Mercurial > repos > iuc > progressivemauve

annotate xmfa2gff3.py @ 5:ce795616bd9c draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit fcddceef74e33d544e239d1036467f65ef11767f"
author iuc
date Sat, 27 Nov 2021 12:13:25 +0000
parents 97a43bcbf44d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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diff changeset
1 #!/usr/bin/env python
1
bca52822843e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
iuc
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2 import argparse
bca52822843e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
iuc
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3 import logging
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74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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4 import sys
1
bca52822843e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
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5
bca52822843e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
iuc
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6 from BCBio import GFF
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74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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7 from Bio import SeqIO
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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8 from Bio.Seq import Seq
1
bca52822843e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
iuc
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9 from Bio.SeqFeature import (
bca52822843e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
iuc
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10 FeatureLocation,
bca52822843e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
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11 SeqFeature
bca52822843e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
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12 )
0
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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13 from Bio.SeqRecord import SeqRecord
1
bca52822843e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
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14
0
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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15 logging.basicConfig(level=logging.INFO)
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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16 log = logging.getLogger(__name__)
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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17
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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18
3
97a43bcbf44d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit fc61c9d4850614a6580d25f92e3032dc8edbc10d"
iuc
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19 # Patch bcbio gff to work around url encoding issue. This is clearly
97a43bcbf44d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit fc61c9d4850614a6580d25f92e3032dc8edbc10d"
iuc
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20 # sub-optimal but we should transition to the newer library.
97a43bcbf44d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit fc61c9d4850614a6580d25f92e3032dc8edbc10d"
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21 def _new_format_keyvals(self, keyvals):
97a43bcbf44d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit fc61c9d4850614a6580d25f92e3032dc8edbc10d"
iuc
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22 return ";".join(["%s=%s" % (k, ",".join(v)) for (k, v) in sorted(keyvals.items())])
97a43bcbf44d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit fc61c9d4850614a6580d25f92e3032dc8edbc10d"
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23
97a43bcbf44d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit fc61c9d4850614a6580d25f92e3032dc8edbc10d"
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24
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25 GFF.GFFOutput.GFF3Writer._format_keyvals = _new_format_keyvals
97a43bcbf44d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit fc61c9d4850614a6580d25f92e3032dc8edbc10d"
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26
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27
0
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28 def parse_xmfa(xmfa):
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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29 """Simple XMFA parser until https://github.com/biopython/biopython/pull/544
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30 """
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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31 current_lcb = []
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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32 current_seq = {}
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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33 for line in xmfa.readlines():
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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34 if line.startswith('#'):
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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35 continue
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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36
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37 if line.strip() == '=':
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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38 if 'id' in current_seq:
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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39 current_lcb.append(current_seq)
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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40 current_seq = {}
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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41 yield current_lcb
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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42 current_lcb = []
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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43 else:
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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44 line = line.strip()
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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45 if line.startswith('>'):
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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46 if 'id' in current_seq:
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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47 current_lcb.append(current_seq)
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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48 current_seq = {}
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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49 data = line.strip().split()
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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50 id, loc = data[1].split(':')
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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51 start, end = loc.split('-')
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52 current_seq = {
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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53 'rid': '_'.join(data[1:]),
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54 'id': id,
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55 'start': int(start),
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56 'end': int(end),
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57 'strand': 1 if data[2] == '+' else -1,
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58 'seq': ''
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59 }
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60 else:
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61 current_seq['seq'] += line.strip()
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62
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63
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64 def _percent_identity(a, b):
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65 """Calculate % identity, ignoring gaps in the host sequence
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66 """
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67 match = 0
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68 mismatch = 0
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69 for char_a, char_b in zip(list(a), list(b)):
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70 if char_a == '-':
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71 continue
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72 if char_a == char_b:
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73 match += 1
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74 else:
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75 mismatch += 1
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76
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77 if match + mismatch == 0:
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78 return 0
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79 return 100 * float(match) / (match + mismatch)
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80
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81
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82 def _id_tn_dict(sequences):
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83 """Figure out sequence IDs
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84 """
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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85 label_convert = {}
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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86 if sequences is not None:
