Mercurial > repos > iuc > progressivemauve

annotate xmfa2gff3.py @ 2:bdb752f3c6bb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 7e386c24c2f9f0293abd4877eff708c1fa285751
author iuc
date Thu, 07 Feb 2019 05:24:24 -0500
parents bca52822843e
children 97a43bcbf44d
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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
parents: 0
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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
parents: 0
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3 import logging
0
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
iuc
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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
iuc
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11 SeqFeature
bca52822843e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
iuc
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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
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18
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19 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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20 """Simple XMFA parser until https://github.com/biopython/biopython/pull/544
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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21 """
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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22 current_lcb = []
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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23 current_seq = {}
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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24 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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25 if line.startswith('#'):
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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26 continue
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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27
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28 if line.strip() == '=':
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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29 if 'id' in current_seq:
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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30 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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31 current_seq = {}
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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32 yield current_lcb
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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33 current_lcb = []
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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34 else:
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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35 line = line.strip()
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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36 if line.startswith('>'):
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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37 if 'id' in current_seq:
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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38 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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39 current_seq = {}
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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40 data = line.strip().split()
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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41 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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42 start, end = loc.split('-')
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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43 current_seq = {
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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44 'rid': '_'.join(data[1:]),
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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45 'id': id,
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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46 'start': int(start),
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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47 'end': int(end),
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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48 'strand': 1 if data[2] == '+' else -1,
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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49 'seq': ''
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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50 }
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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51 else:
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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52 current_seq['seq'] += line.strip()
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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53
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54
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55 def _percent_identity(a, b):
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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56 """Calculate % identity, ignoring gaps in the host sequence
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57 """
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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58 match = 0
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59 mismatch = 0
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60 for char_a, char_b in zip(list(a), list(b)):
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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61 if char_a == '-':
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62 continue
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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63 if char_a == char_b:
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64 match += 1
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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65 else:
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66 mismatch += 1
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67
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68 if match + mismatch == 0:
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69 return 0
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70 return 100 * float(match) / (match + mismatch)
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71
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72
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73 def _id_tn_dict(sequences):
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74 """Figure out sequence IDs
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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75 """
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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76 label_convert = {}
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77 if sequences is not None:
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78 if len(sequences) == 1:
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79 for i, record in enumerate(SeqIO.parse(sequences[0], 'fasta')):
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80 label_convert[str(i + 1)] = record.id
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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81 else:
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82 for i, sequence in enumerate(sequences):
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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83 for record in SeqIO.parse(sequence, 'fasta'):
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
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84 label_convert[str(i + 1)] = record.id
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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85 continue
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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86 return label_convert
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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87
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88
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89 def convert_xmfa_to_gff3(xmfa_file, relative_to='1', sequences=None, window_size=1000):
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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90 label_convert = _id_tn_dict(sequences)
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91
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92 lcbs = parse_xmfa(xmfa_file)
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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93
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94 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
iuc
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95 for lcb in lcbs:
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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96 ids = [seq['id'] for seq in lcb]
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97
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98 # Doesn't match part of our sequence
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99 if relative_to not in ids:
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100 continue
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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101
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102 # Skip sequences that are JUST our "relative_to" genome
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103 if len(ids) == 1:
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104 continue
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105
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106 parent = [seq for seq in lcb if seq['id'] == relative_to][0]
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107 others = [seq for seq in lcb if seq['id'] != relative_to]
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108
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109 for other in others:
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parents:
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110 other['feature'] = SeqFeature(
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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111 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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112 type="match", strand=parent['strand'],
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113 qualifiers={
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114 "source": "progressiveMauve",
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115 "target": label_convert.get(other['id'], other['id']),
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116 "ID": label_convert.get(other['id'], 'xmfa_' + other['rid'])
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117 }
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118 )
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119
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120 for i in range(0, len(lcb[0]['seq']), window_size):
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121 block_seq = parent['seq'][i:i + window_size]
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122 real_window_size = len(block_seq)
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iuc
parents:
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123 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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124 real_end = real_start + real_window_size - block_seq.count('-')
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125
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126 if (real_end - real_start) < 10:
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127 continue
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128
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129 if parent['start'] < 0:
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130 strand = -1
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iuc
parents:
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131 else:
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132 strand = 1
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133
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iuc
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134 for other in others:
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135 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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parents:
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136 # Ignore 0% identity sequences
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137 if pid == 0:
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iuc
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138 continue
1
bca52822843e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
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parents: 0
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139
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parents: 0
diff changeset
140 # Support for Biopython 1.68 and above, which removed sub_features
bca52822843e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
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parents: 0
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141 if not hasattr(other['feature'], "sub_features"):
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parents: 0
diff changeset
142 other['feature'].sub_features = []
0
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
diff changeset
143 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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144 SeqFeature(
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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145 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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146 type="match_part", strand=strand,
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147 qualifiers={
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148 "source": "progressiveMauve",
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149 'score': pid
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150 }
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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151 )
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
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152 )
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
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153
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iuc
parents:
diff changeset
154 for other in others:
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iuc
parents:
diff changeset
155 records[0].features.append(other['feature'])
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
diff changeset
156 return records
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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157
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
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158
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
diff changeset
159 if __name__ == '__main__':
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
diff changeset
160 parser = argparse.ArgumentParser(description='Convert XMFA alignments to gff3', prog='xmfa2gff3')
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
diff changeset
161 parser.add_argument('xmfa_file', type=file, help='XMFA File')
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
diff changeset
162 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
iuc
parents:
diff changeset
163 parser.add_argument('--relative_to', type=str, help='Index of the parent sequence in the MSA', default='1')
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
diff changeset
164 parser.add_argument('--sequences', type=file, nargs='+',
74093fb62bdf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit 2645abbd04dd68266f995b8259e991c31388cda8
iuc
parents:
diff changeset
165 help='Fasta files (in same order) passed to parent for reconstructing proper IDs')
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iuc
parents:
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166 parser.add_argument('--version', action='version', version='%(prog)s 1.0')
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parents:
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167
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iuc
parents:
diff changeset
168 args = parser.parse_args()
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169
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parents:
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170 result = convert_xmfa_to_gff3(**vars(args))
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 GFF.write(result, sys.stdout)