genomepy.files

Utility functions with files

Functions

bgzip_and_name(fname[, bgzip_file])	Bgzip file if requested.
extract_archive(fname[, outfile, concat])	Extract files from an archive.
extract_gzip(fname[, outfile])	Gunzips the file if gzipped.
extract_tarball(fname[, outfile, concat])	Convert tar of multiple FASTAs to one file.
extract_zip(fname[, outfile, concat])	Unzips the file if zipped.
extracted_file(fname)	Context manager to work with (b)gzipped file.
filter_fasta(infa[, outfa, regex, invert_match])	Filter fasta file based on regex.
get_file_info(fname)	Returns the lower case file type of a file, and if it is (g)zipped
glob_ext_files(dirname[, ext])	Return (gzipped) file names in directory containing the given extension.
gzip_and_name(fname[, gzip_file])	Gzip file if requested.
parse_file(fpath[, skip])	basic file parsing
read_readme(readme)	Parse a readme file.
update_readme(readme[, updated_metadata, ...])	Update a readme file with supplied information.
write_readme(readme, metadata[, lines])	Create a new readme file with supplied information.