HybPiper version 2.1.8
·
154 commits
to master
since this release
- Add new subcommand
hybpiper filter_by_length
, used to filter the sequence output ofhybpiper retrieve sequences
by absolute length and/or length relative to mean length in target file representatives. This is done on a per-sample/per-gene basis, rather than the sample-level filtering available inhybpiper retrieve_sequences
. See wiki for more information. - Update the regex used to check target file fasta header formatting, to capture scenarios where a name contains multiple dashes and also ends with a dash.
- In the
fix_targetfile.py
module, remove the import ofBio.Align.Applications.MafftCommandline
and callMAFFT
viasubprocess
(see issue#147). - In the
gene_recovery_heatmap.py
module, cast the dataframe from theseq_lengths_file
to objectdtype
to avoid a deprecation warning . - Add option
--no_heatmap
to commandhybpiper paralog_retriever
(see issue#150). - Fix an Exonerate-related debug message in
exonerate_hits.py
.