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87 if len(sequences) == 1:
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88 for i, record in enumerate(SeqIO.parse(sequences[0], 'fasta')):
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89 label_convert[str(i + 1)] = record.id
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90 else:
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91 for i, sequence in enumerate(sequences):
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92 for record in SeqIO.parse(sequence, 'fasta'):
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93 label_convert[str(i + 1)] = record.id
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94 continue
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95 return label_convert
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96
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97
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parents:
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98 def convert_xmfa_to_gff3(xmfa_file, relative_to='1', sequences=None, window_size=1000):
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99 label_convert = _id_tn_dict(sequences)
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100
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101 lcbs = parse_xmfa(xmfa_file)
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102
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103 records = [SeqRecord(Seq("A"), id=label_convert.get(relative_to, relative_to))]
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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104 for lcb in lcbs:
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105 ids = [seq['id'] for seq in lcb]
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106
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107 # Doesn't match part of our sequence
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108 if relative_to not in ids:
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109 continue
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110
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parents:
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111 # Skip sequences that are JUST our "relative_to" genome
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112 if len(ids) == 1:
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113 continue
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114
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parents:
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115 parent = [seq for seq in lcb if seq['id'] == relative_to][0]
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116 others = [seq for seq in lcb if seq['id'] != relative_to]
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117
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118 for other in others:
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119 other['feature'] = SeqFeature(
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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120 FeatureLocation(parent['start'], parent['end'] + 1),
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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121 type="match", strand=parent['strand'],
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122 qualifiers={
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123 "source": "progressiveMauve",
3
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124 "Target": " ".join(map(str, [label_convert.get(other['id'], other['id']), other['start'], other['end'], '+' if other['strand'] > 0 else '-'])),
0
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125 "ID": label_convert.get(other['id'], 'xmfa_' + other['rid'])
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126 }
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127 )
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128
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129 for i in range(0, len(lcb[0]['seq']), window_size):
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130 block_seq = parent['seq'][i:i + window_size]
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131 real_window_size = len(block_seq)
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132 real_start = abs(parent['start']) - parent['seq'][0:i].count('-') + i
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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133 real_end = real_start + real_window_size - block_seq.count('-')
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134
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135 if (real_end - real_start) < 10:
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136 continue
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137
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iuc
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138 if parent['start'] < 0:
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139 strand = -1
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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parents:
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140 else:
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141 strand = 1
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142
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143 for other in others:
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144 pid = _percent_identity(block_seq, other['seq'][i:i + real_window_size])
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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145 # Ignore 0% identity sequences
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146 if pid == 0:
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147 continue
1
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148
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parents: 0
diff changeset
149 # Support for Biopython 1.68 and above, which removed sub_features
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150 if not hasattr(other['feature'], "sub_features"):
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parents: 0
diff changeset
151 other['feature'].sub_features = []
0
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parents:
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152 other['feature'].sub_features.append(
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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parents:
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153 SeqFeature(
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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154 FeatureLocation(real_start, real_end),
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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parents:
diff changeset
155 type="match_part", strand=strand,
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
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156 qualifiers={
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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157 "source": "progressiveMauve",
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158 'score': pid
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159 }
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160 )
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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diff changeset
161 )
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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162
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163 for other in others:
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iuc
parents:
diff changeset
164 records[0].features.append(other['feature'])
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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parents:
diff changeset
165 return records
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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166
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167
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parents:
diff changeset
168 if __name__ == '__main__':
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iuc
parents:
diff changeset
169 parser = argparse.ArgumentParser(description='Convert XMFA alignments to gff3', prog='xmfa2gff3')
3
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diff changeset
170 parser.add_argument('xmfa_file', type=argparse.FileType('r'), help='XMFA File')
0
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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parents:
diff changeset
171 parser.add_argument('--window_size', type=int, help='Window size for analysis', default=1000)
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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parents:
diff changeset
172 parser.add_argument('--relative_to', type=str, help='Index of the parent sequence in the MSA', default='1')
3
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diff changeset
173 parser.add_argument('--sequences', type=argparse.FileType('r'), nargs='+',
0
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
diff changeset
174 help='Fasta files (in same order) passed to parent for reconstructing proper IDs')
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iuc
parents:
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175 parser.add_argument('--version', action='version', version='%(prog)s 1.0')
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176
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parents:
diff changeset
177 args = parser.parse_args()
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178
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parents:
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179 result = convert_xmfa_to_gff3(**vars(args))
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180 GFF.write(result, sys.stdout)