Mercurial > repos > public-health-bioinformatics > assign_clades

--- 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.
--- /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()
+
--- /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 @@
+<tool id="assign_clades" name="Assign Clades" version="0.0.1">
+  <requirements>
+    <requirement type="package" version="1.70">biopython</requirement>
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[
+    python $__tool_directory__/assign_clades.py
+    '$input_fasta'
+    '$clade_definitions'
+    '$output_file'
+  ]]></command>
+  <inputs>
+    <param name="input_fasta" format="fasta" type="data" />
+    <param name="clade_definitions" format="csv" type="data" />
+  </inputs>
+  <outputs>
+    <data name="output_file" format="fasta"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input_fasta" value="input_fasta.fasta" />
+      <param name="clade_definitions" value="clades.csv" />
+      <output name="output_file" value="output.fasta" />
+    </test>
+  </tests>
+  <help><![CDATA[
+  ]]></help>
+  <citations>
+  </citations>
+</tool>
--- /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,,,,,,,,,,,,,,,,,,
--- /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
--- /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
--- 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()
--- 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 @@
-<tool id="aggregate_linelisting" name="Aggregate Line List" version="0.0.1">
-  <requirements>
-    <requirement type="package" version="1.70">biopython</requirement>
-  </requirements>
-  <command detect_errors="exit_code"><![CDATA[
-    aggregate_linelisting.py
-    '$input_fasta'
-    '$ref_fasta'
-    '$index_array_csv'
-    '$clade_def_csv'
-    '$output_file'
-  ]]></command>
-  <inputs>
-    <param name="input_fasta" format="fasta" type="data" label="Sample Sequences fasta."/>
-    <param name="ref_fasta" format="fasta" type="data" label="Reference Sequence fasta."/>
-    <param name="index_array_csv" format="csv" type="data" label="Antigenic Site Index Array File."/>
-    <param name="clade_def_csv" format="csv" type="data" label="Clade Definition File."/>
-  </inputs>
-  <outputs>
-    <data name="output_file" format="csv"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="input_fasta" value="2017_summer_Nov23_2017_antigenic_maps.fasta"/>
-      <param name="ref_fasta" value="MAP_3C.2a_A_Hong_Kong_4801_2014_X-263B_EGG.fasta" />
-      <param name="index_array_csv" value="FluA_H3_antigenic_aa_indices.csv" />
-      <param name="clade_def_csv" value="Flu_Clade_Definitions_H3_20171121.csv" />
-      <output name="output_file" value="test_output.csv"/>
-    </test>
-  </tests>
-  <help><![CDATA[
-  ]]></help>
-  <citations>
-  </citations>
-</tool>
--- 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
--- 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,,,,,,,,,,,,,,,,,,,,,,,,
--- 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
--- 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
--- 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()
-
--- 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 @@
-<tool id="antigenic_site_extraction" name="Antigenic Site Extraction" version="0.0.1">
-  <requirements>
-    <requirement type="package" version="1.70">biopython</requirement>
-  </requirements>
-  <command detect_errors="exit_code"><![CDATA[
-    antigenic_site_extraction.py
-    '$input_fasta'
-    '$index_array'
-    '$output_file'
-    #if $csv
-    	-c
-    #end if
-  ]]></command>
-  <inputs>
-    <param name="input_fasta" format="fasta" type="data" />
-    <param name="index_array" format="csv" type="data" />
-    <param name="csv" type="boolean" label="Output to csv ?" />
-  </inputs>
-  <outputs>
-      <data format="fasta" name="output_file">
-        <change_format>
-            <when input="csv" value="true" format="csv" />
-        </change_format>
-      </data>
-  </outputs>
-  <tests>
-    <test>
-      <param name="input_fasta" value="14_H3_aa_seqs_aligned.fasta" />
-      <param name="index_array" value="FluA_H3_antigenic_aa_indices.csv" />
-      <output name="output_file" value="output.fasta" />
-    </test>
-  </tests>
-  <help><![CDATA[
-    Upload a fasta file containing full length flu sequences and an index array csv file.
