gstf_preparation: gstf_preparation.py annotate

annotate gstf_preparation.py @ 1:a36645976342 draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 68cf06ec77e20eaf057d77d5bea19e201c4ab27e-dirty

author	earlhaminst
date	Thu, 16 Mar 2017 12:41:51 -0400
parents	28879ca33b5f
children	7e11a7f4bdba

rev	line source
0 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 parents: diff changeset	2
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	3 import collections
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	4 import json
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	5 import optparse
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	6 import sqlite3
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	7 import sys
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	8
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	9 version = "0.3.0"
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	10 gene_count = 0
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	11
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	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 earlhaminst parents: diff changeset	13
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	14
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	15 def FASTAReader_gen(fasta_filename):
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	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 parents: diff changeset	17 line = fasta_file.readline()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	18 while True:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	19 if not line:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	20 return
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	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 parents: diff changeset	22 header = line.rstrip()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	23 sequence_parts = []
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	24 line = fasta_file.readline()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	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 parents: diff changeset	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 parents: diff changeset	27 line = fasta_file.readline()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	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 parents: diff changeset	29 yield Sequence(header, sequence)
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	30
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	31
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	32 def create_tables(conn):
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	33 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	34
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	35 cur.execute('''CREATE TABLE meta (
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	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 earlhaminst parents: diff changeset	37
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	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 parents: diff changeset	39 (version, ))
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	40
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	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 parents: diff changeset	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 earlhaminst parents: diff changeset	43 gene_symbol VARCHAR,
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	44 species VARCHAR NOT NULL,
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	45 gene_json VARCHAR NOT NULL)''')
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	46 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 earlhaminst parents: diff changeset	47
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	48 cur.execute('''CREATE TABLE transcript (
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	49 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 earlhaminst parents: diff changeset	50 protein_id VARCHAR UNIQUE,
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	51 protein_sequence VARCHAR,
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	52 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 earlhaminst parents: diff changeset	53
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	54 cur.execute('''CREATE VIEW transcript_species AS
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	55 SELECT transcript_id, species
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	56 FROM transcript JOIN gene
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	57 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 earlhaminst parents: diff changeset	58
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	59 conn.commit()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	60
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	61
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	62 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 earlhaminst parents: diff changeset	63 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 earlhaminst parents: diff changeset	64
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	65
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	66 def remove_type_from_id(id_):
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	67 colon_index = id_.find(':')
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	68 if colon_index >= 0:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	69 return id_[colon_index + 1:]
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	70 else:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	71 return id_
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	72
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	73
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	74 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 earlhaminst parents: diff changeset	75 d = {
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	76 'end': int(cols[4]),
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	77 'start': int(cols[3]),
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	78 }
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	79 for attr in cols[8].split(';'):
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	80 if '=' in attr:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	81 (tag, value) = attr.split('=')
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	82 if tag == 'ID':
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	83 tag = 'id'
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	84 value = remove_type_from_id(value)
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	85 elif tag == 'Parent':
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	86 value = remove_type_from_list_of_ids(value)
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	87 d[tag] = value
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	88 if cols[6] == '+':
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	89 d['strand'] = 1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	90 elif cols[6] == '-':
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	91 d['strand'] = -1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	92 else:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	93 raise Exception("Unrecognized strand '%s'" % cols[6])
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	94 if parent_dict is not None and 'Parent' in d:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	95 # a 3' UTR can be split among multiple exons
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	96 # a 5' UTR can be split among multiple exons
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	97 # a CDS can be part of multiple transcripts
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	98 for parent in d['Parent'].split(','):
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	99 if parent not in parent_dict:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	100 parent_dict[parent] = [d]
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	101 else:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	102 parent_dict[parent].append(d)
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	103 return d
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	104
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	105
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	106 def 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	107 global gene_count
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	108 gene = feature_to_dict(cols)
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	109 gene.update({
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	110 'member_id': gene_count,
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	111 'object_type': 'Gene',
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	112 'seq_region_name': cols[0],
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	113 'species': species,
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	114 'Transcript': [],
1 a36645976342 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 68cf06ec77e20eaf057d77d5bea19e201c4ab27e-dirty earlhaminst parents: 0 diff changeset	115 'display_name': gene.get('Name', None)
0 28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	116 })
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	117 if gene['id']:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	118 gene_dict[gene['id']] = gene
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	119 gene_count = gene_count + 1
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	120
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	121
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	122 def 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	123 transcript = feature_to_dict(cols)
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	124 transcript.update({
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	125 'object_type': 'Transcript',
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	126 'seq_region_name': cols[0],
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	127 'species': species,
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	128 })
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	129 transcript_dict[transcript['id']] = transcript
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	130
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	131
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	132 def 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	133 exon = feature_to_dict(cols, 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	134 exon.update({
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	135 'length': int(cols[4]) - int(cols[3]) + 1,
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	136 'object_type': 'Exon',
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	137 'seq_region_name': cols[0],
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	138 'species': species,
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	139 })
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	140 if 'id' not in exon and 'Name' in exon:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	141 exon['id'] = exon['Name']
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	142
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	143
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	144 def add_cds_to_dict(cols, 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	145 cds = feature_to_dict(cols, 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	146 if 'id' not in cds:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	147 if 'Name' in cds:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	148 cds['id'] = cds['Name']
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	149 elif 'Parent' in cds and ',' not in cds['Parent']:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	150 cds['id'] = cds['Parent']
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	151
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	152
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	153 def 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: diff changeset	154 for parent, exon_list in exon_parent_dict.items():
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	155 if parent in transcript_dict:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	156 exon_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	157 transcript_dict[parent]['Exon'] = exon_list
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	158
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	159 for transcript_id, transcript in transcript_dict.items():
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	160 translation = {
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	161 'CDS': [],
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	162 'id': None,
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	163 'end': transcript['end'],
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	164 'object_type': 'Translation',
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	165 'species': transcript['species'],
