althonos/pyhmmer: v0.6.0

Published May 1, 2022 | Version v0.6.0

Software Open

Added

pyhmmer.daemon module with an client implementation to communicate to a hmmpgmd server.
Pipeline.arguments methods to get a list of CLI arguments from the parameters used to initialize the Pipeline.
Setters for name, accession and description properties of plan7.Hit.
Constructor for individual plan7.Trace objects outside a plan7.Traces list.
plan7.Trace.from_sequence constructor to create a faux trace from a single sequence.
manually_include and manually_drop methods to plan7.Hit for manually selecting the inclusion status of a Hit in a TopHits instance.
compare_ranking method to plan7.TopHits for comparing the order of the hits compared to a previous run on the same targets stored in an easel.KeyHash object.
Pipeline.iterate_seq and Pipeline.iterate_hmm to run iterative queries like JackHMMER.
repr implementations for easel.MSAFile, easel.SequenceFile and easel.HMMFile showing the path or file object they were created from.
repr implementation for easel.Randomness showing the seed and the RNG algorithm in use.
str implementation for plan7.Alignment using HMMER original code to display a domain alignment like in search/scan results.

Changed

plan7.Trace.posterior_probabilities property may now be None in case no memory is allocated for the posteriors in the P7_TRACE struct.
TopHits.to_msa can now add additional sequences passed as arguments to the alignment.
plan7.HMMPressedFile now raises an exception on attempts to create a new instance manually.
ignore_gaps argument of easel.SequenceFile is now deprecated.
repr implementations for easel types now use the fully qualified class name.

Fixed

easel.SequenceFile.readinto docstring not rendering properly in documentation.
Type annotations of hits_included and hits_reported of plan7.TopHits marking these properties as bool instead of int.
Setters of name, accession, description and author properties of easel.MSA crashing when given None values.
Exception value raised from Easel code not being properly extracted.
Plain strings being used in example for easel.TextSequence and easel.TextMSA constructors where byte strings are expected (#20).

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althonos/pyhmmer-v0.6.0.zip md5:57cd4624045b05ab1157b9c7445cb49f	8.8 MB	Preview Download