Mercurial > repos > earlhaminst > gstf_preparation

annotate gstf_preparation.py @ 7:9ef7661e8e9c draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 79c2cb2362b64134df778cc484e426642eb6895e
author earlhaminst
date Wed, 25 Apr 2018 11:06:03 -0400
parents 56bbdbfe3eaa
children 92f3966d5bc3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
1 from __future__ import print_function
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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2
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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3 import collections
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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4 import json
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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5 import optparse
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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6 import sqlite3
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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7 import sys
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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8
6
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earlhaminst
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9 version = "0.4.0"
0
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earlhaminst
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10 gene_count = 0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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earlhaminst
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12 Sequence = collections.namedtuple('Sequence', ['header', 'sequence'])
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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15 def FASTAReader_gen(fasta_filename):
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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16 with open(fasta_filename) as fasta_file:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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17 line = fasta_file.readline()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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18 while True:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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19 if not line:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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20 return
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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21 assert line.startswith('>'), "FASTA headers must start with >"
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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22 header = line.rstrip()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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23 sequence_parts = []
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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24 line = fasta_file.readline()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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25 while line and line[0] != '>':
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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26 sequence_parts.append(line.rstrip())
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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27 line = fasta_file.readline()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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28 sequence = "\n".join(sequence_parts)
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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29 yield Sequence(header, sequence)
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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32 def create_tables(conn):
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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33 cur = conn.cursor()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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34
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35 cur.execute('''CREATE TABLE meta (
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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36 version VARCHAR PRIMARY KEY NOT NULL)''')
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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37
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38 cur.execute('INSERT INTO meta (version) VALUES (?)',
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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39 (version, ))
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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41 cur.execute('''CREATE TABLE gene (
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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42 gene_id VARCHAR PRIMARY KEY NOT NULL,
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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43 gene_symbol VARCHAR,
6
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earlhaminst
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44 seq_region_name VARCHAR NOT NULL,
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
earlhaminst
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45 seq_region_start INTEGER NOT NULL,
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
earlhaminst
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46 seq_region_end INTEGER NOT NULL,
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
earlhaminst
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47 seq_region_strand INTEGER NOT NULL,
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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48 species VARCHAR NOT NULL,
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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49 gene_json VARCHAR NOT NULL)''')
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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50 cur.execute('CREATE INDEX gene_symbol_index ON gene (gene_symbol)')
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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51
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52 cur.execute('''CREATE TABLE transcript (
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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53 transcript_id VARCHAR PRIMARY KEY NOT NULL,
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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54 protein_id VARCHAR UNIQUE,
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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55 protein_sequence VARCHAR,
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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56 gene_id VARCHAR NOT NULL REFERENCES gene(gene_id))''')
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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57
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58 cur.execute('''CREATE VIEW transcript_species AS
6
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
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59 SELECT transcript_id, species, seq_region_name
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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60 FROM transcript JOIN gene
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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61 ON transcript.gene_id = gene.gene_id''')
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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62
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63 conn.commit()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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64
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65
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66 def remove_type_from_list_of_ids(l):
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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67 return ','.join(remove_type_from_id(_) for _ in l.split(','))
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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68
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69
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70 def remove_type_from_id(id_):
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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71 colon_index = id_.find(':')
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72 if colon_index >= 0:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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73 return id_[colon_index + 1:]
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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74 else:
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75 return id_
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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76
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77
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78 def feature_to_dict(cols, parent_dict=None):
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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79 d = {
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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80 'end': int(cols[4]),
