Mercurial > repos > public-health-bioinformatics > aggregate_linelisting

annotate aggregate_linelisting.py @ 0:515c0c885f5d draft default tip

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planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
author public-health-bioinformatics
date Thu, 04 Jul 2019 19:40:13 -0400
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515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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1 #!/usr/bin/env python
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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2 '''Reads in a fasta file of antigenic maps and one with the reference antigenic map as
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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3 protein SeqRecords. Compares amino acids of sample antigenic maps to corresponding sites
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4 in the reference and masks identical amino acids with dots. Writes headers (including
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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5 amino acid position numbers read from the respective index array), the reference amino
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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6 acid sequence and column headings required for both non-aggregated and aggregated line lists.
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7 Outputs all headers and modified (i.e. dotted) sample sequences to a csv file.'''
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8
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9 '''Author: Diane Eisler, Molecular Microbiology & Genomics, BCCDC Public Health Laboratory, Jan 2018'''
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11 import sys,string,os, time, Bio, re, argparse
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12 from Bio import Seq, SeqIO, SeqUtils, Alphabet, SeqRecord
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13 from Bio.SeqRecord import SeqRecord
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14 from Bio.Alphabet import IUPAC
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15 from Bio.Seq import Seq
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17 inputAntigenicMaps = sys.argv[1] #batch fasta file with antigenic map sequences
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18 refAntigenicMap = sys.argv[2] #fasta file of reference antigenic map sequence
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19 antigenicSiteIndexArray = sys.argv[3] #antigenic site index array csv file
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20 cladeDefinitionFile = sys.argv[4] #clade definition csv file
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21 outFileHandle = sys.argv[5] #user-specifed output filename
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23 agg_lineListFile = open(outFileHandle,'w') #open a writable output file
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25 indicesLine = "" #comma-separated antigenic site positions
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26 cladeList = [] #list of clade names read from clade definition file
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27 ref_seq = "" #reference antigenic map (protein sequence)
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28 seqList = [] #list of aa sequences to compare to reference
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30 BC_list = [] #empty list for BC samples
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31 AB_list = [] #empty list for AB samples
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32 ON_list = [] #empty list for ON samples
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33 QC_list = [] #empty list for QC samples
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34 nonprov_list = [] #empty list for samples not in above 4 provinces
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35 #dictionary for location-separated sequence lists
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36 prov_lists = {'1_BC':BC_list,'2_AB':AB_list,'3_ON':ON_list,'4_QC': QC_list, '5_nonprov': nonprov_list}
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38 def replace_matching_aa_with_dot(record):
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39 """Compare amino acids in record to reference, mask identical symbols with dots, and return modified record."""
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40 orig_seq = str(record.seq) #sequence string from SeqRecord
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41 mod_seq = ""
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42 #replace only those aa's matching the reference with dots
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43 for i in range(0, len(orig_seq)):
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44 if (orig_seq[i] == ref_seq[i]):
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45 mod_seq = mod_seq + '.'
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46 else:
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47 mod_seq = mod_seq + orig_seq[i]
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48 #assign modified sequence to new SeqRecord and return it
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49 rec = SeqRecord(Seq(mod_seq,IUPAC.protein), id = record.id, name = "", description = "")
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50 return rec
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51
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52 def extract_clade(record):
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53 """Extract clade name (or 'No_Match') from sequence name and return as clade name. """
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54 if record.id.endswith('No_Match'):
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55 clade_name = 'No_Match'
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56 else: #
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57 for clade in cladeList:
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58 if record.id.endswith(clade):
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59 clade_name = clade
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60 return clade_name
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61
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62 def extract_sample_name(record, clade):
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63 """Extract sample name from sequence name and return sample name. """
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64 end_index = record.id.index(clade)
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65 sample_name = record.id[:end_index -1]
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66 #return sample name as sequence name minus underscore and clade name
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67 return sample_name
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68
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69 def sort_by_location(record):
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70 """Search sequence name for province name or 2-letter province code and add SeqRecord to
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71 province-specific dictionary."""
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72 seq_name = record.id
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73 if ('-BC-' in seq_name) or ('/British_Columbia/' in seq_name):
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74 BC_list.append(record) #add Sequence record to BC_list
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75 elif ('-AB-' in seq_name) or ('/Alberta/' in seq_name):
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76 AB_list.append(record) #add Sequence record to AB_list
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77 elif ('-ON-' in seq_name) or ('/Ontario/' in seq_name):
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78 ON_list.append(record) #add Sequence record to ON_list
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79 elif ('-QC-' in seq_name) or ('/Quebec/' in seq_name):
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80 QC_list.append(record) #add Sequence record to QC_list
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81 else:
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82 nonprov_list.append(record) #add Sequence record to nonprov_list
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83 return
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84
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85 def extract_province(record):
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86 """Search sequence name for province name or 2-letter province code and return province."""
