def pull_pantherfamily():
outfile = f'{PANTHERFAMILY}/family.csv'
pull_via_ftp(
'ftp.pantherdb.org',
'/sequence_classifications/current_release/PANTHER_Sequence_Classification_files/',
'PTHR16.0_human',
outfilename=outfile)
def pull_pubchem():
files = ['CID-MeSH', 'CID-Synonym-filtered.gz', 'CID-Title.gz']
for f in files:
outfile = f'PUBCHEM/{f}'
pull_via_ftp('ftp.ncbi.nlm.nih.gov',
'/pubchem/Compound/Extras',
f,
outfilename=outfile)
def pull_ncbigene(filenames):
remotedir = 'https://ftp.ncbi.nih.gov/gene/DATA/'
for fn in filenames:
pull_via_ftp('ftp.ncbi.nih.gov',
'/gene/DATA',
fn,
decompress_data=False,
outfilename=f'NCBIGene/{fn}')
def pull_chebi():
pull_via_ftp('ftp.ebi.ac.uk',
'/pub/databases/chebi/SDF/',
'ChEBI_complete.sdf.gz',
decompress_data=True,
outfilename='CHEBI/ChEBI_complete.sdf')
pull_via_ftp('ftp.ebi.ac.uk',
'/pub/databases/chebi/Flat_file_tab_delimited/',
'database_accession.tsv',
outfilename='CHEBI/database_accession.tsv')
def pull_chembl(moleculefilename):
fname = get_latest_chembl_name()
if not fname is None:
# fname should be like chembl_28.0_molecule.ttl.gz
#Pull via ftp is going to add the download_dir, so this is a hack until pull_via_ftp is nicer.
oname = 'CHEMBLCOMPOUND/' + moleculefilename.split('/')[-1]
pull_via_ftp('ftp.ebi.ac.uk',
'/pub/databases/chembl/ChEMBL-RDF/latest/',
fname,
decompress_data=True,
outfilename=oname)
pull_via_ftp('ftp.ebi.ac.uk',
'/pub/databases/chembl/ChEMBL-RDF/latest/',
'cco.ttl.gz',
decompress_data=True,
outfilename='CHEMBL/cco.ttl')
def pull_pubchem_labels():
print('LABEL PUBCHEM')
f_name = 'CID-Title.gz'
cname = pull_via_ftp('ftp.ncbi.nlm.nih.gov','/pubchem/Compound/Extras/', f_name, outfilename=f_name)
fname = make_local_name('labels', subpath='PUBCHEM.COMPOUND')
with open(fname, 'w') as outf, gzip.open(cname,mode='rt',encoding='latin-1') as inf:
for line in inf:
x = line.strip().split('\t')
outf.write(f'PUBCHEM.COMPOUND:{x[0]}\t{x[1]}\n')
def test_pull_gzip_to_memory():
"""Pull a gzipped file into memory, decompressed"""
data = pull_via_ftp('ftp.ncbi.nlm.nih.gov',
'gene/DATA/',
'gene_group.gz',
decompress_data=True)
lines = data.split('\n')
assert len(lines) > 1000
assert lines[0].startswith('#tax_id')
def test_pull_gzip_to_compressed_file():
"""Pull a gzipped file into memory, decompressed"""
ofname = 'test_gz.gz'
outname = pull_via_ftp('ftp.ncbi.nlm.nih.gov',
'gene/DATA/',
'gene_group.gz',
outfilename=ofname)
with gzip.open(outname, 'rt') as inf:
lines = inf.read().split('\n')
assert len(lines) > 1000
assert lines[0].startswith('#tax_id')
def test_pull_text_to_file():
"""Pull a text file into local file"""
ofname = 'test_text'
outname = pull_via_ftp('ftp.ncbi.nlm.nih.gov',
'gene/DATA/',
'stopwords_gene',
outfilename=ofname)
with open(outname, 'r') as inf:
lines = inf.read().split('\n')
assert len(lines) > 100
assert lines[0] == 'a'
def pull_pubchem_synonyms():
f_name = 'CID-Synonym-filtered.gz'
sname = pull_via_ftp('ftp.ncbi.nlm.nih.gov', '/pubchem/Compound/Extras/', f_name, outfilename=f_name)
fname = make_local_name('synonyms', subpath='PUBCHEM.COMPOUND')
with open(fname, 'w') as outf, gzip.open(sname,mode='rt',encoding='latin-1') as inf:
for line in inf:
x = line.strip().split('\t')
if x[1].startswith('CHEBI'):
continue
if x[1].startswith('SCHEMBL'):
continue
outf.write(f'PUBCHEM.COMPOUND:{x[0]}\thttp://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym\t{x[1]}\n')
def pull_hgnc():
data = pull_via_ftp('ftp.ebi.ac.uk', '/pub/databases/genenames/new/json', 'hgnc_complete_set.json')
hgnc_json = loads(data)
lname = make_local_name('labels', subpath='HGNC')
sname = make_local_name('synonyms', subpath='HGNC')
with open(lname,'w') as lfile, open(sname,'w') as sfile:
for gene in hgnc_json['response']['docs']:
hgnc_id =gene['hgnc_id']
symbol = gene['symbol']
lfile.write(f'{hgnc_id}\t{symbol}\n')
name = gene['name']
sfile.write(f'{hgnc_id}\thttp://www.geneontology.org/formats/oboInOwl#hasExactSynonym\t{name}\n')
if 'alias_symbol' in gene:
alias_symbols = gene['alias_symbol']
for asym in alias_symbols:
sfile.write(f'{hgnc_id}\thttp://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym\t{asym}\n')
if 'alias_name' in gene:
alias_names = gene['alias_name']
for asym in alias_names:
sfile.write(f'{hgnc_id}\thttp://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym\t{asym}\n')
def pull_ncbitaxon():
pull_via_ftp('ftp.ncbi.nih.gov',
'/pub/taxonomy',
'taxdump.tar.gz',
decompress_data=True,
outfilename=f'{NCBITAXON}/taxdump.tar')
def pull_hgnc():
outfile = 'HGNC/hgnc_complete_set.json'
pull_via_ftp('ftp.ebi.ac.uk',
'/pub/databases/genenames/new/json',
'hgnc_complete_set.json',
outfilename=outfile)
def pull_hgncfamily():
outfile = f'{HGNCFAMILY}/family.csv'
pull_via_ftp('ftp.ebi.ac.uk',
'/pub/databases/genenames/new/csv/genefamily_db_tables',
'family.csv',
outfilename=outfile)
def pull_mesh():
pull_via_ftp('ftp.nlm.nih.gov',
'/online/mesh/rdf',
'mesh.nt.gz',
decompress_data=True,
outfilename='MESH/mesh.nt')
def test_pull_text_to_memory():
"""Pull a text file into memory so it will be usable"""
data = pull_via_ftp('ftp.ncbi.nlm.nih.gov', 'gene/DATA/', 'stopwords_gene')
lines = data.split('\n')
assert len(lines) > 100
assert lines[0] == 'a'