def info(release: str = typer.Option(
None,
'--release', '-r',
help='release'),
species: str = typer.Option(
None,
'--species', '-s',
help='valid values are Mm and Hs'),
verbose: int = typer.Option(
0, '--verbose', '-v', count=True)):
"""
Stats annotation database <filename> for <term>
"""
try:
configure_logging(verbose)
LOG = get_logger()
LOG.debug('Stats database...')
db = dbs.get_database(release, species, ensimpl_dbs_dict)
db_meta = meta.db_meta(db)
statistics = meta.stats(db)
print(f'Release: {db_meta["release"]}')
print(f'Species: {db_meta["species"]}, {db_meta["assembly_patch"]}')
arr = []
for stat in sorted(statistics):
arr.append([stat, statistics[stat]])
print(tabulate(arr))
except Exception as e:
print(e)
def create(directory: Path = typer.Option(
None, '--directory', '-d',
help='defaults to current directory'),
release: Optional[List[str]] = typer.Option(
None,
help='release, can be listed multiple times, None for all'),
species: Optional[List[str]] = typer.Option(
None,
help='valid values are Mm and Hs'),
resource: Path = typer.Option(
None, '--resource', '-r',
help='ensimpl configuration file'),
verbose: int = typer.Option(
0, '--verbose', '-v', count=True)):
"""
Creates a new ensimpl database <filename> using Ensembl <version>.
"""
try:
configure_logging(verbose)
LOG = get_logger()
if directory is None:
directory = os.getcwd()
if resource is None:
resource = os.path.dirname(os.path.abspath(__file__))
resource = os.path.abspath(os.path.join(resource, 'config/ensimpl.ensembl.conf'))
LOG.info('Creating database...')
tstart = time.time()
create_ensimpl.create(release, species, directory, resource)
tend = time.time()
LOG.info(f'Creation time: {format_time(tstart, tend)}')
except Exception as e:
print(e)
def gene(id: str = typer.Argument(
...,
help='Ensembl ID'),
release: str = typer.Option(
None,
'--release', '-r',
help='release'),
species: str = typer.Option(
None,
'--species', '-s',
help='valid values are Mm and Hs'),
format: SearchOutput = typer.Option(
SearchOutput.pretty,
'--format', '-f',
case_sensitive=False),
verbose: int = typer.Option(
0, '--verbose', '-v', count=True)):
"""
Get gene information from annotation database.
"""
try:
configure_logging(verbose)
LOG = get_logger()
LOG.debug(f'Release: {release}')
LOG.debug(f'Species: {species}')
LOG.debug(f'Format: {format}')
LOG.debug(f'ID: {id}')
ensembl_ids = [id]
db = dbs.get_database(release, species, ensimpl_dbs_dict)
tstart = time.time()
results = genesdb.get(db, ids=ensembl_ids, details=True)
tend = time.time()
headers = [
'ID',
'VERSION',
'SPECIES',
'SYMBOL',
'NAME',
'SYNONYMS',
'EXTERNAL_IDS',
'CHR',
'START',
'END',
'STRAND'
]
tbl = []
delim = '"\t"' if format.value == 'tab' else '","'
if format.value in ('tab', 'csv'):
print('"{}"'.format(delim.join(headers)))
for i in results:
r = results[i]
line = list()
line.append(r['id'])
line.append(r.get('ensembl_version', ''))
line.append(r['species_id'])
line.append(r.get('symbol', ''))
line.append(r.get('name', ''))
line.append('||'.join(r.get('synonyms', [])))
external_ids = r.get('external_ids', [])
external_ids_str = ''
if external_ids:
ext_ids_tmp = []
for ext in external_ids:
ext_ids_tmp.append('{}/{}'.format(ext['db'], ext['db_id']))
external_ids_str = '||'.join(ext_ids_tmp)
line.append(external_ids_str)
line.append(r['chromosome'])
line.append(r['start'])
line.append(r['end'])
line.append(r['strand'])
if format.value in ('tab', 'csv'):
print('"{}"'.format(delim.join(map(str, line))))
elif format.value == 'json':
tbl.append(r)
else:
tbl.append(line)
if format.value in ('tab', 'csv'):
pass
elif format.value == 'json':
print(json.dumps({'data': tbl}, indent=2))
else:
print(tabulate(tbl, headers))
pass
LOG.info('Search time: {format(format_time(tstart, tend)}')
except Exception as e:
print(e)
def search(term: str = typer.Argument(
...,
help='search term'),
release: str = typer.Option(
None,
'--release', '-r',
help='release'),
species: str = typer.Option(
None,
'--species', '-s',
help='valid values are Mm and Hs'),
exact: bool = typer.Option(
False,
help='exact match or not'),
format: SearchOutput = typer.Option(
SearchOutput.pretty,
'--format', '-f',
case_sensitive=False),
max: int = typer.Option(
-1,
'--max', '-m',
help='limit the number of matches'),
verbose: int = typer.Option(
0, '--verbose', '-v', count=True)):
"""
Search ensimpl database <filename> for <term>
"""
configure_logging(verbose)
LOG = get_logger()
LOG.info('Search database...')
maximum = max if max >= 0 else None
try:
db = dbs.get_database(release, species, ensimpl_dbs_dict)
LOG.debug(f'Database: {db}')
tstart = time.time()
results = searchdb.search(db, term, exact, maximum)
tend = time.time()
LOG.debug(f'Number of Results: {results.num_results}')
count = 0
if len(results.matches) == 0:
print('No results found')
sys.exit()
headers = [
'ID',
'SYMBOL',
'IDS',
'POSITION',
'MATCH_REASON',
'MATCH_VALUE'
]
tbl = []
if format.value in ('tab', 'csv'):
delim = '\t' if format.value == 'tab' else ','
print(delim.join(headers))
for match in results.matches:
line = list()
line.append(match.ensembl_gene_id)
line.append(match.symbol)
if match.external_ids:
ext_ids = []
for ids in match.external_ids:
ext_ids.append(f'{ids["db"]}/{ids["db_id"]}')
line.append('||'.join(ext_ids))
else:
line.append('')
line.append(f'{match.chromosome}:{match.position_start}-{match.position_end}')
line.append(match.match_reason)
line.append(match.match_value)
if format.value in ('tab', 'csv'):
print(delim.join(map(str, line)))
elif format.value == 'json':
tbl.append(dict(zip(headers, line)))
else:
tbl.append(line)
count += 1
if count >= max > 0:
break
if format.value in ('tab', 'csv'):
pass
elif format.value == 'json':
print(json.dumps({'data': tbl}, indent=4))
else:
print(tabulate(tbl, headers))
LOG.info(f'Search time: {format_time(tstart, tend)}')
except Exception as e:
print(e)
from collections import OrderedDict
import os
import sqlite3
from typing import Dict
from typing import List
from ensimpl import utils
from ensimpl.db import dbs
LOG = utils.get_logger()
def chromosomes(db: str) -> List:
"""Get the chromosomes.
Args:
db: The Ensimpl database.
Returns:
A list of dicts.
"""
sql_statement = 'SELECT * FROM chromosomes ORDER BY chromosome_num '
# prevent erroneously creating a database
if not os.path.isfile(db):
raise FileNotFoundError(db)
conn = sqlite3.connect(db)
conn.row_factory = sqlite3.Row