Utils

A module for shared utilities used in GFFtk.

gfftk.utils.check_file_type(filepath)

Checks if a file is text, gzipped binary, or other binary.

gfftk.utils.filter_annotations(annotations, grep=None, grepv=None)

Filter annotations based on grep and grepv patterns.

Parameters:

  • annotations (dict) – GFFtk annotation dictionary keyed by gene ID

  • grep (list, optional) – List of patterns to keep (format: “key:pattern” or “key:pattern:flags”)

  • grepv (list, optional) – List of patterns to remove (format: “key:pattern” or “key:pattern:flags”)

Returns:

Filtered annotation dictionary

Return type:

dict

Examples

# Keep only genes with “kinase” in product filtered = filter_annotations(genes, grep=[“product:kinase”])

# Remove genes from specific source filtered = filter_annotations(genes, grepv=[“source:augustus”])

# Case-insensitive matching filtered = filter_annotations(genes, grep=[“product:kinase:i”])

gfftk.utils.is_gzipped(filepath)

Checks if a file is gzipped.

gfftk.utils.is_text_file(filepath)

Checks if a file is likely a text file.

gfftk.utils.test_table2asn_functional()

Test if table2asn binary is functional by running it with -help flag.

Returns:

True if table2asn runs successfully, False otherwise

Return type:

bool

gfftk.utils.zopen(filename, mode='r', buff=1048576, external=2)

Open pipe, zipped, or unzipped file automagically

# external == 0: normal zip libraries # external == 1: (zcat, gzip) or (bzcat, bzip2) # external == 2: (pigz -dc, pigz) or (pbzip2 -dc, pbzip2)