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	166 'start': transcript['start'],
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	167 }
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	168 found_cds = False
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	169 derived_translation_start = None
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	170 derived_translation_end = None
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	171 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	172 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	173 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	174 if len(cds_ids) > 1:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	175 raise Exception("Transcript %s has multiple CDSs: this is not supported by Ensembl JSON format" % parent)
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	176 translation['id'] = cds_ids.pop()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	177 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	178 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	179 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	180 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	181 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	182 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	183 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	184 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	185 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	186 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	187 else:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	188 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	189 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	190 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	191 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	192 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	193 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	194 else:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	195 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	196 if derived_translation_start 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	197 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	198 if derived_translation_start > translation['start']:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	199 raise Exception("UTR overlaps with CDS")
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	200 else:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	201 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	202 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	203 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	204 if derived_translation_end < translation['end']:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	205 raise Exception("UTR overlaps with CDS")
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	206 else:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	207 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	208 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	209 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	210
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	211 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	212 if 'Parent' in transcript:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	213 # 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	214 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	215 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	216 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	217
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	218
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	219 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	220 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	221
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	222 for gene in gene_dict.values():
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	223 gene_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	224 cur.execute('INSERT INTO gene (gene_id, gene_symbol, species, gene_json) VALUES (?, ?, ?, ?)',
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	225 (gene_id, gene.get('display_name', None), gene['species'], json.dumps(gene)))
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 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	228 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	229 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	230 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	231 try:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	232 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	233 (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	234 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	235 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	236
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	237 conn.commit()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	238
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	239
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	240 def fetch_species_for_transcript(conn, transcript_id):
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	241 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	242
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	243 cur.execute('SELECT species FROM transcript_species WHERE transcript_id=?',
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	244 (transcript_id, ))
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	245 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	246 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	247 return None
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	248 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	249
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	250
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	251 def remove_id_version(s):
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	252 """
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	253 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: diff changeset	254 """
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	255 if s.startswith('ENS'):
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	256 return s.split('.')[0]
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	257 else:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	258 return s
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	259
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	260
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	261 def __main__():
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	262 parser = optparse.OptionParser()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	263 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: diff changeset	264 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: diff changeset	265 parser.add_option('--fasta', action='append', default=[], help='Path of the input FASTA files')
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	266 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 parents: diff changeset	267 parser.add_option('--of', help='Path of the output FASTA file')
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	268 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: diff changeset	269 if args:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	270 raise Exception('Use options to provide inputs')
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	271
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	272 conn = sqlite3.connect(options.output)
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	273 conn.execute('PRAGMA foreign_keys = ON')
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	274 create_tables(conn)
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	275
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	276 for gff3_arg in options.gff3:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	277 try:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	278 (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	279 except ValueError:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	280 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	281 gene_dict = dict()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	282 transcript_dict = dict()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	283 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	284 cds_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	285 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 parents: diff changeset	286 three_prime_utr_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	287 with open(filename) as f:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	288 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	289 line = line.strip()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	290 if not line:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	291 # skip empty lines
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	292 continue
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	293 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	294 # 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	295 continue
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	296 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	297 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	298 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 parents: diff changeset	299 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	300 try:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	301 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	302 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	303 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	304 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	305 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	306 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	307 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	308 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	309 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	310 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	311 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	312 add_cds_to_dict(cols, 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	313 else:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	314 print("Line %i in file '%s': '%s' is not an implemented feature type" % (i, filename, feature_type), file=sys.stderr)
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	315 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	316 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 parents: diff changeset	317
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	318 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: diff changeset	319 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	320
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	321 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: diff changeset	322 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: diff changeset	323 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 parents: diff changeset	324
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	325 with open(options.of, 'w') as output_fasta_file:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	326 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: diff changeset	327 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: diff changeset	328 # 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 parents: diff changeset	329 transcript_id = remove_id_version(entry.header[1:].lstrip().split(' ')[0])
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	330 species_for_transcript = fetch_species_for_transcript(conn, transcript_id)
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	331 if not species_for_transcript:
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	332 print("Transcript '%s' not found in the gene feature information" % transcript_id, file=sys.stderr)
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	333 continue
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	334 # Remove any underscore in the species
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	335 species_for_transcript = species_for_transcript.replace('_', '')
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	336 # Write the FASTA sequence using '>TranscriptId_species' as the header, as required by TreeBest
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	337 output_fasta_file.write(">%s_%s\n%s\n" % (transcript_id, species_for_transcript, entry.sequence))
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	338
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	339 conn.close()
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	340
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	341
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	342 if __name__ == '__main__':
28879ca33b5f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 651fae48371f845578753052c6fe173e3bb35670 earlhaminst parents: diff changeset	343 __main__()

Mercurial > repos > earlhaminst > gstf_preparation

annotate gstf_preparation.py @ 1:a36645976342 draft