Mercurial > repos > iuc > amas_concat

annotate check_interleaved.py @ 0:fb24e1904d08 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
author iuc
date Tue, 02 Dec 2025 09:26:01 +0000
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
iuc
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1 """
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
iuc
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2 Helper script to check if AMAS input files are interleaved.
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
iuc
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3 """
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
iuc
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4 import argparse
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
iuc
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5 import re
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
iuc
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6 import sys
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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7
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8
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9 def check_phylip_interleaved(filepath):
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
iuc
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10 """Check if PHYLIP file is interleaved."""
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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11 with open(filepath, encoding='utf-8') as f:
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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12 # First line is header: ntax nchar
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13 header = next(f).strip().split()
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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14 ntax = int(header[0])
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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15
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16 for idx, line in enumerate(f, 1):
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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17 if line.strip():
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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18 if idx > ntax:
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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19 return True
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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20
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21 return False
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23
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24 def check_nexus_interleaved(filepath):
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25 """Check if NEXUS file is interleaved."""
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26 in_data_block = False
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27 in_matrix = False
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28 ntax = None
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29 seq_lines = 0
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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30
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31 with open(filepath, encoding='utf-8') as f:
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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32 for line in f:
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33 content = line.strip().lower()
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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34
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35 if not content:
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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36 continue
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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37
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38 if in_matrix:
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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39 if content == 'end;':
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40 return seq_lines != ntax if ntax else False
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41
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42 if content != ';':
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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43 seq_lines += 1
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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44 if ntax and seq_lines > ntax:
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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45 return True
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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46 continue
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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47
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48 if not in_data_block:
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49 if content.startswith('begin'):
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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50 words = content.split()
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51 if len(words) > 1 and (
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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52 words[1].startswith('data')
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53 or words[1].startswith('characters')):
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54 in_data_block = True
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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55 continue
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56
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57 if content.startswith('dimensions') and ntax is None:
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58 match = re.search(r'ntax=(\d+)', content)
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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59 if match:
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60 ntax = int(match.group(1))
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61
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62 elif content.startswith('format'):
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63 if re.search(r'\binterleave(?:;|=yes;?)?\b', content):
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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64 return True
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65
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66 elif content.startswith('matrix'):
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67 in_matrix = True
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68
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69 return False
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70
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71
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72 def check_fasta_interleaved(filepath):
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73 """FASTA files are not interleaved."""
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74 return False
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75
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76
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77 def main():
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78 parser = argparse.ArgumentParser(
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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79 description='Check if AMAS input files are interleaved'
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80 )
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81 parser.add_argument('input_files', nargs='+', help='Input sequence files')
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82 parser.add_argument('--format', required=True,
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83 choices=['fasta', 'phylip', 'nexus'],
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84 help='Input format')
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85
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86 args = parser.parse_args()
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87
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88 interleaved_status = []
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89 for filepath in args.input_files:
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90 if args.format == 'phylip':
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91 is_interleaved = check_phylip_interleaved(filepath)
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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92 elif args.format == 'nexus':
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93 is_interleaved = check_nexus_interleaved(filepath)
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94 else:
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95 is_interleaved = check_fasta_interleaved(filepath)
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96
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97 interleaved_status.append(is_interleaved)
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98
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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99 interleaved_status = list(set(interleaved_status))
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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100 if len(interleaved_status) > 1:
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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101 raise Exception("Error: Input files are a mix of interleaved/sequential formats")
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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102
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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103 if interleaved_status[0]:
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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104 print(f"{args.format}-int")
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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105 else:
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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106 print(args.format)
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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107
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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108 return 0
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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109
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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110
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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111 if __name__ == '__main__':
fb24e1904d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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112 sys.exit(main())