gene_scaffolding.py

#!/usr/bin/env python3

import datetime
import argparse
import os
from string import Template
from bel_functions import bel_term

""" Generates Gene Scaffolding BEL script document used in Phase III.
Given the urls for gene/protein domain .belns files, uses the
encodings to generate transcribedTo and translatedTo BEL statements. """

namespaces = {'HGNC': 'hgnc-human-genes.belns',
              'MGI': 'mgi-mouse-genes.belns',
              'RGD': 'rgd-rat-genes.belns'}
base_url = 'http://resources.openbel.org/belframework/testing/namespace/'
output_file = 'gene_scaffolding_document_9606_10090_10116.bel'


def translated_to(value, ns):
    """ Create bel translatedTo statement, given
    namespace keyword string and value. """
    source = bel_term(value, ns, 'r')
    target = bel_term(value, ns, 'p')
    s = Template('${source} translatedTo ${target}').substitute(
        source=source, target=target)
    return s


def transcribed_to(value, ns):
    """ Create bel transcribedTo statement, given
    namespace keyword string and value. """
    source = bel_term(value, ns, 'g')
    target = bel_term(value, ns, 'r')
    s = Template('${source} transcribedTo ${target}').substitute(
        source=source, target=target)
    return s


def micro_rna(value, ns):
    """ Create bel transcribedTo statement for microRNA,
    given namespace keyword string and value. """
    source = bel_term(value, ns, 'g')
    target = bel_term(value, ns, 'm')
    s = Template('${source} transcribedTo ${target}').substitute(
        source=source, target=target)
    return s


def scaffold(belns_filename, ns):
    """ Returns set of gene scaffolding statements from .belns,
    along with species, name, and date values needed for annotations. """
    field = ''
    statements = set()
    with open(belns_filename, 'r') as belns:
        for line in iter(belns):
            # line = line.decode('ISO-8859-1')
            if not line.strip():
                continue
            if line.startswith('['):
                field = line.strip()
                continue
            elif '[Namespace]' in field:
                if line.startswith('SpeciesString='):
                    species = line.split('=')[1].strip()
                elif line.startswith('NameString='):
                    name = line.split('=')[1].strip()
                elif line.startswith('CreatedDateTime'):
                    date = line.split('=')[1].strip()
            elif '[Values]' in field:
                (value, encoding) = line.split('|')
                encoding = encoding.strip()
                if encoding == 'G':
                    continue
                elif encoding == 'GR':
                    statements.add(transcribed_to(value, ns))
                elif encoding == 'GRM':
                    statements.add(micro_rna(value, ns))
                elif encoding == 'GRP':
                    statements.add(transcribed_to(value, ns))
                    statements.add(translated_to(value, ns))
    return statements, name, species, date

annotations = {
    'Species': 'http://resources.openbel.org/belframework/testing/annotation/species-taxonomy-id.belanno'}
today = datetime.date.today()
version = today.strftime('%Y%m%d')
separator = '#' * 50

parser = argparse.ArgumentParser(
    description="""Gene scaffolding from HGNC, RGD, and MGI .belns files.""")

parser.add_argument("-n", required=True, metavar="DIRECTORY",
                    help="directory with .belns files")
args = parser.parse_args()

belns_dir = args.n

if os.path.exists(args.n):
    os.chdir(args.n)
else:
    print('Data directory {0} not found'.format(args.n))
    exit()

with open(output_file, 'w') as bel:
    print('\nWriting file {0} ...'.format(output_file))
    bel.write(separator)
    bel.write('\n# Document Properties Section\n')
    bel.write('SET DOCUMENT Name = "Phase III Gene Scaffolding"\n')
    bel.write(
        'SET DOCUMENT Description = "Gene scaffolding for use with the BEL compiler."\n')
    bel.write('SET DOCUMENT Version = "{0}"\n'.format(version))
    bel.write('SET DOCUMENT Copyright = "Copyright (c) {0}, OpenBEL Project. This work is licensed under a Creative Commons Attribution 3.0 Unported License."\n'.format(
        str(today.year)))
    bel.write('SET DOCUMENT Authors = "OpenBEL"\n')
    bel.write('\n' + separator + '\n')
    bel.write('# Definitions Section\n')
    for ns_prefix, ns_name in namespaces.items():
        bel.write(
            'DEFINE NAMESPACE {0} AS URL "{1}{2}"\n'.format(
                ns_prefix, base_url, ns_name))
    bel.write('\n')
    for anno, url in annotations.items():
        bel.write('DEFINE ANNOTATION {0} AS URL "{1}"\n'.format(anno, url))
    bel.write(separator + '\n')
    bel.write('# Statements Section\n\n')
    for ns_prefix, ns_name in namespaces.items():
        statements, name, species, date = scaffold(ns_name, ns_prefix)
        bel.write('SET Species = {0}\n'.format(species))
        bel.write(
            'SET Citation = {3}"Online Resource", "{0}", "{1}{5}", "{2}", "", ""{4}\n\n'.format(
                name, base_url, date, '{', '}', ns_name))
        print('\n\tGenerated {0} scaffolding statements for {1}. '.format(
            str(len(statements)), name))
        for s in sorted(statements):
            bel.write(s + '\n')
        bel.write('\n\n')