Mercurial > repos > iss > eurl_vtec_wgs_pt

annotate scripts/GetConsensus.py @ 4:32b5625795ea draft

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planemo upload commit 906fafe94520fdbabb0fb94cdbe93ffeab43867a
author iss
date Thu, 19 Oct 2023 19:07:24 +0000
parents c6bab5103a14
children
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1 #!/usr/bin/env python3
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2 # -*- coding: utf-8 -*-
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3 """
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4 ############################################################################
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5 # Istituto Superiore di Sanita'
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6 # European Union Reference Laboratory (EU-RL) for Escherichia coli, including Verotoxigenic E. coli (VTEC)
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7 # Developer: Arnold Knijn arnold.knijn@iss.it
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8 ############################################################################
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9 """
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10
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11 import argparse
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12 import sys
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13 import os
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14 import subprocess
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15 import shutil
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16
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17 def __main__():
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18 parser = argparse.ArgumentParser()
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19 parser.add_argument('-i', '--input', dest='input', help='input alignment file')
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20 parser.add_argument('-o', '--output', dest='output', help='output consensus file')
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21 args = parser.parse_args()
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22
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23 sequences = []
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24 varsequences = []
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25 # read input
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26 with open(args.input) as alignments:
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27 for alignment in alignments:
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28 if alignment[0] != ">":
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29 sequences.append(alignment.rstrip())
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30 numsequences = len(sequences)
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31 for j in range(0, numsequences + 1):
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32 varsequences.append("")
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33 lstnumvariants = []
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34 lstnumhyphens = []
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35 # loop over the columns
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36 for i in range(0, len(sequences[0])):
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37 variants = []
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38 numhyphens = 0
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39 # loop over the original rows to obtain variants
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40 for j in range(0, numsequences):
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41 if sequences[j][i:i+1] == "-":
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42 numhyphens = numhyphens + 1
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43 if sequences[j][i:i+1] not in variants and sequences[j][i:i+1] != "-":
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44 variants.append(sequences[j][i:i+1])
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45 lstnumvariants.append(len(variants))
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46 lstnumhyphens.append(numhyphens)
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47 # create varsequences with a template of the variants
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48 for j in range(0, numsequences):
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49 if lstnumhyphens[i] == 0:
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50 varsequences[j] = varsequences[j] + "-"
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51 elif lstnumvariants[i] < 2:
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52 varsequences[j] = varsequences[j] + "-"
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53 else:
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54 varsequences[j] = varsequences[j] + sequences[j][i:i+1]
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55 if lstnumvariants[i] == 1 and lstnumhyphens[i] > 0:
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56 varsequences[numsequences] = varsequences[numsequences] + variants[0]
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57 else:
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58 varsequences[numsequences] = varsequences[numsequences] + "-"
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59 # loop over the columns, apply single variant
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60 for i in range(0, len(sequences[0])):
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61 if lstnumvariants[i] == 1 and lstnumhyphens[i] > 0:
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62 # loop over all the rows to apply single variant to "-"
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63 for j in range(0, len(sequences)):
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64 if sequences[j][i:i+1] == "-":
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65 lstsequence = list(sequences[j])
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66 lstsequence[i] = varsequences[numsequences][i:i+1]
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67 sequences[j] = ''.join(lstsequence)
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68 # loop over the rows of the sequences, apply multiple variants
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69 for j in range(0, len(sequences)):
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70 # loop over the columns
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71 for i in range(0, len(sequences[0])):
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72 variants = []
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73 if sequences[j][i:i+1] == "-" and lstnumvariants[i] > 1:
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74 # loop over the rows of the varsequences
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75 for k in range(0, numsequences):
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76 if varsequences[k][i:i+1] not in variants and varsequences[k][i:i+1] != "-":
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77 variants.append(varsequences[k][i:i+1])
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78 if len(variants) == 1:
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79 lstsequence = list(sequences[j])
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80 lstsequence[i] = variants[0]
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81 sequences[j] = ''.join(lstsequence)
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82 else:
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83 lstsequence[i] = variants[len(variants) - 1]
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84 sequences.append(''.join(lstsequence))
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85 # eliminate duplicate sequences
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86 sequences_unique = list(set(sequences))
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87 # write consensus sequences to output
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88 consensus = open(args.output, 'w')
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89 n = 1
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90 for sequence in sequences_unique:
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91 consensus.write(">consensus_" + str(n) + "\n")
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92 consensus.write(sequence + "\n")
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93 n = n + 1
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94
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95
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96 if __name__ == "__main__":
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97 __main__()