-  ]]></help>
-  <citations>
-  </citations>
-</tool>
--- 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
--- 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
--- 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()
-
--- 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 @@
-<tool id="assign_clades" name="Assign Clades" version="0.0.1">
-  <requirements>
-    <requirement type="package" version="1.70">biopython</requirement>
-  </requirements>
-  <command detect_errors="exit_code"><![CDATA[
-    assign_clades.py
-    '$input_fasta'
-    '$clade_definitions'
-    '$output_file'
-  ]]></command>
-  <inputs>
-    <param name="input_fasta" format="fasta" type="data" />
-    <param name="clade_definitions" format="csv" type="data" />
-  </inputs>
-  <outputs>
-    <data name="output_file" format="fasta"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="input_fasta" value="input_fasta.fasta" />
-      <param name="clade_definitions" value="clades.csv" />
-      <output name="output_file" value="output.fasta" />
-    </test>
-  </tests>
-  <help><![CDATA[
-  ]]></help>
-  <citations>
-  </citations>
-</tool>
--- 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,,,,,,,,,,,,,,,,,,
--- 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
--- 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
--- 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()
--- 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 @@
-<tool id="change_fasta_deflines" name="Change Fasta Deflines" version="0.0.1">
-  <requirements>
-    <requirement type="package" version="1.70">biopython</requirement>
-  </requirements>
-  <command detect_errors="exit_code"><![CDATA[
-    change_fasta_deflines.py
-    '$key_value_pairs'
-    '$input_fasta'
-    '$output_file'
-    #if $tab_delim
-      -t
-    #end if
-  ]]></command>
-  <inputs>
-    <param name="input_fasta" format="fasta" type="data" />
-    <param name="tab_delim" type="boolean" label="Names file is tab-delimited." checked="false" />
-    <param name="key_value_pairs" format="csv" type="data" />
-  </inputs>
-  <outputs>
-    <data name="output_file" format="fasta"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="input_fasta" value="fasta_2_rename.fasta" />
-      <param name="key_value_pairs" value="csv_rename_file.csv" />
-      <output name="output_file" value="output.fasta" />
-    </test>
-    <test>
-      <param name="input_fasta" value="fasta_2_rename.fasta" />
-      <param name="key_value_pairs" value="tab_delim_rename_file.txt" />
-      <param name="tab_delim" value="true" />
-      <output name="output_file" value="output.fasta" />
-    </test>
-  </tests>
-  <help><![CDATA[
-  ]]></help>
-  <citations>
-  </citations>
-</tool>
--- 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
--- 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
--- 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
--- 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
--- 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 @@
-<tool id="linelisting" name="Line List" version="0.0.1">
-  <requirements>
-    <requirement type="package" version="1.70">biopython</requirement>
-  </requirements>
-  <command detect_errors="exit_code"><![CDATA[
-    linelisting.py
-    '$input_fasta'
-    '$ref_fasta'
-    '$index_array_csv'
-    '$clade_def_csv'
-    '$output_file'
-  ]]></command>
-  <inputs>
-    <param name="input_fasta" format="fasta" type="data" label="Sample Sequences fasta."/>
-    <param name="ref_fasta" format="fasta" type="data" label="Reference Sequence fasta."/>
-    <param name="index_array_csv" format="csv" type="data" label="Antigenic Site Index Array File."/>
-    <param name="clade_def_csv" format="csv" type="data" label="Clade Definition File."/>
-  </inputs>
-  <outputs>
-    <data name="output_file" format="csv"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="input_fasta" value="2017_summer_Nov23_2017_antigenic_maps.fasta"/>
-      <param name="ref_fasta" value="MAP_3C.2a_A_Hong_Kong_4801_2014_X-263B_EGG.fasta" />
-      <param name="index_array_csv" value="FluA_H3_antigenic_aa_indices.csv" />
-      <param name="clade_def_csv" value="Flu_Clade_Definitions_H3_20171121.csv" />
-      <output name="output_file" value="test_output.csv"/>
-    </test>
-  </tests>
-  <help><![CDATA[
-  ]]></help>
-  <citations>
-  </citations>
-</tool>
--- 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
--- 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,,,,,,,,,,,,,,,,,,,,,,,,
--- 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
--- 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
--- 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()
--- 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 @@
-<tool id="reformat_usearch_collapsed_fasta" name="Reformat USearch-Collapsed Fasta" version="0.0.1">
-  <requirements>
-    <requirement type="package" version="1.70">biopython</requirement>
-  </requirements>
-  <command detect_errors="exit_code"><![CDATA[
-    reformat_usearch_collapsed_fasta.py
-    '$input_fasta'
-    '$output_file'
-  ]]></command>
-  <inputs>
-    <param name="input_fasta" format="fasta" type="data" />
-  </inputs>
-  <outputs>
-    <data name="output_file" format="fasta"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="input_fasta" value="fasta_2_rename.fasta" />
-      <output name="output_file" value="output.fasta" />
-    </test>
-    <test>
-      <param name="input_fasta" value="usearch_collapsed_sequences.fasta" />
-      <output name="output_file" value="output.fasta" />
-    </test>
-  </tests>
-  <help><![CDATA[
-  ]]></help>
-  <citations>
-  </citations>
-</tool>
--- 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