGQNKKLFVSKYNVPRTKNSNTGVTQNKSAIRSKSSKNTHLNYTAL -NTMNNEQFDKLIVGTDKDIFLAQSRTKRSAVIPNIGSIPSRIKGILNSTIQSSPGKKSEF -VRIACRYVKHS - ->A-ON-003-2018_3C.2a_+_N121K_+_S144K -QNSSIEIDSQLENIQGQNKKLFVSKYNVPRTKNSNTGVTQNKSAIRSKSSKNTHLNYTAL -NTMNNEQFDKLIVGTDKDIFLAQSRTKRSAVIPNIGSIPSRIKGILNSTIQSSPGKKSEF -VRIACRYVKHS - ->A-ON-309-2017_No_Match -QNSSIEIDSQLENIQGQNKKLFVSKYNVPRTNNSNTGVKQNTSAIKSSSSRNTHLNYKAL -NTMNNEQFDKLIVGTDKDIFLAQSKTKISAVIPNIGSIPSRIKGILNSTIQSSPGKKSEF -VRIACRYVKHS - ->A-BC-330-2017_No_Match -QNSSIEIDSQLENIQGQNKKLFVSKYNVPRTNNSNTGVKQNTSAIKSRSSRNTHLNYTAL -NTMNNEQFDKLIVGTDKDIFLAQSRTKRSAVIPNIGSIPSRIKGILNSTIQSSPGKKSEF -VRIACRYVKHS - ->A-AB-415-2017_3C.2a_+_T131K_+_R142K_+_R261Q -QNSSIEIDSQLENIQGQNKKLFVSRYNVPRTNNSNTGVKQNTSAIKSSSSRNTHLNYTAL -NTMNNEQFDKLIVGTDKDIFLAQSRTKRSAVIPNIGFIPSRIKGILNSTIQSSPGKKSEF -VRIACRYVKHS - ->A-AB-400-2017_3C.2a_+_T131K_+_R142K_+_R261Q -QNSSIEIDSQLENIQGQNKKLFVSRYNVPRTNNSNTGVKQNTSAIKSSSSRNTHLNYTAL -NTMNNEQFDKLIVGTDKDIFLAQSRTKRSAVIPNIGSIPSRIKGILNSTIQSSPGKKSEF -VRIACRYVKHS - ->A-AB-416-2017_3C.2a_+_T131K_+_R142K_+_R261Q -QNSSIEIDSQLENIQGQNKKLFVSRYNVPRTNNSNTGVKQNTSAIKSSSSRNTHLNYTAL -NTMNNEQFDKLIVGTDKDIFLAQSRTKRSAVIPNIGSIPSRIKGILNSTIQSSPGKKSEF -VRIACRYVKHS - ->A-QC-316-2017_3C.2a_+_T131K_+_R142K_+_R261Q -QNSSIEIDSQLENIQGQNKKLFVSRYNVPRTNNSNTGVKQNTSAIKSSSSRNTHLNYTAL -NTMNNEQFDKLIVGTDKDIFLAQSRTKRSAVIPNIGSIPSRIKGILNSTIQSSPGKKSEF -VRIACRYVKHS diff -r 1dc65ec11a40 -r 0d3dad155413 tools/antigenic_site_extraction/antigenic_site_extraction.py --- a/tools/antigenic_site_extraction/antigenic_site_extraction.py Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,95 +0,0 @@ -#!/usr/bin/env python - -'''Accepts fasta files of amino acid sequence, extracts specific amino acids (defined in a csv index array), -and outputs extracted sequences - representing flu antigenic sites - to fasta (default) or csv.''' - -'''Author: Diane Eisler, Molecular Microbiology & Genomics, BCCDC Public Health Laboratory,Sept 2017''' - -import sys,string,os, time, Bio, argparse -from Bio import Seq, SeqIO, SeqUtils, Alphabet, SeqRecord -from Bio.SeqRecord import SeqRecord -from Bio.Alphabet import IUPAC -from Bio.Seq import Seq - -#parse command line arguments -parser = argparse.ArgumentParser() -parser.add_argument("-c","--csv",help="export extracted antigenic sites to csv file",action="store_true") -parser.add_argument("inFileHandle1") #batch fasta file with sequences to be parsed -parser.add_argument("inFileHandle2") # .csv file containing positions of aa's to extract -parser.add_argument("outFileHandle") #user-specified name for output file of extracted aa seq's -args = parser.parse_args() - -#inFileHandle1 = sys.argv[1] #batch fasta file with sequences to be parsed -#inFileHandle2 = sys.argv[2] # .csv file containing positions of aa's to extract -#outFileHandle = sys.argv[3] #user-specified name for output file of extracted aa seq's - -outFile= open(args.outFileHandle,'w') #open a writable, appendable output file -localtime = time.asctime(time.localtime(time.time())) #date and time of analysis -seqList = [] #list of aa sequence objects to parse for oligo sequences -indexArray = [] # .csv list of aa's corresponding to antigenic site positions -extractedSeqList = [] #list of extracted antigenic sites extracted from seqList - -def extract_aa_from_sequence(record): - """Extract specific amino acids from SeqRecord, create new SeqRecord and append to list.""" - original_sequence = str(record.seq) #pull out the SeqRecord's Seq object and ToString it - new_sequence = "" #set variable to empty - new_id = record.id #store the same sequence id as the original sequence - #iterate over each position in index array, extract corresponding aa and add to string - for pos in indexArray: - char = original_sequence[pos-1] #aa positions must be zero indexed - new_sequence = new_sequence + char - rec = SeqRecord(Seq(new_sequence,IUPAC.protein), id = record.id, name = "", description = "") - extractedSeqList.append(rec) #add new SeqRecord object to the list - -with open (args.inFileHandle2,'r') as inFile2: - '''Open csv file containing amino acid positions to extract and add to list.''' - #read items separated by comma's to position list - positionList = "" - for line in inFile2: - #remove whitespace from the end of each line - strippedLine = line.rstrip() - #split the line at commas and assigned the returned list as indexArray - positionList = strippedLine.split(',') - #Convert string items in positionList from strings to int and add to indexArray - for item in positionList: - indexArray.append(int(item)) - #print number of amino acids to extract and array to console as user check - print "Amino Acid positions to extract: %i " %(len(indexArray)) - print indexArray - -with open(args.inFileHandle1,'r') as inFile: - '''Open fasta of amino acid sequences to parse, uppercase and add to protein Sequence list.''' - #read in Sequences from fasta file, uppercase and add to seqList - for record in SeqIO.parse(inFile, "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 "\n%i flu sequences will be extracted for antigenic sites..." % len(seqList) - #parse each target sequence object - for record in seqList: - extract_aa_from_sequence(record) - -#print original and extracted sequence -for x in range(0, len(seqList)): - print "Original %s: %i amino acids,\tExtracted: %i" % (seqList[x].id,len(seqList[x]),len(extractedSeqList[x])) - -#determine if output format is fasta (default) or csv -if args.csv: - #write csv file of extracted antigenic sits - for record in extractedSeqList: - #outFile.write(record.id),"," - name_part = (record.id).rstrip() + ',' - sequence = str(record.seq).strip() - csv_seq = ",".join(sequence) - comma_separated_sequence = name_part + csv_seq + "\n" - print comma_separated_sequence - outFile.write(comma_separated_sequence) -else: - #write fasta file of extracted antigenic sites - SeqIO.write(extractedSeqList,outFile,"fasta") - -print("\n%i Sequences Extracted to Output file: %s" % ((len(extractedSeqList),args.outFileHandle))) -inFile.close() -inFile2.close() -outFile.close() - diff -r 1dc65ec11a40 -r 0d3dad155413 tools/antigenic_site_extraction/antigenic_site_extraction.xml --- a/tools/antigenic_site_extraction/antigenic_site_extraction.xml Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ - - - biopython - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 1dc65ec11a40 -r 0d3dad155413 tools/antigenic_site_extraction/test-data/14_H3_aa_seqs_aligned.fasta --- a/tools/antigenic_site_extraction/test-data/14_H3_aa_seqs_aligned.fasta Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ ->Seq1(3C.2a.3) -QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVKQNGTSSACIRKSSSSFFSRLNWLTHLNYTYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIQSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKHSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHNVYRDEALNNRFQIKGVELKSGYKDW ->Seq2(3C.2a.4) -QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFKDESFNWTGVTQNGTSSACIRRSKSSFFSRLNWLTHLNYTYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNIIAPRGYFKIRNGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKHSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHNVYRDEALNNRFQIKGVELKSGYKDW ->Seq3(3C.2a.3) -QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICNSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVKQNGTSSACIRKSSSSFFSRLNWLTHLNYTYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQISLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIQSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKHSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHNVYRDEALNNRFQIKGVELKSGYKDW ->Seq4(3C.2a.2) -QKIPGNDNSMATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVTQNGTSSACMRRSSSSFFSRLNWLTHLNYTYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAKSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIQSGKSSIMRSNAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKHSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMMDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYDAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHNVYRDEALNNRFHIKGVELKSGYKDW ->Seq5(3C.2a.3) -QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVKQNGTSSACIRKSSSSFFSRLNWLTHLNYTYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQISLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIQSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKHSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHNVYRDEALNNRFQIKGVELKSGYKDW ->Seq5(3C.2a.4) -QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASFGTLEFKNESFNWTGVTQNGTSSACIRRSKSSFFSRLNWLTHLNYTYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGYRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKHSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHNVYRDEALNNRFQIKGVELKSGYKDW ->Seq6(3C.3a) -QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERNKAYSSCYPYDVPDYASLRSLVASSGTLEFNNESFNWAGVTQNGTSSSCIRGSKSSFFSRLNWLTHLNSKYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQISLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKQSTLKLATGMRNVPERQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHNVYRDEALNNRFQIKGVELKSGYKDW ->Seq7(3C.3a) -QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERNKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWAGVTQNGTSSSCIRGSKSSFFSRLNWLTHLNSKYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQISLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKQSTLKLATGMRNVPERQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHSVYRDEALNNRFQIKGVELKSGYKDW ->Seq8(3C.2a.1) -QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFKNESFNWTGVTQNGKSSACIRRSSSSFFSRLNWLTHLNYTYPALNVTMPNKEQFDKLYIWGVHHPGTDKDQIFLYAQPSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKHSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRVQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIESIRNETYDHNVYRDEALNNRFQIKGVELKSGYKDW ->Clade_3C.2a_A/Hong_Kong/5738/2014 -QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVTQNGTSSACIRRSSSSFFSRLNWLTHLNYTYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKH?TLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHNVYRDEALNNRFQIKGVELKSGYKDW ->Clade_3C.3a_A/Switzerland/9715293/2013 -QKLPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWAGVTQNGTSSSCIRGSNSSFFSRLNWLTHLNSKYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKQSTLKLATGMRNVPERQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIKGVELKSGYKDW ->Seq9(3C.2a.1) -QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVTQNGTSSACIRRSSSSFFSRLNWLTHLNYTYPALNVTMPNKEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKHSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRVQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNETYDHNVYRDEALNNRFQIKGVELKSGYKDW ->Seq10(3C.2a.1) -QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFKNESFNWTGVTQNGKSSACIRRSSSSFFSRLNWLTHLNYTYPALNVTMPNKEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKHSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRVQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIESIRNETYDHNVYRDEALNNRFQIKGVELKSGYKDW ->Clade_3C.2a.1_A/Bolzano/7/2016 -QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVTQNGTSSACIRRSSSSFFSRLNWLTHLNYTYPALNVTMPNKEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKHSTLKLATGMRNVPEKQARGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRVQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNETYDHNVYRDEALNNRFQIKGVELKSGYKDW diff -r 1dc65ec11a40 -r 0d3dad155413 tools/antigenic_site_extraction/test-data/FluA_H3_antigenic_aa_indices.csv --- a/tools/antigenic_site_extraction/test-data/FluA_H3_antigenic_aa_indices.csv Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -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 1dc65ec11a40 -r 0d3dad155413 tools/assign_clades/assign_clades.py --- a/tools/assign_clades/assign_clades.py Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,133 +0,0 @@ -#!/usr/bin/env python - -'''Accepts fasta files containing amino acid sequence, reading them in as -amino acid sequence objects. Reads influenza clade defintions (i.e. amino -acids at certain positions) from .csv file into dictionary structure. Searches -each of the amino acid sequence objects for a list of matching clades, assigns -the most 'evolved' (i.e. child as opposed to parent clade) to the sequence. Appends -"_cladename" to the Sequence name and generates a fasta file of original sequences with -modified names.''' - -'''Author: Diane Eisler, Molecular Microbiology & Genomics, BCCDC Public Health Laboratory, Oct 2017''' - -import sys,string,os, time, Bio -from Bio import Seq, SeqIO, SeqUtils, Alphabet, SeqRecord -from Bio.SeqRecord import SeqRecord -from Bio.Alphabet import IUPAC -from Bio.Seq import Seq - -localtime = time.asctime(time.localtime(time.time())) #date and time of analysis -inFileHandle1 = sys.argv[1] #batch fasta file with sequences to be parsed -inFileHandle2 = sys.argv[2] # .csv file containing clade definitions and "depth" -outFileHandle = sys.argv[3] #user-specified name for output file of aa seq's with clade suffixes -outFile= open(outFileHandle,'w') #open a writable, appendable output file -seqList = [] #list of aa sequence objects to parse for clade definitions -cladeList = [] #empty list to hold clade tuples i.e. ("3C.3a", 1 ,{"3":"I", "9":"V"..