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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81 'start': int(cols[3]),
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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82 }
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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83 for attr in cols[8].split(';'):
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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84 if '=' in attr:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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85 (tag, value) = attr.split('=')
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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86 if tag == 'ID':
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87 tag = 'id'
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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88 value = remove_type_from_id(value)
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89 elif tag == 'Parent':
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earlhaminst
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90 value = remove_type_from_list_of_ids(value)
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91 d[tag] = value
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92 if cols[6] == '+':
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93 d['strand'] = 1
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94 elif cols[6] == '-':
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95 d['strand'] = -1
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96 else:
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97 raise Exception("Unrecognized strand '%s'" % cols[6])
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98 if parent_dict is not None and 'Parent' in d:
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99 # a 3' UTR can be split among multiple exons
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100 # a 5' UTR can be split among multiple exons
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101 # a CDS can be part of multiple transcripts
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102 for parent in d['Parent'].split(','):
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103 if parent not in parent_dict:
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104 parent_dict[parent] = [d]
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105 else:
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106 parent_dict[parent].append(d)
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107 return d
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108
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109
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110 def add_gene_to_dict(cols, species, gene_dict):
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111 global gene_count
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112 gene = feature_to_dict(cols)
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113 gene.update({
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114 'member_id': gene_count,
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115 'object_type': 'Gene',
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116 'seq_region_name': cols[0],
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117 'species': species,
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118 'Transcript': [],
1
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119 'display_name': gene.get('Name', None)
0
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120 })
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121 if gene['id']:
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122 gene_dict[gene['id']] = gene
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123 gene_count = gene_count + 1
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124
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125
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126 def add_transcript_to_dict(cols, species, transcript_dict):
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127 transcript = feature_to_dict(cols)
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128 transcript.update({
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129 'object_type': 'Transcript',
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130 'seq_region_name': cols[0],
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131 'species': species,
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132 })
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133 transcript_dict[transcript['id']] = transcript
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134
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135
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136 def add_exon_to_dict(cols, species, exon_parent_dict):
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137 exon = feature_to_dict(cols, exon_parent_dict)
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138 exon.update({
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earlhaminst
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139 'length': int(cols[4]) - int(cols[3]) + 1,
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140 'object_type': 'Exon',
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141 'seq_region_name': cols[0],
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142 'species': species,
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143 })
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144 if 'id' not in exon and 'Name' in exon:
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145 exon['id'] = exon['Name']
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146
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147
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148 def add_cds_to_dict(cols, cds_parent_dict):
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149 cds = feature_to_dict(cols, cds_parent_dict)
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150 if 'id' not in cds:
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151 if 'Name' in cds:
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152 cds['id'] = cds['Name']
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153 elif 'Parent' in cds and ',' not in cds['Parent']:
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154 cds['id'] = cds['Parent']
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155
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156
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157 def join_dicts(gene_dict, transcript_dict, exon_parent_dict, cds_parent_dict, five_prime_utr_parent_dict, three_prime_utr_parent_dict):
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158 for parent, exon_list in exon_parent_dict.items():
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159 if parent in transcript_dict:
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160 exon_list.sort(key=lambda _: _['start'])
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161 transcript_dict[parent]['Exon'] = exon_list
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162
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163 for transcript_id, transcript in transcript_dict.items():
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164 translation = {
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165 'CDS': [],
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166 'id': None,
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167 'end': transcript['end'],
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168 'object_type': 'Translation',
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169 'species': transcript['species'],
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170 'start': transcript['start'],
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171 }
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172 found_cds = False
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173 derived_translation_start = None
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174 derived_translation_end = None
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diff changeset
175 if transcript_id in cds_parent_dict:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
176 cds_list = cds_parent_dict[transcript_id]
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
177 cds_ids = set(_['id'] for _ in cds_list)
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
178 if len(cds_ids) > 1:
5
b3ba0c84667c planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
earlhaminst
parents: 4
diff changeset
179 raise Exception("Transcript %s has multiple CDSs: this is not supported by Ensembl JSON format" % transcript_id)
b3ba0c84667c planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
earlhaminst
parents: 4
diff changeset
180 cds_id = cds_ids.pop()
b3ba0c84667c planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
earlhaminst
parents: 4
diff changeset
181 translation['id'] = cds_id
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
182 cds_list.sort(key=lambda _: _['start'])
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
183 translation['CDS'] = cds_list
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
184 translation['start'] = cds_list[0]['start']
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
185 translation['end'] = cds_list[-1]['end']
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
186 found_cds = True
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