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87 seq_name = record.id
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88 if ('-BC-' in seq_name) or ('/British_Columbia/' in seq_name):
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89 province = 'British Columbia'
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90 elif ('-AB-' in seq_name) or ('Alberta' in seq_name):
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91 province = '/Alberta/'
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92 elif ('-ON-' in seq_name) or ('/Ontario/' in seq_name):
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93 province = 'Ontario'
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94 elif ('-QC-' in seq_name) or ('/Quebec/' in seq_name):
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95 province = 'Quebec'
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96 else:
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97 province = "other"
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98 return province
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99
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100 def get_sequence_length(record):
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101 """Return length of sequence in a SeqRecord."""
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102 sequenceLength = len(str((record.seq)))
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103 return sequenceLength
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104
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105 def get_antigenic_site_substitutions(record):
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106 """Count number of non-dotted amino acids in SeqRecord sequence and return as substitutions."""
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107 sequenceLength = get_sequence_length(record)
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108 seqString = str(record.seq)
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109 matches = seqString.count('.')
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110 substitutions = sequenceLength - matches
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111 return substitutions
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112
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113 def calculate_percent_id(record, substitutions):
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114 """Calculate percent sequence identity to reference sequence, based on substitutions
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115 and sequence length and return percent id as a ratio (i.e. 0.90 no 90%)."""
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116 sequenceLength = get_sequence_length(record)
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117 percentID = (1.00 - (float(substitutions)/float(sequenceLength)))
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118 return percentID
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119
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120 def output_aggregated_linelist(a_list):
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121 """Output aggregated line list of SeqRecords in csv format."""
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122 sequevars = {} #dict of sequevar: SeqRecord list
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123 firstRecordID = None
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124 #examine dotted/masked sequences in list and assign unique ones as dict keys
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125 for rec in a_list:
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126 rec = replace_matching_aa_with_dot(rec)
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127 sequence =str(rec.seq)
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128 #if the sequence is a key in the dict, add SeqRecord to list
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129 if sequence in sequevars:
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130 #if sequence already in dict as a key, increment the value
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131 sequevars[sequence].append(rec)
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132 else:
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133 #if sequence not in dict, add is as new key with list of 1 SeqRecord
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134 sequevars[sequence] = [rec]
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135 #get list of sorted unique sequence keys
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136 sorted_unique_seq_keys = sorted(sequevars.keys())
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137 #process each list of SeqRecords sharing a unique sequence
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138 for u in sorted_unique_seq_keys:
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139 #access list of sequences by unique sequence
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140 listOfSeqs = sequevars[u]
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141 #sort this list of SeqRecords by record.id (i.e. name)
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142 listOfSeqs = [f for f in sorted(listOfSeqs, key = lambda x : x.id)]
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143 N = len(listOfSeqs)
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144 #output details of first SeqRecord to csv
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145 firstRecord = listOfSeqs[0]
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146 province = extract_province(firstRecord)
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147 clade = extract_clade(firstRecord)
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148 substitutions = get_antigenic_site_substitutions(firstRecord)
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149 percentID = calculate_percent_id(firstRecord,substitutions)
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150 name = extract_sample_name(firstRecord, clade)
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151 name_part = name.rstrip() + ','
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152 N_part = str(N) + ','
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153 clade_part = clade + ','
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154 substitutions_part = str(substitutions) + ','
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155 percID_part = str(percentID) + ','
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156 col = " ," #empty column
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157 sequence = str(firstRecord.seq).strip()
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158 csv_seq = ",".join(sequence) +","
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159 comma_sep_output = name_part + N_part + clade_part + col + csv_seq + substitutions_part + percID_part + "\n"
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160 #write first member of unique sequence list to csv
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161 agg_lineListFile.write(comma_sep_output)
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162 #print sequence records in sequevar to console
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163 print("\n\t\t%i SeqRecords matching Sequevar: %s" % (len(listOfSeqs), u))
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164
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165 #to uncollapse sequevar group, print each member of the sequevar list to csv output
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166 '''for i in range(1,len(listOfSeqs)):
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167 currentRec = listOfSeqs[i]
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168 province = extract_province(currentRec)
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169 clade = extract_clade(currentRec)
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170 substitutions = get_antigenic_site_substitutions(currentRec)
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171 percentID = calculate_percent_id(currentRec,substitutions)
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172 name_part = (currentRec.id).rstrip() + ','
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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173 N_part = "n/a" + ','
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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174 clade_part = clade + ','
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175 substitutions_part = str(substitutions) + ','
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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176 percID_part = str(percentID) + ','
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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177 col = " ," #empty column
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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178 sequence = str(currentRec.seq).strip()
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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179 csv_seq = ",".join(sequence) +","
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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180 comma_sep_output = name_part + N_part + clade_part + col + csv_seq + substitutions_part + percID_part + "\n"
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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181 agg_lineListFile.write(comma_sep_output) '''
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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182 return
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183
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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184 with open (antigenicSiteIndexArray,'r') as siteIndices:
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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185 """Read amino acid positions from antigenic site index array and print as header after one empty row."""