}) - -'''Searches record for required amino acids at defined positions. If found, assigns -clade name to sequence name by appending underscore and clade name to record id.''' -def call_clade(record): - print "---------------------------------------------------------------------" - print "Parsing %s for matching flu clade definitions..." % (record.id) - matchList = [] #empty list to hold clades that match 100% - #iterate over each tuple in the clade list - for clade in cladeList: - cladeName = clade[0] #temp variable for name - depth = clade[1] #temp variable for depth - sites = clade[2] #temp variable for aa def dictionary - shouldFind = len(sites) #number of sites that should match - found = 0 #a counter to hold matches to antigenic sites - #iterate over each position in sites dictionary - for pos, aa in sites.iteritems(): - #translate pos to corresponding index in target sequence - index = int(pos) - 1 - #if record at index has same amino acid as 'aa', increment 'found' - if record[index] == aa: - found += 1 - if (found == shouldFind): - #add the matching clade tuple to the list of matches - matchList.append(clade) - return matchList - -'''Compares depth level of clades in a list and returns the most granular one''' -def decide_clade_by_depth(matchList): - #empty variable for maximum depth encountered - max_depth = 0 - best_match_name = '' #variable to hold most granular clade - #for each matching clade, check depth of the corresponding tuple - for clade in matchList: - #if the current clade is 'deeper' than the one before it - if clade[1] > max_depth: - #store this depth - max_depth = clade[1] - #store name of the clade - best_match_name = clade[0] - return best_match_name - -'''opens the .csv file of clade definitions and clade "depth" ''' -with open (inFileHandle2, 'r') as clade_file: - #remove whitespace from the end of each line and split elements at commas - for line in clade_file: - #print "Current Line in File:" + line - sites={} #initialize a dictionary for clade - elementList = line.rstrip().split(',') - new_list = [] #start a new list to put non-empty strings into - #remove empty stings in list - for item in elementList: - if item != '': - new_list.append(item) - name = new_list.pop(0) #move 1st element to name field - depth = int(new_list.pop(0)) #move 2nd element to depth field - #read remaining pairs of non-null elements into clade def dictionary - for i in range(0, len(new_list), 2): - #move next 2 items from the list into the dict - pos = new_list[i] - aa = new_list[i + 1] - sites[pos] = aa - #add the clade info as a tuple to the cladeList[] - oneClade =(name, depth, sites) - cladeList.append(oneClade) - print "The List of Clades:" - for clade in cladeList: - print "Clade Name: %s Depth: %i Antigenic Sites: %i" % (clade[0], clade[1], len(clade[2])) - for pos, aa in clade[2].iteritems(): - print "Pos: %s\tAA: %s" % (pos,aa) - -'''opens readable input file of sequences to parse using filename from cmd line, - instantiates as AA Sequence objects, with ppercase sequences''' -with open(inFileHandle1,'r') as inFile: - #read in Sequences from fasta file, uppercase and add to seqList - for record in SeqIO.parse(inFile, "fasta", alphabet=IUPAC.protein): - record = record.upper() - seqList.append(record) #add Seq to list of Sequences - print "\n%i flu HA sequences will be compared to current clade definitions..." % len(seqList) - #parse each target sequence object - for record in seqList: - clade_call = '' #empty variale for final clade call on sequence - matchingCladeList = call_clade(record) #holds matching clade tuples - #if there is more than one clade match - if len(matchingCladeList) > 1: - #choose the most granular clade based on depth - clade_call = decide_clade_by_depth(matchingCladeList) - #if there is only one clade call - elif len(matchingCladeList) > 0: - clade = matchingCladeList[0] #take the first tuple in the list - clade_call = clade[0] #clade name is the first item in the tuple - #empty list return, no matches - else: - clade_call = "No_Match" - print clade_call - seq_name = record.id - mod_name = seq_name + "_" + clade_call - print "New Sequence Name: " + mod_name - record.id = mod_name - - -#output fasta file with clade calls appended to sequence names -SeqIO.write(seqList,outFile,"fasta") - -#print("\n%i Sequences Extracted to Output file: %s" % ((len(extractedSeqList),outFileHandle))) -inFile.close() -clade_file.close() -outFile.close() - diff -r 1dc65ec11a40 -r 0d3dad155413 tools/assign_clades/assign_clades.xml --- a/tools/assign_clades/assign_clades.xml Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,29 +0,0 @@ - - - biopython - - - - - - - - - - - - - - - - - - - - diff -r 1dc65ec11a40 -r 0d3dad155413 tools/assign_clades/test-data/clades.csv --- a/tools/assign_clades/test-data/clades.csv Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,15 +0,0 @@ -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_+_Q197K_+_R261Q,2,3,I,144,S,145,S,159,Y,160,T,197,K,225,D,261,Q,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_(w/o_N121K),3,3,I,144,S,145,S,159,Y,160,T,171,K,225,D,311,H,406,V,484,E,489,N,,,,,,,, -3C.2a1_+_N121K,4,3,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_+_R142G_+_I242V,4,3,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.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_+_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_+_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_+_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_+_R142G,4,3,I,142,G,144,S,145,S,159,Y,160,T,171,K,225,D,311,H,406,V,484,E,489,N,,,,,, -3C.2a1_+_S47T_+_G78S,4,3,I,47,T,78,S,144,S,145,S,159,Y,160,T,171,K,225,D,311,H,406,V,484,E,489,N,,,, -3C.3a,1,128,A,138,S,142,G,145,S,159,S,225,D,,,,,,,,,,,,,,,,,, diff -r 1dc65ec11a40 -r 0d3dad155413 tools/assign_clades/test-data/output.fa --- a/tools/assign_clades/test-data/output.fa Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ ->test_3C.3a test -QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILD -GENCTLIDALLGDPQCDGFQNKKWDLFVERNKAYSSCYPYDVPDYASLRSLVASSGTLEF -NNESFNWAGVTQNGTSSSCIRGSKSSFFSRLNWLTHLNSKYPALNVTMPNNEQFDKLYIW -GVHHPGTDKDQISLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPG -DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRI -TYGACPRYVKQSTLKLATGMRNVPERQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEG -RGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDL -WSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGS -IRNGTYDHNVYRDEALNNRFQIKGVELKSGYKDW diff -r 1dc65ec11a40 -r 0d3dad155413 tools/assign_clades/test-data/test_input.fasta --- a/tools/assign_clades/test-data/test_input.fasta Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ ->test -QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERNKAYSSCYPYDVPDYASLRSLVASSGTLEFNNESFNWAGVTQNGTSSSCIRGSKSSFFSRLNWLTHLNSKYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQISLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKQSTLKLATGMRNVPERQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHNVYRDEALNNRFQIKGVELKSGYKDW diff -r 1dc65ec11a40 -r 0d3dad155413 tools/change_fasta_deflines/change_fasta_deflines.py --- a/tools/change_fasta_deflines/change_fasta_deflines.py Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,62 +0,0 @@ -#!