forgi.utilities.commandline_utils module¶

exception forgi.utilities.commandline_utils.WrongFileFormat[source]¶

Bases: exceptions.ValueError

Error raised if the input file has the wrong file format or the file format could not be detected.

forgi.utilities.commandline_utils.cgs_from_args(args, rna_type='any', enable_logging=True, return_filenames=False, skip_errors=False)[source]¶

Given an Namespace from argparse, return a list of CoarseGrainRNA objects (or BulgeGraph objects).

Parameters:

Parameters:	args – A argparse Namespace. rna_type – See documentation of load_rna enable_logging – In addition to loading the CoarseGrainRNA objects, call logging.basicConfig() and use args.verbose and args.debug to set the level for different loggers. return_filenames – Instead of returning a list of rnas, return a tuple `rnas, filenames`, where filenames is a list of filenames of equal length as the returned list of CoarseGrainRNA objects and with corresponding order. If a file contains two seperate RNA molecules, the filename will thus be found twice in the list of filenames. skip_errors – Boolean. Log GraphConstructionErrors and continue with the next filename instead of letting the error propagate.

args – A argparse Namespace.
rna_type – See documentation of load_rna
enable_logging – In addition to loading the CoarseGrainRNA objects, call logging.basicConfig() and use args.verbose and args.debug to set the level for different loggers.
return_filenames – Instead of returning a list of rnas, return a tuple rnas, filenames, where filenames is a list of filenames of equal length as the returned list of CoarseGrainRNA objects and with corresponding order. If a file contains two seperate RNA molecules, the filename will thus be found twice in the list of filenames.
skip_errors – Boolean. Log GraphConstructionErrors and continue with the next filename instead of letting the error propagate.

Usage:

parser = get_rna_input_parser()
args = parser.parse_args()
rnas = cgs_from_args(args)

forgi.utilities.commandline_utils.get_rna_input_parser(helptext, nargs=1, rna_type='any', enable_logging=True, parser_kwargs={})[source]¶

forgi.utilities.commandline_utils.hide_traceback(*args, **kwds)[source]¶: A context manager that catches errors of the specified class and outputs only the error message before calling sys.exit(1).

forgi.utilities.commandline_utils.load_rna(filename, rna_type='any', allow_many=True, pdb_chain=None, pdb_remove_pk=True, pdb_dotbracket='', dissolve_length_one_stems=True, pdb_annotation_tool=None, pdb_allow_www_query=False)[source]¶

Parameters:

Parameters:	rna_type – One of “any”, and “3d” and “pdb” ”any”: Return either BulgeGraph or CoarseGrainRNA object, depending on the input format ”only_cg”: Only accept cg-files. ”3d”: Return CoarseGrainRNA objects, if the file contains 3D information, raise an error otherwise ”pdb”: only accept pdb files allow_many – If True, return a list. If False, return a single CoarseGrainRNA object or raise a WrongFileFormat, if more than one RNA is present. pdb_chain – Extract the given chain from the file. Only applicable if filename corresponds to a pdb file pdb_remove_pk – Detect pseudoknot-free structures from the pdb. pdb_dotbracket – Only applicable, if filename corresponds to a pdb file and pdb_chain is given. dissolve_length_one_stems – Ignored if input is in forgi bg/cg format. pdb_annotation_tool – Use DSSR, MC-Annotate or forgi heuristic for basepair-detection in PDB/MMCIF files (None for auto-detect). Ignored for other file-types.
Retuns:	A list of RNAs or a single RNA

rna_type –
One of “any”, and “3d” and “pdb”
- ”any”: Return either BulgeGraph or CoarseGrainRNA object,
  
  depending on the input format
- ”only_cg”: Only accept cg-files.
- ”3d”: Return CoarseGrainRNA objects,
  
  if the file contains 3D information, raise an error otherwise
- ”pdb”: only accept pdb files
allow_many – If True, return a list. If False, return a single CoarseGrainRNA object or raise a WrongFileFormat, if more than one RNA is present.
pdb_chain – Extract the given chain from the file. Only applicable if filename corresponds to a pdb file
pdb_remove_pk – Detect pseudoknot-free structures from the pdb.
pdb_dotbracket – Only applicable, if filename corresponds to a pdb file and pdb_chain is given.
dissolve_length_one_stems – Ignored if input is in forgi bg/cg format.
pdb_annotation_tool – Use DSSR, MC-Annotate or forgi heuristic for basepair-detection in PDB/MMCIF files (None for auto-detect). Ignored for other file-types.

Retuns:

A list of RNAs or a single RNA

forgi.utilities.commandline_utils.open_for_out(*args, **kwds)[source]¶: From http://stackoverflow.com/a/17603000/5069869

forgi.utilities.commandline_utils.sniff_filetype(file)[source]¶

forgi 2.0.0 documentation

forgi.utilities.commandline_utils module¶