187 if transcript_id in five_prime_utr_parent_dict:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
188 five_prime_utr_list = five_prime_utr_parent_dict[transcript_id]
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
189 five_prime_utr_list.sort(key=lambda _: _['start'])
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
190 if transcript['strand'] == 1:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
191 derived_translation_start = five_prime_utr_list[-1]['end'] + 1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
192 else:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
193 derived_translation_end = five_prime_utr_list[0]['start'] - 1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
194 if transcript_id in three_prime_utr_parent_dict:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
195 three_prime_utr_list = three_prime_utr_parent_dict[transcript_id]
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
196 three_prime_utr_list.sort(key=lambda _: _['start'])
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
197 if transcript['strand'] == 1:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
198 derived_translation_end = three_prime_utr_list[0]['start'] - 1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
199 else:
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earlhaminst
parents:
diff changeset
200 derived_translation_start = three_prime_utr_list[-1]['end'] + 1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
201 if derived_translation_start is not None:
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earlhaminst
parents:
diff changeset
202 if found_cds:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
203 if derived_translation_start > translation['start']:
5
b3ba0c84667c planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
earlhaminst
parents: 4
diff changeset
204 raise Exception("Transcript %s has the start of CDS %s overlapping with the UTR end" % (transcript_id, cds_id))
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
205 else:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
206 translation['start'] = derived_translation_start
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
207 if derived_translation_end is not None:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
208 if found_cds:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
209 if derived_translation_end < translation['end']:
5
b3ba0c84667c planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
earlhaminst
parents: 4
diff changeset
210 raise Exception("Transcript %s has the end of CDS %s overlapping with the UTR start" % (transcript_id, cds_id))
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
211 else:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
212 translation['end'] = derived_translation_end
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
213 if found_cds or derived_translation_start is not None or derived_translation_end is not None:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
214 transcript['Translation'] = translation
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
215
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earlhaminst
parents:
diff changeset
216 for transcript in transcript_dict.values():
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
217 if 'Parent' in transcript:
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earlhaminst
parents:
diff changeset
218 # A polycistronic transcript can have multiple parents
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
219 for parent in transcript['Parent'].split(','):
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
220 if parent in gene_dict:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
221 gene_dict[parent]['Transcript'].append(transcript)
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
222
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earlhaminst
parents:
diff changeset
223
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earlhaminst
parents:
diff changeset
224 def write_gene_dict_to_db(conn, gene_dict):
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
225 cur = conn.cursor()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
226
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
227 for gene in gene_dict.values():
3
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earlhaminst
parents: 1
diff changeset
228 if gene is None:
7e11a7f4bdba planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 77ed525b753e34d3e9dd4f07a239592ce764f7e6-dirty
earlhaminst
parents: 1
diff changeset
229 # This can happen when loading a JSON file from Ensembl
7e11a7f4bdba planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 77ed525b753e34d3e9dd4f07a239592ce764f7e6-dirty
earlhaminst
parents: 1
diff changeset
230 continue
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
231 gene_id = gene['id']
6
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
earlhaminst
parents: 5
diff changeset
232 cur.execute('INSERT INTO gene (gene_id, gene_symbol, seq_region_name, seq_region_start, seq_region_end, seq_region_strand, species, gene_json) VALUES (?, ?, ?, ?, ?, ?, ?, ?)',
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
earlhaminst
parents: 5
diff changeset
233 (gene_id, gene.get('display_name', None), gene['seq_region_name'], gene['start'], gene['end'], gene['strand'], gene['species'], json.dumps(gene)))
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
234
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
235 if "Transcript" in gene:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
236 for transcript in gene["Transcript"]:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
237 transcript_id = transcript['id']
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
238 protein_id = transcript.get('Translation', {}).get('id', None)
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
239 try:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
240 cur.execute('INSERT INTO transcript (transcript_id, protein_id, gene_id) VALUES (?, ?, ?)',
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
241 (transcript_id, protein_id, gene_id))
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
242 except Exception as e:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
243 raise Exception("Error while inserting (%s, %s, %s) into transcript table: %s" % (transcript_id, protein_id, gene_id, e))
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
244
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
245 conn.commit()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
246
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
247
6
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
earlhaminst
parents: 5
diff changeset
248 def fetch_species_and_seq_region_for_transcript(conn, transcript_id):
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
249 cur = conn.cursor()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
250
6
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
earlhaminst
parents: 5
diff changeset
251 cur.execute('SELECT species, seq_region_name FROM transcript_species WHERE transcript_id=?',
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
252 (transcript_id, ))
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
253 results = cur.fetchone()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
254 if not results:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
255 return None
6
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
earlhaminst
parents: 5
diff changeset
256 return results
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
257
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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diff changeset
258
4
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
parents: 3
diff changeset
259 def fetch_gene_id_for_transcript(conn, transcript_id):
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
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diff changeset
260 cur = conn.cursor()
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
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parents: 3
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261
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earlhaminst
parents: 3
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262 cur.execute('SELECT gene_id FROM transcript WHERE transcript_id=?',
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
parents: 3
diff changeset
263 (transcript_id, ))
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
parents: 3
diff changeset
264 results = cur.fetchone()
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
parents: 3
diff changeset
265 if not results:
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
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parents: 3
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266 return None
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
parents: 3
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267 return results[0]
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
parents: 3
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268
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
parents: 3
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269
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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270 def remove_id_version(s):
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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271 """
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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272 Remove the optional '.VERSION' from an Ensembl id.