/usr/bin/env python -import sys, argparse -'''Accepts either csv (default) or tab-delimited files with old/new sequence names, creating a dictionary of -respective key:value pairs. Parses an input fasta file for 'old' names, replacing them with 'new' names, writing -renamed sequences to a fasta file. NOTE: use of tab-delim text file for renaming requires '-t' on cmd line.''' -#USAGE EXAMPLE 1: python change_fasta_def_lines.py csv_rename_file.csv fasta_2_rename.fasta renamedSequences.fasta -#USAGE EXAMPLE 2: python change_fasta_def_lines.py tab_delim_rename_file.txt -t fasta_2_rename.fasta renamedSequences.fasta - -'''Author: Diane Eisler, Molecular Microbiology & Genomics, BCCDC Public Health Laboratory,Sept 2017''' - -#parse command line arguments -parser = argparse.ArgumentParser() -parser.add_argument ("-t", "--tab_delim", help = "name fasta definition lines from tab-delim file", action = "store_true") -parser.add_argument("inFileHandle") #csv file with current fasta file names in column 1 and desired names in col 2 -parser.add_argument("inFileHandle2") #fasta file containing sequences requiring name replacement -parser.add_argument("outFileHandle") #user-specified output filename -args = parser.parse_args() - -#open a writable output file that will be over-written if it already exists -outfile= open(args.outFileHandle,'w') -dict = {} #dictionary to hold old_name:new_name key:value pairs -splitter = ',' #default char to split lines at -#determine if input naming file is csv (default) or tab delim text -if args.tab_delim: - splitter = '\t' #change splitter to tab if comd line args contain '-t' - -#create dictionary using key/value pairs from csv file of old/new names -with open(args.inFileHandle,'r') as inputFile: -#read in each line and split at comma into key:value pairs - for line in inputFile: - #remove whitespace from end of lines, split at comma, assigning to key:value pairs - line2 = line.rstrip() - splitLine = line2.split(splitter) - old_name = splitLine[0] - new_name = splitLine[1] - dict[old_name] = new_name - -#parse fasta deflines for 'old' names and, if found, replace with new names -with open(args.inFileHandle2,'r') as inputFile2: - for line in inputFile2: - #find the definition lines, remove trailing whitespace & '>' - if ">" in line: - originalDefline = line.rstrip().replace(">","",1) - #check for a match to any of the dict key - if dict.has_key(originalDefline): - #find the index of that item in the list - newDefline= dict[originalDefline] - #print("the new name"), newDefline - # print each item to make sure the right name is being entered - outfile.write(">" + newDefline + "\n") - else: - #write out the original defline sequence name - print ("Defline not in dictionary: "), originalDefline - outfile.write(">" + originalDefline + "\n") - else: - #in lines without ">", write out sequence as it was - seq = line.rstrip() - outfile.write(seq+"\n") - -inputFile.close() -inputFile2.close() -outfile.close() diff -r 1dc65ec11a40 -r 0d3dad155413 tools/change_fasta_deflines/change_fasta_deflines.xml --- a/tools/change_fasta_deflines/change_fasta_deflines.xml Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,39 +0,0 @@ - - - biopython - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 1dc65ec11a40 -r 0d3dad155413 tools/change_fasta_deflines/test-data/csv_rename_file.csv --- a/tools/change_fasta_deflines/test-data/csv_rename_file.csv Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -s1,sample_1 -s2,sample_2 -s3,sample_3 -s4,sample_4 -s5,sample_5 -s6,sample_6 -s7,sample_7 -s8,sample_8 -s9,sample_9 -s10,sample_10 diff -r 1dc65ec11a40 -r 0d3dad155413 tools/change_fasta_deflines/test-data/fasta_2_rename.fasta --- a/tools/change_fasta_deflines/test-data/fasta_2_rename.fasta Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ ->s1 -QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVKQNGTSSACIRKSSSSFFSRLNWLTHLNYTYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIQSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKHSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHNVYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVALLGFIMWACQKGNIRCNICI ->s2 -QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVKQNGTSSACIRKSSSSFFSRLNWLTHLNYTYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIQSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKHSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHNVYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVALLGFIMWACQKGNIRCNICI ->s3 -QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVKQNGTSSACIRKSSSSFFSRLNWLTHLNYTYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIQSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKHSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHNVYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVALLGFIMWACQKGNIRCNICI ->s4 -QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGGNCTLIDALLGDPQCDGFQNKKWDLFVERSRAYSNCYPYDVPDYASLRSLVASSGTLEFKNESFNWTGVTQNGTSSACIRGSSSSFFSRLNWLTHLNYTYPALNVTMPNKEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKQSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRVQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNETYDHNVYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCIALLGFIMWACQKGNIRCNICI ->s5 -QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVKQNGTSSACIRKSSSSFFSRLNWLTHLNYTYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIQSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKHSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHNVYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVALLGFIMWACQKGNIRCNICI ->s6 -QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVKQNGTSSACIRKSSSSFFSRLNWLTHLNYTYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIQSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKHSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHNVYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVALLGFIMWACQKGNIRCNICI ->s7 -QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVKQNGTSSACIRKSSSSFFSRLNWLTHLNYTYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIQSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKHSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHNVYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVALLGFIMWACQKGNIRCNICI ->s8 -QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVKQNGTSSACIRKSSSSFFSRLNWLTHLNYTYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIQSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKHSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHNVYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVALLGFIMWACQKGNIRCNICI ->s9 -QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVKQNGTSSACIRKSSSSFFSRLNWLTHLNYTYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIQSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKHSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHNVYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVALLGFIMWACQKGNIRCNICI ->s10 -QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSRAYSNCYPYDVPDYASLRSLVASSGTLEFKNESFNWTGVTQNGNSSACIRRSSSSFFSRLNWLTHLNYTYPALNVTMPNKEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKQSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRVQDLEKYIEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNETYDHNVYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVALLGFIMWACQKGNIRCNICI diff -r 1dc65ec11a40 -r 0d3dad155413 tools/change_fasta_deflines/test-data/tab_delim_rename_file.txt --- a/tools/change_fasta_deflines/test-data/tab_delim_rename_file.txt Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -s1 sample_1 -s2 sample_2 -s3 sample_3 -s4 sample_4 -s5 sample_5 -s6 sample_6 -s7 sample_7 -s8 sample_8 -s9 sample_9 -s10 sample_10 diff -r 1dc65ec11a40 -r 0d3dad155413 tools/linelisting/linelisting.py --- a/tools/linelisting/linelisting.py Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,219 +0,0 @@ -#!/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 1dc65ec11a40 -r 0d3dad155413 tools/linelisting/linelisting.xml --- a/tools/linelisting/linelisting.xml Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,35 +0,0 @@ - - - biopython - - - - - - - - - - - - - - - - - - - - - - - - diff -r 1dc65ec11a40 -r 0d3dad155413 tools/linelisting/test-data/FluA_H3_antigenic_aa_indices.csv --- a/tools/linelisting/test-data/FluA_H3_antigenic_aa_indices.csv Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -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 1dc65ec11a40 -r 0d3dad155413 tools/linelisting/test-data/Flu_Clade_Definitions_H3_20171121.csv --- a/tools/linelisting/test-data/Flu_Clade_Definitions_H3_20171121.csv Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -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 1dc65ec11a40 -r 0d3dad155413 tools/linelisting/test-data/MAP_3C.2a_A_Hong_Kong_4801_2014_X-263B_EGG.fasta --- a/tools/linelisting/test-data/MAP_3C.2a_A_Hong_Kong_4801_2014_X-263B_EGG.fasta Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->Clade_3C.2a_A/Hong_Kong/4801/2014_X-263B_EGG -QNSSIEIDSQLENIQGQNKKLFVSKYSVPRTNNSNTGVTQNTSAIRSSSSRNTHLNYKAL -NTMNNEQFDKLIVGTDKDIFPAQSRXKRSAVIPNIGSIPSRIKGILNSTIRSSPGKKSEF -VRIACRYVKHS diff -r 1dc65ec11a40 -r 0d3dad155413 tools/linelisting/test-data/fluA_H3_clade_assigned_antigenic_sites_extracted.fasta --- a/tools/linelisting/test-data/fluA_H3_clade_assigned_antigenic_sites_extracted.fasta Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,94 +0,0 @@ ->A-ON-314-2017_3C.3a -QNSSIEIDSQLENIQGQNKKLFVNKYNVPRTNNSNAGVTQNTSSIGSKSSRNTHLNSKAL -NTMNNEQFDKLIVGTDKDISLAQSRTKRSAVIPNIGSIPSRIKGILNSTIRSSPGKKSEF -VRIACRYVKQS - ->A-AB-399-2017_3C.2a_+_N31S_+_D53N_+_R142G_+_S144R_+_N171K_+_I192T_+_Q197H -QNSSIEINSQLENIQGQNKKLFVSKYNVPRTNNSNTGVTQNTSAIGSRSSRNTHLNYTAL -NTMNKEQFDKLIVGTDKDTFLAHSRTKRSAVIPNIGSIPSRIKGLLNSTIRSSPGKKSEF -VRIACRYVKHS - ->A-QC-303-2017_3C.2a_+_N31S_+_D53N_+_R142G_+_S144R_+_N171K_+_I192T_+_Q197H -QNSSIEINSQLENIQGQNKKLFVSKYNVPRTNNSNTGVTQNTSAIGSRSSRNTHLNYTAL -NTMNKEQFDKLIVGTDKDTFLAHSRTKRSAVIPNIGSIPSRIKGLLNSTIRSSPGKKSEF -VRIACRYVKHS - ->A-AB-319-2017_3C.2a_+_N31S_+_D53N_+_R142G_+_S144R_+_N171K_+_I192T_+_Q197H -QNSSIEINSQLENIQGQNKKLFVSKYNVPRTNNSNTGVTQNTSAIGSRSSRNTHLNYTAL -NTMNKEQFDKLIVGTDKDTFLAHSRTKRSAVIPNIGSIPSRIKGLLNSTIRSSPGKKSEF -VRIACRYVKHS - ->A-AB-308-2017_3C.2a1_+_N121K_+_T135K -QNSSIEIDSQLENIQDQNKKLFVSKHNVPRTKDSNTGVTQNKSAIRSSSSRNTHLNYTAL -NTMNKEQFDKLIIGTDKDIFLAQSRTKRSAVIPNIGSIPSRIKGILNSTIRSSPGKKSEF -VRIACRYVKHS - ->A-AB-341-2017_3C.2a1_+_N121K_+_T135K -QNSSIEIDSQLENIQDQNKKLFVSKHNVPRTKDSNTGVTQNKSAIRSSSSRNTHLNYTAL -NTMNKEQFDKLIIGTDKDIFLAQSRTKRSAVIPNIGSIPSRIKGILNSTIRSSPGKKSEF -VRIACRYVKHS - ->A-BC-024-2018_3C.2a1_+_N121K_+_T135K -QNSSIEIDSQLENIQDQNKKLFVSKHNVPRTKNSNTGVTQNKSAIRSSSSRNTHLNYTAL -NTMNKEQFDKLIIGTDKDIFLAQSRTKRSAVIPNIGSIPSRIKGILNSTIRSSPGKKSEF -VRIACRYVKHS - ->A-QC-309-2017_3C.2a1_+_N121K_+_K92R_+_H311Q -QNSSIEIDSQLGNIQDQNKKLFVSRYNVPRTKDSNTGVTQNKSAIGSSSSRNTHLNYTAL -NTMNKEQFDKLIVGTDKDIFLAQSRTKRSAVIPNIGSIPSRIKGILNSTIRSSPGKKSEF -VRIACRYVKQS - ->A-BC-324-2017_3C.2a1_+_N121K_+_K92R_+_H311Q -QNSSMEIDSQLGNIQGQNKKLFVSRYNVPRTKNSNTGVTQNKSAIGSSSSRNTHLNYTAL -NTMNKEQFDKLIVGTDKDIFLAQSRTKRSAVIPNIGSIPSRIKGILNSTIRSSPGKKSEF -VRIACRYVKQS - ->A-QC-315-2017_3C.2a1_+_N121K_+_K92R_+_H311Q -QNSSIEIDSQLGNIQGQNKKLFVSRYNVPRTKNSNAGVTQNKSAIGSSSSRNTHLNYTAL -NTMNKEQFDKLIVGTDKDIFLAQSRTKRSAVIPNIGSIPSRIKGILNSTIRSSPGKKSEF -VRIACRYVKQS - ->A-ON-016-2018_3C.2a_+_N121K_+_S144K -QNSSIEIDSQLENIQGQNKKLFVSKYNVPRTKNSNTGVTQNKSAIRSKSSKNTHLNYTAL -NTMNNEQFDKLIVGTDKDIFLAQSRTKRSAVIPNIGSIPSRIKGILNSTIQSSPGKKSEF -VRIACRYVKHS - ->A-BC-325-2017_3C.2a_+_N121K_+_S144K -QNSSIEIDSQLENIQGQNKKLFVSKYNVPRTKNSNTGVTQNKSAIRSKSSKNTHLNYTAL -NTMNNEQFDKLIVGTDKDIFLAQSRTKRSAVIPNIGSIPSRIKGILNSTIQSSPGKKSEF -VRIACRYVKHS - ->A-ON-003-2018_3C.2a_+_N121K_+_S144K -QNSSIEIDSQLENIQGQNKKLFVSKYNVPRTKNSNTGVTQNKSAIRSKSSKNTHLNYTAL -NTMNNEQFDKLIVGTDKDIFLAQSRTKRSAVIPNIGSIPSRIKGILNSTIQSSPGKKSEF -VRIACRYVKHS - ->A-ON-309-2017_No_Match -QNSSIEIDSQLENIQGQNKKLFVSKYNVPRTNNSNTGVKQNTSAIKSSSSRNTHLNYKAL -NTMNNEQFDKLIVGTDKDIFLAQSKTKISAVIPNIGSIPSRIKGILNSTIQSSPGKKSEF -VRIACRYVKHS - ->A-BC-330-2017_No_Match -QNSSIEIDSQLENIQGQNKKLFVSKYNVPRTNNSNTGVKQNTSAIKSRSSRNTHLNYTAL -NTMNNEQFDKLIVGTDKDIFLAQSRTKRSAVIPNIGSIPSRIKGILNSTIQSSPGKKSEF -VRIACRYVKHS - ->A-AB-415-2017_3C.2a_+_T131K_+_R142K_+_R261Q -QNSSIEIDSQLENIQGQNKKLFVSRYNVPRTNNSNTGVKQNTSAIKSSSSRNTHLNYTAL -NTMNNEQFDKLIVGTDKDIFLAQSRTKRSAVIPNIGFIPSRIKGILNSTIQSSPGKKSEF -VRIACRYVKHS - ->A-AB-400-2017_3C.2a_+_T131K_+_R142K_+_R261Q -QNSSIEIDSQLENIQGQNKKLFVSRYNVPRTNNSNTGVKQNTSAIKSSSSRNTHLNYTAL -NTMNNEQFDKLIVGTDKDIFLAQSRTKRSAVIPNIGSIPSRIKGILNSTIQSSPGKKSEF -VRIACRYVKHS - ->A-AB-416-2017_3C.2a_+_T131K_+_R142K_+_R261Q -QNSSIEIDSQLENIQGQNKKLFVSRYNVPRTNNSNTGVKQNTSAIKSSSSRNTHLNYTAL -NTMNNEQFDKLIVGTDKDIFLAQSRTKRSAVIPNIGSIPSRIKGILNSTIQSSPGKKSEF -VRIACRYVKHS - ->A-QC-316-2017_3C.2a_+_T131K_+_R142K_+_R261Q -QNSSIEIDSQLENIQGQNKKLFVSRYNVPRTNNSNTGVKQNTSAIKSSSSRNTHLNYTAL -NTMNNEQFDKLIVGTDKDIFLAQSRTKRSAVIPNIGSIPSRIKGILNSTIQSSPGKKSEF -VRIACRYVKHS diff -r 1dc65ec11a40 -r 0d3dad155413 tools/reformat_usearch_collapsed_fasta/reformat_usearch_collapsed_fasta.py --- a/tools/reformat_usearch_collapsed_fasta/reformat_usearch_collapsed_fasta.py Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,42 +0,0 @@ -#!