Mercurial > repos > mbernt > fasta_regex_finder

annotate fastaregexfinder.py @ 1:9a811adb714f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe commit c318cd3f894f89c13d7eb257678673da70f72212
author iuc
date Wed, 25 Jan 2023 14:03:52 +0000
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269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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1 #!/usr/bin/env python
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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3 import argparse
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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4 import operator
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iuc
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5 import re
9a811adb714f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe commit c318cd3f894f89c13d7eb257678673da70f72212
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6 import sys
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269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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8 VERSION = "0.1.1"
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10 parser = argparse.ArgumentParser(
9a811adb714f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe commit c318cd3f894f89c13d7eb257678673da70f72212
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11 description="""
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269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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13 DESCRIPTION
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269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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15 Search a fasta file for matches to a regex and return a bed file with the
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9a811adb714f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe commit c318cd3f894f89c13d7eb257678673da70f72212
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16 coordinates of the match and the matched sequence itself.
9a811adb714f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe commit c318cd3f894f89c13d7eb257678673da70f72212
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269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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18 Output bed file has columns:
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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19 1. Name of fasta sequence (e.g. chromosome)
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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20 2. Start of the match
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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21 3. End of the match
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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22 4. ID of the match
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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23 5. Length of the match
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9a811adb714f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe commit c318cd3f894f89c13d7eb257678673da70f72212
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24 6. Strand
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25 7. Matched sequence as it appears on the forward strand
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269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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27 For matches on the reverse strand it is reported the start and end position on the
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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28 forward strand and the matched string on the forward strand (so the G4 'GGGAGGGT'
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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29 present on the reverse strand is reported as ACCCTCCC).
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269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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31 Note: Fasta sequences (chroms) are read in memory one at a time along with the
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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32 matches for that chromosome.
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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33 The order of the output is: chroms as they are found in the inut fasta, matches
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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34 sorted within chroms by positions.
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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36 EXAMPLE:
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37 ## Test data:
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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38 echo '>mychr' > /tmp/mychr.fa
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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39 echo 'ACTGnACTGnACTGnTGAC' >> /tmp/mychr.fa
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269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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41 fastaRegexFinder.py -f /tmp/mychr.fa -r 'ACTG'
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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42 mychr 0 4 mychr_0_4_for 4 + ACTG
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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43 mychr 5 9 mychr_5_9_for 4 + ACTG
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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44 mychr 10 14 mychr_10_14_for 4 + ACTG
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46 fastaRegexFinder.py -f /tmp/mychr.fa -r 'ACTG' --maxstr 3
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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47 mychr 0 4 mychr_0_4_for 4 + ACT[3,4]
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48 mychr 5 9 mychr_5_9_for 4 + ACT[3,4]
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49 mychr 10 14 mychr_10_14_for 4 + ACT[3,4]
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51 less /tmp/mychr.fa | fastaRegexFinder.py -f - -r 'A\\w\\wGn'
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52 mychr 0 5 mychr_0_5_for 5 + ACTGn
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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53 mychr 5 10 mychr_5_10_for 5 + ACTGn
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54 mychr 10 15 mychr_10_15_for 5 + ACTGn
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56 DOWNLOAD
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57 fastaRegexFinder.py is hosted at https://github.com/dariober/bioinformatics-cafe/tree/master/fastaRegexFinder
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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58
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59 """,
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60 formatter_class=argparse.RawTextHelpFormatter,
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61 )
0
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62
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63 parser.add_argument(
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64 "--fasta",
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65 "-f",
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66 type=str,
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67 help="Input fasta file to search. Use '-' to read the file from stdin.",
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68 required=True,
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69 )
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70
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71 parser.add_argument(
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72 "--regex",
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73 "-r",
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74 type=str,
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75 help="""Regex to be searched in the fasta input.
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76 Matches to the reverse complement will have - strand.
