Mercurial > repos > galaxyp > filter_by_fasta_ids

annotate filter_by_fasta_ids.py @ 3:3c623e81be77 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
author galaxyp
date Fri, 15 Feb 2019 16:38:31 -0500
parents 1bd985f14938
children cd22452edec2
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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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9
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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
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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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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2
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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()
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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31 while True:
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32 if not line:
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33 return
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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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, search_entry, pattern='>([^| ]+)'):
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45 ''' Matches '''
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46 search_entry = search_entry.upper()
3c623e81be77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
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47 m = re.search(pattern,search_entry)
3c623e81be77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
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48 if m:
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49 target = m.group(len(m.groups()))
3c623e81be77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
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50 if target in targets:
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51 return target
3c623e81be77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
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52 else:
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53 print( 'No ID match: %s' % search_entry, file=sys.stdout)
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54 return None
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56
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57 def main():
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58 ''' the main function'''
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59
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60 parser = argparse.ArgumentParser()
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61 parser.add_argument('-i', required=True, help='Path to input FASTA file')
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62 parser.add_argument('-o', required=True, help='Path to output FASTA file')
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63 parser.add_argument('-d', help='Path to discarded entries file')
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64 header_criteria = parser.add_mutually_exclusive_group()
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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65 header_criteria.add_argument('--id_list', help='Path to the ID list file')
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66 parser.add_argument('--pattern', help='regex earch attern for ID in Fasta entry')
2
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67 header_criteria.add_argument('--header_regexp', help='Regular expression pattern the header should match')
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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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
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76 if options.pattern:
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77 pattern = options.pattern
3c623e81be77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
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78 if not re.match('^.*[(](?![?]:).*[)].*$',pattern):
3c623e81be77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
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79 print('pattern: "%s" did not include capture group "()" in regex ' % pattern)
3c623e81be77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
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80 exit(1)
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81
2
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82 if options.min_length is not None and options.max_length is None:
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83 options.max_length = sys.maxsize
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84 if options.header_regexp:
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85 regexp = re.compile(options.header_regexp)
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86 if options.sequence_regexp:
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87 regexp = re.compile(options.sequence_regexp)
1
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88
2
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89 work_summary = {'found': 0}
1
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90
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91 if options.dedup:
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92 used_sequences = set()
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93 work_summary['duplicates'] = 0
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94
2
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95 if options.id_list:
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96 targets = []
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97 with open(options.id_list) as f_target:
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98 for line in f_target.readlines():
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99 targets.append(line.strip().upper())
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100 work_summary['wanted'] = len(targets)
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101
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102 homd_db = FASTAReader_gen(options.i)
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103 if options.d:
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104 discarded = open(options.d, 'w')
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105
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106 with open(options.o, "w") as output:
1
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107 for entry in homd_db:
2
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108 print_entry = True
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109 if options.id_list:
3
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110 target_matched_results = target_match(targets, entry.header, pattern=pattern)
2
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111 if target_matched_results:
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112 work_summary['found'] += 1
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113 targets.remove(target_matched_results)
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114 else:
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115 print_entry = False
3
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116
2
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117 elif options.header_regexp:
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118 if regexp.search(entry.header) is None:
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119 print_entry = False
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120 if options.min_length is not None:
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121 sequence_length = len(entry.sequence)
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122 if not(options.min_length <= sequence_length <= options.max_length):
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123 print_entry = False
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124 elif options.sequence_regexp:
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125 if regexp.search(entry.sequence) is None:
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126 print_entry = False
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127 if print_entry:
1
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128 if options.dedup:
2
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129 if entry.sequence in used_sequences:
1
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130 work_summary['duplicates'] += 1
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131 continue
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132 else:
2
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133 used_sequences.add(entry.sequence)
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134 entry.print(output)
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135 elif options.d:
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136 entry.print(discarded)
1
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137
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138 for parm, count in work_summary.items():
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139 print('%s ==> %d' % (parm, count))
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140
2
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141
1
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142 if __name__ == "__main__":
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143 main()