goatools.base module

Utilities used in Gene Ontology Enrichment Analyses.

goatools.base.get_logger(name: str)

Return a logger with a default ColoredFormatter.

goatools.base.nopen(f, mode='r')

Open a file that’s gzipped or return stdin for ‘-‘.

If f is a number, the result of nopen(sys.argv[f]) is returned.

>>> nopen('-') == sys.stdin, nopen('-', 'w') == sys.stdout
(True, True)
>>> nopen(sys.argv[0])
<...file...>

Expands user and vars ($HOME):

>>> nopen("~/.bashrc").name == nopen("$HOME/.bashrc").name
True

An already open file:

>>> nopen(open(sys.argv[0]))
<...file...>
>>> nopen(0)
<...file...>

Or provide nicer access to Popen.stdout:

>>> files = list(nopen("|ls"))
>>> assert 'setup.py\n' in files or b'setup.py\n' in files, files

goatools.base.ungzipper(fh, blocksize=16384)

work-around to get streaming download of http://…/some.gz

goatools.base.download_go_basic_obo(obo='go-basic.obo', prt=sys.stdout)

Download Ontologies, if necessary.

goatools.base.download_ncbi_associations(gene2go='gene2go', prt=sys.stdout)

Download associations from NCBI, if necessary

goatools.base.gunzip(gzip_file, file_gunzip=None)

Unzip .gz file. Return filename of unzipped file.

goatools.base.get_godag(fin_obo='go-basic.obo', prt=sys.stdout, optional_attrs=None)

Return GODag object. Initialize, if necessary.

goatools.base.dnld_gaf(species_txt, prt=sys.stdout)

Download GAF file if necessary.

goatools.base.dnld_gafs(species_list, prt=sys.stdout)

Download GAF files if necessary.

goatools.base.http_get(url, fout=None)

Download a file from http. Save it in a file named by fout

goatools.base.ftp_get(fin_src: str, fout: str)

Download a file from an ftp server, e.g., ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz

goatools.base.dnld_file(src_ftp, dst_file, prt=sys.stdout)

Download specified file if necessary.

goatools.base.gzip_open_to(fin_gz, fout)

Unzip a file.gz file.