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77 The default regex is '([gG]{3,}\\w{1,7}){3,}[gG]{3,}' which searches
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78 for G-quadruplexes.""",
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79 default="([gG]{3,}\\w{1,7}){3,}[gG]{3,}",
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80 )
0
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81
1
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82 parser.add_argument(
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83 "--matchcase",
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84 "-m",
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85 action="store_true",
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86 help="""Match case while searching for matches. Default is
0
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87 to ignore case (I.e. 'ACTG' will match 'actg').
1
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88 """,
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89 )
0
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90
1
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91 parser.add_argument(
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92 "--noreverse",
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93 action="store_true",
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94 help="""Do not search the reverse complement of the input fasta.
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95 Use this flag to search protein sequences.""",
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96 )
0
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97
1
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98 parser.add_argument(
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99 "--maxstr",
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100 type=int,
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101 required=False,
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102 default=10000,
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103 help="""Maximum length of the match to report in the 7th column of the output.
0
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104 Default is to report up to 10000nt.
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105 Truncated matches are reported as <ACTG...ACTG>[<maxstr>,<tot length>]
1
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106 """,
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107 )
0
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108
1
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109 parser.add_argument(
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110 "--seqnames",
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111 "-s",
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112 type=str,
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113 nargs="+",
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114 default=[None],
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115 required=False,
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116 help="""List of fasta sequences in --fasta to
0
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117 search. E.g. use --seqnames chr1 chr2 chrM to search only these crhomosomes.
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118 Default is to search all the sequences in input.
1
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119 """,
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120 )
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121 parser.add_argument(
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122 "--quiet",
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123 "-q",
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124 action="store_true",
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125 help="""Do not print progress report (i.e. sequence names as they are scanned).
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126 """,
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127 )
0
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128
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129
1
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130 parser.add_argument("--version", "-v", action="version", version="%(prog)s " + VERSION)
0
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131
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132
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133 args = parser.parse_args()
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134
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135 " --------------------------[ Check and parse arguments ]---------------------- "
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136
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137 if args.matchcase:
1
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138 flag = 0
0
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139 else:
1
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140 flag = re.IGNORECASE
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141
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142 " ------------------------------[ Functions ]--------------------------------- "
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143
1
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144
0
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145 def sort_table(table, cols):
1
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146 """Code to sort list of lists
0
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147 see http://www.saltycrane.com/blog/2007/12/how-to-sort-table-by-columns-in-python/
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148
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149 sort a table by multiple columns
1
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150 table: a list of lists (or tuple of tuples) where each inner list
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151 represents a row
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152 cols: a list (or tuple) specifying the column numbers to sort by
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153 e.g. (1,0) would sort by column 1, then by column 0
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154 """
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155 for col in reversed(cols):
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156 table = sorted(table, key=operator.itemgetter(col))
1
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157 return table
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158
0
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159
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160 def trimMatch(x, n):
1
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161 """Trim the string x to be at most length n. Trimmed matches will be reported
0
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162 with the syntax ACTG[a,b] where Ns are the beginning of x, a is the length of
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163 the trimmed strng (e.g 4 here) and b is the full length of the match
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164 EXAMPLE:
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165 trimMatch('ACTGNNNN', 4)
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166 >>>'ACTG[4,8]'
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167 trimMatch('ACTGNNNN', 8)
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168 >>>'ACTGNNNN'
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169 """
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170 if len(x) > n and n is not None:
1
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171 m = x[0:n] + "[" + str(n) + "," + str(len(x)) + "]"
0
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172 else:
1
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173 m = x
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174 return m
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175
0
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176
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177 def revcomp(x):
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178 """Reverse complement string x. Ambiguity codes are handled and case conserved.