/usr/bin/env python -import sys, re - -'''Accepts a sequence-collapsed fasta output from USEARCH (drive5) software and reformats the fasta -definition lines by replacing occurences of ';size=N;' with '_xN' and writing output to fasta -(N = number of identical sequences represented by the collapsed sequence). If N is not greater -than 1 (i.e. only 1 sample with that sequence), replaces ';size=N;' with ''. For example, -'>sequence_A;size=2;' is replaced with '>sequence_A_x2', whereas '>sequence_B;size=1;' is -replaced with 'sequence_B'. -#USAGE EXAMPLE: python reformat_usearch_collapsed_fasta.py usearch_collapsed_sequences.fasta output.fasta - -Author: Diane Eisler, Molecular Microbiology & Genomics, BCCDC Public Health Laboratory,Feb 2018''' - -inFileHandle = sys.argv[1] #input fasta filename -outFileHandle = sys.argv[2] #output fasta filename -outFile = open(outFileHandle,'w') #open a writable output file - -separator = "_x" #the string separating sequence name from number of sequences, N -regex = re.compile(";size=[0-9]{0,};") #regex snippet from debuggex - -#parse fasta definition lines for pattern matching regex -with open(inFileHandle,'r') as inFile: - for line in inFile: - if ">" in line: - #look for regex pattern in fasta definition line - matchArray = regex.findall(line) - if len(matchArray) > 0: #replace the matching substring - substringToReplace = matchArray[0] - endIndex = len(substringToReplace) - digits = substringToReplace[6:endIndex -1] #digits between ';size=' and ';' - if int(digits) > 1: #show number of sequences if greater than 1 - replacementString = separator + digits - else: - replacementString = "" #otherwise, just display sequence name - newDefline = line.rstrip().replace(substringToReplace, replacementString) - outFile.write(newDefline + "\n") - else: #in lines without ">", write out sequence unmodified - seq = line.rstrip() - outFile.write(seq+"\n") - -inFile.close() -outFile.close() diff -r 1dc65ec11a40 -r 0d3dad155413 tools/reformat_usearch_collapsed_fasta/reformat_usearch_collapsed_fasta.xml --- a/tools/reformat_usearch_collapsed_fasta/reformat_usearch_collapsed_fasta.xml Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ - - - biopython - - - - - - - - - - - - - - - - - - - - - - diff -r 1dc65ec11a40 -r 0d3dad155413 tools/reformat_usearch_collapsed_fasta/test-data/10_usearch_collapsed_sequences.fasta --- a/tools/reformat_usearch_collapsed_fasta/test-data/10_usearch_collapsed_sequences.fasta Wed Jan 09 15:33:32 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,210 +0,0 @@ ->SampleA;size=40; -CAAAAAATTCCTGGAAATGACAATAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAATGGAACGATAGTGAA -AACAATCACAAATGACCGAATTGAAGTTACTAATGCTACTGAGTTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACA -GTCCTCATCAGATCCTTGATGGAGAGAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTTCAA -AATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTC -CCTTAGGTCACTAGTTGCCTCATCTGGCACACTGGAGTTTAAAAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACG -GAACAAGTTCTGCTTGCATAAGGGGATCTAGTAGTAGTTTCTTTAGTAGATTAAATTGGTTGACCCACTTAAACTACACA -TATCCAGCATTGAACGTGACTATGCCAAACAAGGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTAC -GGACAAGGACCAAATCTTCCTGTATGCTCAATCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAA -TCCCAAATATCGGATCTAGACCCAGAATAAGGGATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGA -GACGTACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAAT -AATGAGATCAGATGCACCCATTGGCAAATGCAAGTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCAT -TCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCATAGCACTCTGAAATTGGCAACAGGAATG -CGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGT -GGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAA -TCGATCAAATCAATGGGAAGCTGAATCGGTTGATCGGAAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCA -GAAGTAGAAGGAAGAGTTCAAGACCTTGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCT -TCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGC -AACTGAGGGAAAATGCTGAGGATATGGGAAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGAATCA -ATAAGAAATGAAACTTATGACCACAATGTGTACAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCT -GAAGTCAGGGTACAAAGATTGG ->SampleB;size=24; -CAAAAAATTCCTGGAAATGACAATAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAA -AACAATCACAAATGACCGAATTGAAGTTACTAATGCTACTGAGTTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACA -GTCCTCATCAGATCCTTGATGGAGAGAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTTCAA -AATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTC -CCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAAAAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACG -GAACAAGTTCTGCTTGCATAAGGGGATCTAGTAGTAGTTTCTTTAGTAGATTAAATTGGTTGACCCACTTAAACTACACA -TATCCAGCATTGAACGTGACTATGCCAAACAAGGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTAC -GGACAAGGACCAAATCTTCCTGTATGCTCAATCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAA -TCCCAAATATCGGATCTAGACCCAGAATAAGGGATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGA -GACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAAT -AATGAGATCAGATGCACCCATTGGCAAATGCAAGTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCAT -TCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCATAGCACTCTGAAATTGGCAACAGGAATG -CGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGT -GGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAA -TCGATCAAATCAATGGGAAGCTGAATCGGTTGATCGGAAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCA -GAAGTAGAAGGAAGAGTTCAAGACCTTGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCT -TCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGC -AACTGAGGGAAAATGCTGAGGATATGGGAAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCA -ATAAGAAATGAAACTTATGACCACAATGTGTACAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCT -GAAGTCAGGGTACAAAGATTGG ->SampleC;size=22; -CAAAAAATTCCTGGAAATGACAATAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAA -AACAATCACAAATGACCGAATTGAAGTTACTAATGCTACTGAGTTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACA -GTCCTCATCAGGTCCTTGATGGAGAGAACTGCACACTAATAGATGCTCTATTGGGGGACCCTCAGTGTGACGGCTTTCAA -AATAAGAAATGGGACCTTTTTGTTGAACGAAGCAGAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTC -CCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAAAAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACG -GAACAAGTTCTGCTTGCATAAGGAGATCTAGTAGTAGTTTCTTTAGTAGATTAAATTGGTTGACCCACTTAAACTACACA -TATCCAGCACTGAACGTGACTATGCCAAACAAGGAACAATTTGACAAATTGTACATTTGGGGGGTCCACCACCCGGGTAC -GGACAAGGACCAAATCTTCCTGTATGCTCGATCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAA -TCCCAAATATCGGATCTAGACCCAGAATAAGGGATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGA -GACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAAT -AATGAGATCAGATGCACCCATTGGCAAATGCAAATCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCAT -TCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAGCACTCTGAAATTGGCAACAGGAATG -CGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGT -GGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAA -TCGATCAAATCAATGGGAAGCTGAATCGATTGATCGGAAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCA -GAAGTAGAAGGAAGAGTTCAAGACCTTGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCT -TCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGC -AACTGAGGGAAAATGCTGAGGATATGGGAAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCA -ATAAGAAATGAAACTTATGACCACAATGTGTACAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCT -GAAGTCAGGGTACAAAGATTGG ->SampleD;size=13; -CAAAAAATTCCTGGAAATGACAATAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAATGGAACGATAGTGAA -AACAATCACAAATGACCGAATTGAAGTTACTAATGCTACTGAGTTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACA -GTCCTCATCAGATCCTTGATGGAGAGAACTGCACACTAATTGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTTCAA -AATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTC -CCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAAAAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACG -GAAAAAGTTCTGCTTGCATAAGGAGATCTAGTAGTAGTTTCTTTAGTAGATTAAATTGGTTGACCCACTTAAACTACACA -TATCCAGCATTGAACGTGAGTATGCCAAACAAGGAACAATTTGACAAATTGTACATTTGGGGGGTTCATCACCCGGGTAC -GGACAAGGACCAAATCTTCCTGTATGCTCAATCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAA -TCCCAAATATCGGATCTAGACCCAGAATAAGGGATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGA -GACATACTTTTGATTAACAGCACAGGAAATCTAATTGCTCCTAGGGGCTACTTCAAAATACGAAGTGGGAAAAGCTCAAT -AATGAGATCAGATGCACCCATTGGCAAATGCAAGTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCAT -TCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCATAGCACTCTGAAATTGGCAACAGGAATG -CGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGT -GGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGGAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAA -TCGATCAAATCAATGGGAAGCTGAATCGGTTGATCGGAAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCA -GAAGTAGAAGGAAGAGTTCAAGACCTTGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCT -TCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGC -AACTGAGGGAAAATGCTGAGGATATGGGAAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGAATCA -ATAAGAAATGAAACTTATGACCACAATGTGTACAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCT -GAAGTCAGGGTACAAAGATTGG ->SampleE;size=9; -CAAAAAATTCCTGGAAATGACAATAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAATGGAACGATAGTGAA -AACAATCACAAATGACCGAATTGAAGTTACTAATGCTACTGAGTTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACA -GTCCTCATCAGATCCTTGATGGAGAGAACTGCACACTAATTGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTTCAA -AATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTC -CCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAAAAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAATG -GAAAAAGTTCTGCTTGCATAAGGAGATCTAGTAGTAGTTTCTTTAGTAGATTAAATTGGTTGACCCACTTAAACTACACA -TATCCAGCATTGAACGTGACTATGCCAAACAAGGAACAATTTGACAAATTGTACATTTGGGGGGTTCATCACCCGGGTAC -GGACAAGGACCAAATCTTCCTGTATGCTCAATCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAA -TCCCAAATATCGGATCTAGACCCAGAATAAGGGATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGA -GACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAAT -AATGAGATCAGATGCACCCATTGGCAAATGCAAGTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCAT -TCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCATAGCACTCTGAAATTGGCAACAGGAATG -CGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGT -GGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAA -TCGATCAAATCAATGGGAAGCTGAATCGGTTGATCGGAAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCA -GAAGTAGAAGGAAGAGTTCAAGACCTTGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCT -TCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGC -AACTGAGGGAAAATGCTGAGGATATGGGAAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGAATCA -ATAAGAAATGAAACTTATGACCACAATGTGTACAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCT -GAAGTCAGGGTACAAAGATTGG ->SampleF;size=8; -CAAAAAATTCCTGGAAATGACAATAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAATGGAACGATAGTGAA -AACAATCACAAATGACCGAATTGAAGTTACTAATGCTACTGAGTTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACA -GTCCTCATCAGATCCTTGATGGAGAGAACTGCACACTAATTGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTTCAA -AATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAGCTGTTACCCTTATGATGTGCCGGATTATGCCTC -CCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAAAAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACG -GAAAAAGTTCTGCTTGCATAAGGAGATCTAGTAGTAGTTTCTTTAGTAGATTAAATTGGTTAACCCACTTAAACTACACA -TATCCAGCATTGAACGTGACTATGCCAAACAAGGAACAATTTGACAAATTGTACATTTGGGGGGTTCATCACCCGGGTAC -GGACAAGGACCAAATCTTCCTGTATGCTCAATCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAA -TCCCAAATATCGGATCTAGACCCAGAATAAGGGATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGA -GACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAAT -AATGAGATCAGATGCACCCATTGGCAAATGCAAGTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCAT -TCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCATAGCACTCTGAAATTGGCAACAGGAATG -CGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGT -GGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAA -TCGATCAAATCAATGGGAAGCTGAATCGGTTGATCGGAAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCA -GAAGTAGAAGGAAGAGTTCAAGACCTTGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCT -TCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGC -AACTGAGGGAAAATGCTGAGGATATGGGAAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGAATCA -ATAAGAAATGAAACTTATGACCACAATGTGTACAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCT -GAAGTCAGGGTACAAAGATTGG ->SampleG;size=8; -CAAAAAATTCCTGGAAATGACAATAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAA -AACAATCACAAATGACCGAATTGAAGTTACTAATGCTACTGAGTTGGTTCAGAATTCCTCAATAGGTGAAATATGCAACA -GTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTTCAA -AATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTC -CCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCAAACAAAACG -GAACAAGTTCTGCTTGTATAAGGAAATCTAGTAGTAGTTTCTTTAGTAGATTAAATTGGTTGACCCACTTAAACTACACA -TATCCAGCATTGAACGTGACTATGCCAAACAATGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTAC -GGACAAGGACCAAATCTCCCTGTATGCTCAATCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAA -TCCCAAATATCGGATCCAGACCCAGAATAAGGGATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGA -GACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACAAAGTGGGAAAAGCTCAAT -AATGAGATCAGATGCACCCATTGGCAAATGCAAGTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCAT -TCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCATAGCACTCTGAAATTGGCAACAGGAATG -CGAAATGTACCAGAGAAACAAACTAGGGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGT -GGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGGGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAA -TCGATCAAATCAATGGGAAGCTGAATCGGTTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCA -GAAGTAGAAGGAAGAATTCAGGACCTTGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCT -TCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGC -AACTGAGGGAAAATGCTGAGGATATGGGAAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGTTCA -ATAAGAAATGGAACTTATGACCACAATGTGTACAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAACT -GAAGTCAGGGTACAAAGATTGG ->SampleH;size=7; -CAAAAAATTCCTGGAAATGACAATAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAA -AACAATCACAAATGACCGAATTGAAGTTACTAATGCTACTGAGTTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACA -GTCCTCATCAGATCCTTGATGGAGAGAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTTCAA -AATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTC -CCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAAAAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACG -GAACAAGTTCTGCTTGCATAAGGGGATCTAGTAGTAGTTTCTTTAGTAGATTAAATTGGTTGACCCACTTAAACTACACA -TATCCAGCATTGAACGTGACTATGCCAAACAAGGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTAC -GGACAAGGACCAAATCTTCCTGTATGCTCAATCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAA -TCCCAAATATCGGATCTAGACCCAGAATAAGGGATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGA -GACATACTTTTGATTAACAGCACGGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAAT -AATGAGATCAGATGCACCCATTGGCAAATGCAAGTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCAT -TCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCATAGCACTCTGAAATTGGCAACAGGAATG -CGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGT -GGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACGCAGGCAGCAA -TCGATCAAATCAATGGGAAGCTGAATCGGTTGATCGGAAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCA -GAAGTAGAAGGAAGAGTTCAAGACCTTGAGAAATATGTTGAGGACACTAAAATAGATCTTTGGTCATACAACGCGGAGCT -TCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGC -AACTGAGGGAAAATGCTGAGGATATGGGAAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCA -ATAAGAAATGAAACTTATGACCACAATGTGTACAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCT -GAAGTCAGGGTACAAAGATTGG ->SampleI;size=6; -CAAAAAATTCCTGGAAATGACAATAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAATGGAACGATAGTGAA -AACAATCACAAATGACCGAATTGAAGTTACTAATGCTACTGAGTTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACA -GTCCTCATCAGATCCTTGATGGAGAGAACTGCACACTAATTGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTTCAA -AATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTC -CCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAAAAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACG -GAAAAAGTTCTGCTTGCATAAGGAGATCTAGTAGTAGTTTCTTTAGTAGATTAAATTGGTTGACCCACTTAAACTACACA -TATCCAGCATTGAACGTGACTATGCCAAACAAGGAACAATTTGACAAATTGTACATTTGGGGGGTTCATCACCCGGGTAC -GGACAAGGACCAAATCTTCCTGTATGCTCAATCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAA -TCCCAAATATCGGATCTAGACCCAGAATAAGGGATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGA -GACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAAT -AATGAGATCAGATGCACCCATTGGCAAATGCAAGTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCAT -TCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCATAGCACTCTGAAATTGGCAACAGGAATG -CGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGT -GGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAA -TCGATCAAATCAATGGGAAGCTGAATCGGTTGATCGGAAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCA -GAAGTAGAAGGAAGAGTTCAAGACCTTGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCT -TCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGC -AACTGAGGGAAAATGCTGAGGATATGGGAAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGAATCA -ATAAGAAATGAAACTTATGACCACAATGTGTACAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCT -GAAGTCAGGGTACAAAGATTGG ->SampleJ;size=5; -CAAAAAATTCCTGGAAATGACAATAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAA -AACAATCACAAATGACCGAATTGAAGTTACTAATGCTACTGAGTTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACA -GTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTTCAA -AATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTC -CCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCAAACAAAACG -GAACAAGTTCTGCTTGTATAAGGAAATCTAGTAGTAGTTTCTTTAGTAGATTAAATTGGTTGACCCACTTAAACTACACA -TATCCAGCATTGAACGTGACTATGCCAAACAATGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTAC -GGACAAGGACCAAATCTTCCTGTATGCTCAATCATCAGGAAAAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAA -TCCCAAATATCGGATCCAGACCCAGAATAAGGGATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGA -GACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACAAAGTGGGAAAAGCTCAAT -AATGAGATCAGATGCACCCATTGGCAAATGCAAGTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCAT -TCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCATAGCACTCTGAAATTGGCAACAGGAATG -CGAAATGTACCAGAGAAACAAACTAGGGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGT -GGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAA -TCGATCAAATCAATGGGAAGCTGAATCGGTTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCA -GAAGTAGAAGGAAGAATTCAGGACCTTGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCT -TCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGC -AACTGAGGGAAAATGCTGAGGATATGGGAAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGTTCA -ATAAGAAATGGAACTTATGACCACAATGTGTACAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCT -GAAGTCAGGGTACAAAGATTGG \ No newline at end of file