General methods

biscot.Misc.agp_to_fasta(contigs_sequence_dict, agp_path, output_file)[source]

Parses an AGP file and thanks to a dict containing contigs sequence, transforms it into a scaffolds FASTA File

Parameters
  • contigs_sequence_dict (dict(str: str)) – Dict containing contigs FASTA sequence

  • agp_path (str) – Path to an AGP file

  • output_file (str) – Path to an output FASTA file

biscot.Misc.check_path(file_paths)[source]

Checks if the files given as input exist

Parameters

file_paths (list(str)) – List of file paths

Raises

FileNotFoundError – If a file is not found

biscot.Misc.load_contigs(contigs_sequence_dict, contigs_path)[source]

Extracts contig sequences from a FASTA file

Parameters
  • contigs_sequence_dict (dict(str: str)) – Dict that will contain contigs FASTA sequence

  • contigs_path (str) – Path to a contigs FASTA file

biscot.Misc.print(*args, **kwargs)[source]

Unbuffured print function

biscot.Misc.setup_logging(debug)[source]

Setups the logging streams

Parameters

debug (bool) – True to activate debug logs