1
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179
0
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180 Test
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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181 x= 'ACGTRYSWKMBDHVNacgtryswkmbdhvn'
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182 revcomp(x)
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183 """
1
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184 compdict = {
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185 "A": "T",
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186 "C": "G",
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iuc
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187 "G": "C",
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188 "T": "A",
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189 "R": "Y",
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190 "Y": "R",
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191 "S": "W",
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192 "W": "S",
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193 "K": "M",
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194 "M": "K",
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195 "B": "V",
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196 "D": "H",
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197 "H": "D",
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198 "V": "B",
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199 "N": "N",
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200 "a": "t",
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201 "c": "g",
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202 "g": "c",
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203 "t": "a",
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204 "r": "y",
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205 "y": "r",
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206 "s": "w",
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207 "w": "s",
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208 "k": "m",
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209 "m": "k",
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210 "b": "v",
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211 "d": "h",
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212 "h": "d",
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213 "v": "b",
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214 "n": "n",
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215 }
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216 xrc = []
0
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217 for n in x:
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218 xrc.append(compdict[n])
1
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219 xrc = "".join(xrc)[::-1]
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220 return xrc
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221
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222
0
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223 # -----------------------------------------------------------------------------
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224
1
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225 psq_re_f = re.compile(args.regex, flags=flag)
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226 # psq_re_r= re.compile(regexrev)
0
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227
1
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228 if args.fasta != "-":
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229 ref_seq_fh = open(args.fasta)
0
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230 else:
1
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231 ref_seq_fh = sys.stdin
0
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232
1
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233 ref_seq = []
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234 line = (ref_seq_fh.readline()).strip()
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235 chr = re.sub("^>", "", line)
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236 line = (ref_seq_fh.readline()).strip()
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237 gquad_list = []
0
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238 while True:
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239 if not args.quiet:
1
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240 sys.stderr.write("Processing %s\n" % (chr))
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241 while line.startswith(">") is False:
0
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242 ref_seq.append(line)
1
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243 line = (ref_seq_fh.readline()).strip()
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244 if line == "":
0
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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245 break
1
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246 ref_seq = "".join(ref_seq)
0
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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247 if args.seqnames == [None] or chr in args.seqnames:
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248 for m in re.finditer(psq_re_f, ref_seq):
1
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249 matchstr = trimMatch(m.group(0), args.maxstr)
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250 quad_id = str(chr) + "_" + str(m.start()) + "_" + str(m.end()) + "_for"
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251 gquad_list.append(
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252 [chr, m.start(), m.end(), quad_id, len(m.group(0)), "+", matchstr]
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253 )
0
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254 if args.noreverse is False:
1
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255 ref_seq = revcomp(ref_seq)
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256 seqlen = len(ref_seq)
0
269c627ae9f4 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/fasta_regex_finder commit 8e118a4d24047e2c62912b962e854f789d6ff559
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257 for m in re.finditer(psq_re_f, ref_seq):
1
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258 matchstr = trimMatch(revcomp(m.group(0)), args.maxstr)
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259 mstart = seqlen - m.end()
9a811adb714f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe commit c318cd3f894f89c13d7eb257678673da70f72212
iuc
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260 mend = seqlen - m.start()
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iuc
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diff changeset
261 quad_id = str(chr) + "_" + str(mstart) + "_" + str(mend) + "_rev"
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262 gquad_list.append(
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263 [chr, mstart, mend, quad_id, len(m.group(0)), "-", matchstr]
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264 )
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265 gquad_sorted = sort_table(gquad_list, (1, 2, 3))
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266 gquad_list = []
0
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267 for xline in gquad_sorted:
1
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268 xline = "\t".join([str(x) for x in xline])
0
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269 print(xline)
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270 chr = re.sub("^>", "", line)
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271 ref_seq = []
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272 line = (ref_seq_fh.readline()).strip()
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273 if line == "":
0
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274 break
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275
1
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276 # gquad_sorted= sort_table(gquad_list, (0,1,2,3))
0
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277 #
1
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278 # for line in gquad_sorted:
0
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279 # line= '\t'.join([str(x) for x in line])
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280 # print(line)
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281 sys.exit()