cathpy.util¶
from cathpy import util
General utility classes and functions
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class
cathpy.util.AlignmentSummary(*, path, dops, aln_length, seq_count, gap_count, total_positions)¶ Stores summary information about an alignment.
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class
cathpy.util.AlignmentSummaryRunner(*, aln_dir=None, aln_file=None, suffix='.sto', skipempty=False)¶ Provides a summary report for sequence alignment files.
Parameters: - aln_dir – input alignment directory
- aln_file – input alignment file
- suffix – filter alignments by suffix
- skipempty – skip empty files
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class
cathpy.util.FunfamFileFinder(base_dir, *, ff_tmpl='__SFAM__-ff-__FF_NUM__.sto')¶ Finds a Funfam alignment file within a directory.
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funfam_id_from_file(ff_file)¶ Extracts a FunfamID from the file name (based on the ff_tmpl)
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search_by_domain_id(domain_id)¶ Return the filename of the FunFam alignment containing the domain id.
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class
cathpy.util.GroupsimResult(*, scores=None)¶ Represents the result from running the groupsim algorithm.
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count_positions¶ Returns the number of positions in the groupsim result.
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classmethod
new_from_file(gs_file)¶ Create a new groupsim result from an output file.
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classmethod
new_from_io(gs_io, *, maxscore=1)¶ Create a new groupsim result from an io source.
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class
cathpy.util.GroupsimRunner(*, groupsim_dir='/home/docs/checkouts/readthedocs.org/user_builds/cathpy/envs/stable/lib/python3.7/site-packages/cathpy-0.1.4-py3.7.egg/cathpy/tools/GroupSim', python2path='python2', column_gap=0.3, group_gap=0.5)¶ Object that provides a wrapper around groupsim.
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run_alignment(alignment, *, column_gap=None, group_gap=None, mclachlan=False)¶ Runs groupsim against a given alignment.
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class
cathpy.util.ScoreconsResult(*, dops, scores)¶ Represents the results from running scorecons.
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to_string¶ Returns the scorecons results as a string (one char per position).
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class
cathpy.util.ScoreconsRunner(*, scorecons_path='/home/docs/checkouts/readthedocs.org/user_builds/cathpy/envs/stable/lib/python3.7/site-packages/cathpy-0.1.4-py3.7.egg/cathpy/tools/linux-x86_64/scorecons', matrix_path='/home/docs/checkouts/readthedocs.org/user_builds/cathpy/envs/stable/lib/python3.7/site-packages/cathpy-0.1.4-py3.7.egg/cathpy/tools/data/PET91mod.mat2')¶ Runs scorecons for a given alignment.
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run_alignment(alignment)¶ Runs scorecons on a given alignment.
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run_fasta(fasta_file)¶ Returns scorecons data (ScoreconsResult) for the provided FASTA file.
Returns: scorecons result Return type: result (ScoreconsResult)
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run_stockholm(sto_file)¶ Returns scorecons data for the provided STOCKHOLM file.
Returns: scorecons result Return type: result (ScoreconsResult)
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class
cathpy.util.StructuralClusterMerger(*, cath_version, sc_file, ff_dir, out_fasta=None, out_sto=None, ff_tmpl='__SFAM__-ff-__FF_NUM__.sto', add_groupsim=True, add_scorecons=True, cath_release=None)¶ Merges FunFams based on a structure-based alignment of representative sequences.
Parameters: - cath_version – version of CATH
- sc_file – structure-based alignment (*.fa) of funfam reps
- ff_dir – path of the funfam alignments (*.sto) to merge
- out_fasta – file to write merged alignment (FASTA)
- out_sto – file to write merged alignment (STOCKHOLM)
- ff_tmpl – template used to find the funfam alignment files
- add_groupsim – add groupsim data (default: True)
- add_scorecons – add scorecons data (default: True)
- cath_release – specify custom release data directory