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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273 """
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
274 if s.startswith('ENS'):
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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275 return s.split('.')[0]
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earlhaminst
parents:
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276 else:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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277 return s
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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278
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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279
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earlhaminst
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280 def __main__():
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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281 parser = optparse.OptionParser()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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parents:
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282 parser.add_option('--gff3', action='append', default=[], help='GFF3 file to convert, in SPECIES:FILENAME format. Use multiple times to add more files')
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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283 parser.add_option('--json', action='append', default=[], help='JSON file to merge. Use multiple times to add more files')
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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284 parser.add_option('--fasta', action='append', default=[], help='Path of the input FASTA files')
4
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
parents: 3
diff changeset
285 parser.add_option('-l', action='store_true', default=False, dest='longestCDS', help='Keep only the longest CDS per gene')
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
parents: 3
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286 parser.add_option('--headers', action='store_true', default=False, help='Change the header line of the FASTA sequences to the >TranscriptId_species format')
6
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
earlhaminst
parents: 5
diff changeset
287 parser.add_option('--regions', default="", help='Comma-separated list of region IDs for which FASTA sequences should be filtered')
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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288 parser.add_option('-o', '--output', help='Path of the output SQLite file')
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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diff changeset
289 parser.add_option('--of', help='Path of the output FASTA file')
6
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
earlhaminst
parents: 5
diff changeset
290 parser.add_option('--ff', help='Path of the filtered sequences output FASTA file')
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
earlhaminst
parents: 5
diff changeset
291
0
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earlhaminst
parents:
diff changeset
292 options, args = parser.parse_args()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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293 if args:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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294 raise Exception('Use options to provide inputs')
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earlhaminst
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295
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earlhaminst
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296 conn = sqlite3.connect(options.output)
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297 conn.execute('PRAGMA foreign_keys = ON')
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298 create_tables(conn)
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299
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earlhaminst
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300 for gff3_arg in options.gff3:
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earlhaminst
parents:
diff changeset
301 try:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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302 (species, filename) = gff3_arg.split(':')
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
303 except ValueError:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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304 raise Exception("Argument for --gff3 '%s' is not in the SPECIES:FILENAME format" % gff3_arg)
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
305 gene_dict = dict()
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earlhaminst
parents:
diff changeset
306 transcript_dict = dict()
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earlhaminst
parents:
diff changeset
307 exon_parent_dict = dict()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
308 cds_parent_dict = dict()
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earlhaminst
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diff changeset
309 five_prime_utr_parent_dict = dict()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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diff changeset
310 three_prime_utr_parent_dict = dict()
5
b3ba0c84667c planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
earlhaminst
parents: 4
diff changeset
311 unimplemented_feature_nlines_dict = dict()
4
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
parents: 3
diff changeset
312
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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diff changeset
313 with open(filename) as f:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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314 for i, line in enumerate(f, start=1):
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
315 line = line.strip()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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diff changeset
316 if not line:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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317 # skip empty lines
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earlhaminst
parents:
diff changeset
318 continue
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
319 if line[0] == '#':
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
320 # skip comment lines
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
321 continue
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
322 cols = line.split('\t')
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
323 if len(cols) != 9:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
324 raise Exception("Line %i in file '%s': '%s' does not have 9 columns" % (i, filename, line))
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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diff changeset
325 feature_type = cols[2]
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
326 try:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
327 if feature_type == 'gene':
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
328 add_gene_to_dict(cols, species, gene_dict)
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
329 elif feature_type in ('mRNA', 'transcript'):
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
330 add_transcript_to_dict(cols, species, transcript_dict)
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
331 elif feature_type == 'exon':
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
332 add_exon_to_dict(cols, species, exon_parent_dict)
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
333 elif feature_type == 'five_prime_UTR':
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
334 feature_to_dict(cols, five_prime_utr_parent_dict)
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
335 elif feature_type == 'three_prime_UTR':
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
336 feature_to_dict(cols, three_prime_utr_parent_dict)
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
337 elif feature_type == 'CDS':
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
338 add_cds_to_dict(cols, cds_parent_dict)
5
b3ba0c84667c planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
earlhaminst
parents: 4
diff changeset
339 elif feature_type in unimplemented_feature_nlines_dict:
b3ba0c84667c planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
earlhaminst
parents: 4
diff changeset
340 unimplemented_feature_nlines_dict[feature_type] += 1
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
341 else:
5
b3ba0c84667c planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
earlhaminst
parents: 4
diff changeset
342 unimplemented_feature_nlines_dict[feature_type] = 0
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
343 except Exception as e:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
344 print("Line %i in file '%s': %s" % (i, filename, e), file=sys.stderr)
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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345
5
b3ba0c84667c planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
earlhaminst
