fetch#
- biotite.database.uniprot.fetch(ids, format, target_path=None, overwrite=False, verbose=False)[source]#
Download files from the UniProt in various formats.
Available databases are UniProtKB, UniRef and UniParc. This function requires an internet connection.
- Parameters:
- idsstr or iterable object of str
A single ID or a list of IDs of the file(s) to be downloaded.
- format{‘fasta’, ‘gff’, ‘txt’, ‘xml’, ‘rdf’, ‘tab’}
The format of the files to be downloaded.
- target_pathstr, optional
The target directory of the downloaded files. By default, the file content is stored in a file-like object (StringIO or BytesIO, respectively).
- overwritebool, optional
If true, existing files will be overwritten. Otherwise the respective file will only be downloaded if the file does not exist yet in the specified target directory.
- verbosebool, optional
If true, the function will output the download progress.
- Returns:
- filesstr or StringIO or BytesIO or list of (str or StringIO or BytesIO)
The file path(s) to the downloaded files. If a single string (a single ID) was given in ids, a single string is returned. If a list (or other iterable object) was given, a list of strings is returned. If no target_path was given, the file contents are stored in either StringIO or BytesIO objects.
Examples
>>> import os.path >>> file = fetch("P12345", "fasta", path_to_directory) >>> print(os.path.basename(file)) P12345.fasta >>> files = fetch(["P12345", "Q8K9I1"], "fasta", path_to_directory) >>> print([os.path.basename(file) for file in files]) ['P12345.fasta', 'Q8K9I1.fasta']
