Mercurial > repos > galaxyp > filter_by_fasta_ids

annotate filter_by_fasta_ids.py @ 2:1bd985f14938 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
author galaxyp
date Sat, 28 Apr 2018 03:49:28 -0400
parents 8d15aebf55fd
children 3c623e81be77
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1 #!/usr/bin/env python
8d15aebf55fd planemo upload commit 88309fbfadbafe82f2d8fb7b96468799f2421e30
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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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5 import argparse
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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6 import re
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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7 import sys
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10 class Sequence(object):
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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11 def __init__(self, header, sequence_parts):
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12 self.header = header
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13 self.sequence_parts = sequence_parts
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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14 self._sequence = None
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16 @property
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17 def sequence(self):
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18 if self._sequence is None:
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19 self._sequence = ''.join(self.sequence_parts)
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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20 return self._sequence
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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22 def print(self, fh=sys.stdout):
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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23 print(self.header, file=fh)
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24 for line in self.sequence_parts:
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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25 print(line, file=fh)
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28 def FASTAReader_gen(fasta_filename):
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29 with open(fasta_filename) as fasta_file:
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30 line = fasta_file.readline()
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31 while True:
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32 if not line:
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33 return
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34 assert line.startswith('>'), "FASTA headers must start with >"
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35 header = line.rstrip()
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36 sequence_parts = []
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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37 line = fasta_file.readline()
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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38 while line and line[0] != '>':
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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39 sequence_parts.append(line.rstrip())
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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40 line = fasta_file.readline()
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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41 yield Sequence(header, sequence_parts)
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43
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44 def target_match(targets, header):
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45 ''' Matches '''
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46 # Remove '>' and initial spaces from the header
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47 header = header[1:].lstrip().upper()
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48 # Search for an exact match among the targets
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49 if header in targets:
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50 return header
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51 # Try to find an exact match for the first "word" in the header
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52 header = header.split()[0]
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53 if header in targets:
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54 return header
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55 return None
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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 = argparse.ArgumentParser()
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62 parser.add_argument('-i', required=True, help='Path to input FASTA file')
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63 parser.add_argument('-o', required=True, help='Path to output FASTA file')
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64 parser.add_argument('-d', help='Path to discarded entries file')
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65 header_criteria = parser.add_mutually_exclusive_group()
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66 header_criteria.add_argument('--id_list', help='Path to the ID list file')
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67 header_criteria.add_argument('--header_regexp', help='Regular expression pattern the header should match')
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68 sequence_criteria = parser.add_mutually_exclusive_group()
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69 sequence_criteria.add_argument('--min_length', type=int, help='Minimum sequence length')
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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70 sequence_criteria.add_argument('--sequence_regexp', help='Regular expression pattern the header should match')
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71 parser.add_argument('--max_length', type=int, help='Maximum sequence length')
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72 parser.add_argument('--dedup', action='store_true', default=False, help='Whether to remove duplicate sequences')
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73 options = parser.parse_args()
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74
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75 if options.min_length is not None and options.max_length is None:
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76 options.max_length = sys.maxsize
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77 if options.header_regexp:
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78 regexp = re.compile(options.header_regexp)
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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79 if options.sequence_regexp:
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80 regexp = re.compile(options.sequence_regexp)
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82 work_summary = {'found': 0}
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84 if options.dedup:
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85 used_sequences = set()
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86 work_summary['duplicates'] = 0
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88 if options.id_list:
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89 targets = []
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90 with open(options.id_list) as f_target:
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91 for line in f_target.readlines():
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92 targets.append(line.strip().upper())
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93 work_summary['wanted'] = len(targets)
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94
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95 homd_db = FASTAReader_gen(options.i)
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96 if options.d:
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97 discarded = open(options.d, 'w')
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98
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99 with open(options.o, "w") as output:
1
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100 for entry in homd_db:
2
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101 print_entry = True
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102 if options.id_list:
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103 target_matched_results = target_match(targets, entry.header)
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104 if target_matched_results:
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105 work_summary['found'] += 1
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106 targets.remove(target_matched_results)
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107 else:
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108 print_entry = False
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109 elif options.header_regexp:
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110 if regexp.search(entry.header) is None:
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111 print_entry = False
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112 if options.min_length is not None:
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113 sequence_length = len(entry.sequence)
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114 if not(options.min_length <= sequence_length <= options.max_length):
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115 print_entry = False
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116 elif options.sequence_regexp:
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117 if regexp.search(entry.sequence) is None:
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118 print_entry = False
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119 if print_entry:
1
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120 if options.dedup:
2
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121 if entry.sequence in used_sequences:
1
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122 work_summary['duplicates'] += 1
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123 continue
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124 else:
2
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125 used_sequences.add(entry.sequence)
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126 entry.print(output)
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127 elif options.d:
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128 entry.print(discarded)
1
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129
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130 for parm, count in work_summary.items():
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131 print('%s ==> %d' % (parm, count))
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132
2
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133
1
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134 if __name__ == "__main__":
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135 main()