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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186 col = "," #empty column
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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187 #read amino acid positions and remove trailing whitespace
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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188 for line in siteIndices:
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189 #remove whitespace from the end of each line
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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190 indicesLine = line.rstrip()
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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191 row1 = "\n"
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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192 #add comma-separated AA positions to header line
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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193 row2 = col + col + col + col + indicesLine + "\n"
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194 #write first (empty) and 2nd (amino acid position) lines to output file
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195 agg_lineListFile.write(row1)
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196 agg_lineListFile.write(row2)
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197
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198 with open (refAntigenicMap,'r') as refMapFile:
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199 """Read reference antigenic map from fasta and output amino acids, followed by column headers."""
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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200 #read sequences from fasta to SeqRecord, uppercase, and store sequence string to ref_seq
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201 record = SeqIO.read(refMapFile,"fasta",alphabet=IUPAC.protein)
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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202 record = record.upper()
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203 ref_seq = str(record.seq).strip() #store sequence in variable for comparison to sample seqs
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204 col = "," #empty column
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205 name_part = (record.id).rstrip() + ','
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206 sequence = str(record.seq).strip()
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207 csv_seq = ",".join(sequence)
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208 #output row with reference sequence displayed above sample sequences
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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209 row3 = name_part + col + col + col + csv_seq + "\n"
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210 agg_lineListFile.write(row3)
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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211 positions = indicesLine.split(',')
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212 numPos = len(positions)
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213 empty_indicesLine = ',' * numPos
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214 #print column headers for sample sequences
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215 row4 = "Sequence Name,N,Clade,Extra Substitutions," + empty_indicesLine + "Number of Amino Acid Substitutions in Antigenic Sites,% Identity of Antigenic Site Residues\n"
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216 agg_lineListFile.write(row4)
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217 print("\nREFERENCE ANTIGENIC MAP: '%s' (%i amino acids)" % (record.id, len(record)))
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218
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219 with open(cladeDefinitionFile,'r') as cladeFile:
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220 """Read clade definition file and store clade names in list."""
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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221 #remove whitespace from the end of each line and split elements at commas
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222 for line in cladeFile:
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223 elementList = line.rstrip().split(',')
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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224 name = elementList[0] #move 1st element to name field
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225 cladeList.append(name)
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226
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227 with open(inputAntigenicMaps,'r') as extrAntigMapFile:
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228 """Read antigenic maps as protein SeqRecords and add to list."""
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229 #read Sequences from fasta file, uppercase and add to seqList
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230 for record in SeqIO.parse(extrAntigMapFile, "fasta", alphabet=IUPAC.protein):
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231 record = record.upper()
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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232 seqList.append(record) #add Seq to list of Sequences
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233
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234 #print number of sequences to be processed as user check
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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235 print("\nCOMPARING %i flu antigenic map sequences to the reference..." % len(seqList))
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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236 for record in seqList:
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237 #assign SeqRecords to province-specific dictionaries
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238 sort_by_location(record)
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239
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240 #access prov segregated lists in order
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241 sorted_prov_keys = sorted(prov_lists.keys())
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242 print("\nSequence Lists Sorted by Province: ")
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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243 for prov in sorted_prov_keys:
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244 current_list = prov_lists[prov]
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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245 #mask AA's identical to reference sequence with dot
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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246 masked_list = [] # empty temporary list to park masked sequences
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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247 for record in current_list:
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248 masked_rec = replace_matching_aa_with_dot(record)
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249 masked_list.append(masked_rec)
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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250 prov_lists[prov] = masked_list #replace original SeqRecord list with masked list
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251
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252 #group sequences in province-sorted list into clades
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253 for prov in sorted_prov_keys:
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254 prov_list = prov_lists[prov]
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255 by_clades_dict = {} #empty dict for clade:seqRecord list groups
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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256 print("\n'%s' List (Amino Acids identical to Reference are Masked): " % (prov))
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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257 for rec in prov_list:
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258 clade = extract_clade(rec)
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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259 if clade in by_clades_dict:
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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260 #if clade already in dict as key, append record to list (value)
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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261 by_clades_dict[clade].append(rec)
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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262 else: #add clade as key to dict, value is list of 1 SeqRecord
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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263 by_clades_dict[clade] = [rec]
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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264 #get list of alphabetically sorted clade keys
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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265 sorted_clade_keys = sorted(by_clades_dict.keys())
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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266 print("\tNumber of clades: ", len(by_clades_dict))
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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267 #group each list of sequences in clade by sequevars
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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268 for key in sorted_clade_keys:
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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269 print("\n\tCLADE: %s Number of Members: %i" % (key, len(by_clades_dict[key])))
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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270 a_list = by_clades_dict[key]
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
public-health-bioinformatics
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271 for seqrec in a_list:
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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272 print("\t %s: %s" %(seqrec.id,str(seqrec.seq)))
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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273 #output the list to csv as aggregated linelist
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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274 output_aggregated_linelist(a_list)
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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275
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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276 print("Aggregated Linelist written to file: '%s\n'" % (outFileHandle))
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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277 extrAntigMapFile.close()
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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278 refMapFile.close()
515c0c885f5d planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
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279 agg_lineListFile.close()