Mercurial > repos > galaxyp > filter_by_fasta_ids

annotate filter_by_fasta_ids.py @ 1:8d15aebf55fd draft

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planemo upload commit 88309fbfadbafe82f2d8fb7b96468799f2421e30
author galaxyp
date Tue, 24 May 2016 13:05:22 -0400
parents
children 1bd985f14938
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1
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1 #!/usr/bin/env python
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2 """ A script to build specific fasta databases """
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3 from __future__ import print_function
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4 import optparse
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5
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6
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7 # ===================================== Iterator ===============================
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8 class Sequence:
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9 ''' Holds protein sequence information '''
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10 def __init__(self):
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11 self.header = ""
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12 self.sequence_parts = []
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13
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14 def get_sequence(self):
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15 return "".join([line.rstrip().replace('\n', '').replace('\r', '') for line in self.sequence_parts])
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16
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17
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18 class FASTAReader:
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19 """
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20 FASTA db iterator. Returns a single FASTA sequence object.
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21 """
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22 def __init__(self, fasta_name):
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23 self.fasta_file = open(fasta_name)
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24 self.next_line = self.fasta_file.readline()
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25
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26 def __iter__(self):
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27 return self
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28
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29 def __next__(self):
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30 ''' Iteration '''
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31 next_line = self.next_line
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32 if not next_line:
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33 raise StopIteration
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34
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35 seq = Sequence()
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36 seq.header = next_line.rstrip().replace('\n', '').replace('\r', '')
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37
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38 next_line = self.fasta_file.readline()
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39 while next_line and next_line[0] != '>':
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40 seq.sequence_parts.append(next_line)
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41 next_line = self.fasta_file.readline()
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42 self.next_line = next_line
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43 return seq
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44
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45 # Python 2/3 compat
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46 next = __next__
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47
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48
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49 def target_match(target, search_entry):
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50 ''' Matches '''
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51 search_entry = search_entry.upper()
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52 for atarget in target:
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53 if search_entry.find(atarget) > -1:
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54 return atarget
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55 return None
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56
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57
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58 def main():
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59 ''' the main function'''
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60
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61 parser = optparse.OptionParser()
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62 parser.add_option('--dedup', dest='dedup', action='store_true', default=False, help='Whether to remove duplicate sequences')
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63 (options, args) = parser.parse_args()
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64
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65 targets = []
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66
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67 with open(args[0]) as f_target:
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68 for line in f_target.readlines():
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69 targets.append(">%s" % line.strip().upper())
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70
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71 print('Read target file, now looking for %d sequences.' % len(targets))
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72
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73 work_summary = {'wanted': len(targets), 'found': 0}
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74 if options.dedup:
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75 used_sequences = set()
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76 work_summary['duplicates'] = 0
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77 homd_db = FASTAReader(args[1])
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78
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79 with open(args[2], "w") as output:
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80 for entry in homd_db:
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81 target_matched_results = target_match(targets, entry.header)
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82 if target_matched_results:
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83 work_summary['found'] += 1
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84 targets.remove(target_matched_results)
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85 sequence = entry.get_sequence()
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86 if options.dedup:
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87 if sequence in used_sequences:
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88 work_summary['duplicates'] += 1
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89 continue
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90 else:
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91 used_sequences.add(sequence)
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92 print(entry.header, file=output)
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93 print(sequence, file=output)
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94
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95 print('Completed filtering.')
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96 for parm, count in work_summary.items():
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97 print('%s ==> %d' % (parm, count))
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98
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99 if __name__ == "__main__":
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100 main()