parents: 4
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346 for unimplemented_feature, nlines in unimplemented_feature_nlines_dict.items():
b3ba0c84667c planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
earlhaminst
parents: 4
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347 print("Skipped %d lines in file '%s': '%s' is not an implemented feature type" % (nlines, filename, unimplemented_feature), file=sys.stderr)
b3ba0c84667c planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
earlhaminst
parents: 4
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348
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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349 join_dicts(gene_dict, transcript_dict, exon_parent_dict, cds_parent_dict, five_prime_utr_parent_dict, three_prime_utr_parent_dict)
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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350 write_gene_dict_to_db(conn, gene_dict)
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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351
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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352 for json_arg in options.json:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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353 with open(json_arg) as f:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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354 write_gene_dict_to_db(conn, json.load(f))
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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355
4
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
parents: 3
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356 if options.longestCDS:
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
parents: 3
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357 gene_transcripts_dict = dict()
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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358 for fasta_arg in options.fasta:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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359 for entry in FASTAReader_gen(fasta_arg):
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
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360 # Extract the transcript id by removing everything after the first space and then removing the version if it is an Ensembl id
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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361 transcript_id = remove_id_version(entry.header[1:].lstrip().split(' ')[0])
4
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
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362
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
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363 gene_id = fetch_gene_id_for_transcript(conn, transcript_id)
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
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364 if not gene_id:
5
b3ba0c84667c planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
earlhaminst
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365 print("Transcript '%s' in file '%s' not found in the gene feature information" % (transcript_id, fasta_arg), file=sys.stderr)
4
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
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diff changeset
366 continue
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
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diff changeset
367
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
parents: 3
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368 if gene_id in gene_transcripts_dict:
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
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369 gene_transcripts_dict[gene_id].append((transcript_id, len(entry.sequence)))
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
parents: 3
diff changeset
370 else:
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
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371 gene_transcripts_dict[gene_id] = [(transcript_id, len(entry.sequence))]
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
parents: 3
diff changeset
372
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
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373 # For each gene, select the transcript with the longest sequence
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
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374 # If more than one transcripts have the same longest sequence for a gene, the
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
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375 # first one to appear in the FASTA file is selected
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
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376 selected_transcript_ids = [max(transcript_id_lengths, key=lambda _: _[1])[0] for transcript_id_lengths in gene_transcripts_dict.values()]
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
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377
6
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378 regions = [_.strip().lower() for _ in options.regions.split(",")]
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
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379 with open(options.of, 'w') as output_fasta_file, open(options.ff, 'w') as filtered_fasta_file:
4
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
parents: 3
diff changeset
380 for fasta_arg in options.fasta:
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
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diff changeset
381 for entry in FASTAReader_gen(fasta_arg):
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
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382 transcript_id = remove_id_version(entry.header[1:].lstrip().split(' ')[0])
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
parents: 3
diff changeset
383 if options.longestCDS and transcript_id not in selected_transcript_ids:
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
parents: 3
diff changeset
384 continue
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
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diff changeset
385
6
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
earlhaminst
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diff changeset
386 species_for_transcript, seq_region_for_transcript = fetch_species_and_seq_region_for_transcript(conn, transcript_id)
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
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diff changeset
387 if not species_for_transcript:
5
b3ba0c84667c planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 95bab1105cf8a7b07c668f08f712399e8775a4ae
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diff changeset
388 print("Transcript '%s' in file '%s' not found in the gene feature information" % (transcript_id, fasta_arg), file=sys.stderr)
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
389 continue
4
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
parents: 3
diff changeset
390
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
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diff changeset
391 if options.headers:
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
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diff changeset
392 # Change the FASTA header to '>TranscriptId_species', as required by TreeBest
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
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diff changeset
393 # Remove any underscore in the species
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
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diff changeset
394 header = ">%s_%s" % (transcript_id, species_for_transcript.replace('_', ''))
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
parents: 3
diff changeset
395 else:
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
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diff changeset
396 header = entry.header
284f64ad9d43 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit cda3ecab1a34376cc7d4d392a34dc810847cbf0b-dirty
earlhaminst
parents: 3
diff changeset
397
6
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
earlhaminst
parents: 5
diff changeset
398 if seq_region_for_transcript.lower() in regions:
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
earlhaminst
parents: 5
diff changeset
399 filtered_fasta_file.write("%s\n%s\n" % (header, entry.sequence))
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
earlhaminst
parents: 5
diff changeset
400 else:
56bbdbfe3eaa planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
earlhaminst
parents: 5
diff changeset
401 output_fasta_file.write("%s\n%s\n" % (header, entry.sequence))
0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
402
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
403 conn.close()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
404
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
405
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
parents:
diff changeset
406 if __name__ == '__main__':
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670
earlhaminst
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diff changeset
407 __main__()