Application and Python module for average nucleotide identity analyses of microbes.
This release fixes Issue #177: input filenames that contain an open or a closed parenthesis produce the message: 'WARNING: At least one BLAST run failed. ANIb may fail.'
This release fixes issues due to pandas
API changes.
pyani
are now found in pandas.errors
not pandas.io.common
This release fixes the bug reported in issue #178 that affected graphical output if all input filenames could be interpreted as floating point numbers.
This release fixes issue #132 (TETRA analysis failing when one or more 4-mers are missing from input sequences).
Thanks to @ghbio for the bug report!
This release implements several changes:
pandas
and other syntax--workers
argument (PR #127 from Özcan Esen)matplotlib
calls use new API ('false', 'off' -> False; 'true', 'on' -> True)ANIblastall
commands are no longer supporteddelta-filter
wrapper for compatibility with SGE/OGE schedulersThis release fixes a PyPI installation problem, resulting from a badly-built .whl
wheel.
ANIm
now uses delta-filter
to remove alignments of repeat regions (issue #91)--filter_exe
option to specify location of delta-filter
utility (issue #91)--format
option so that GenBank downloads work again (issue #89)--SGEargs
option to average_nucleotide_identity.py
for custom qsub settingsREADME.md
badges now clickable--version
switch added to average_nucleotide_identity.py
genbank_get_genomes_by_taxon.py
genbank_get_genomes_by_taxon.py
- should be fewer failed downloadsNUCmer
alignment failsaverage_nucleotide_identity.py
argument documentation improvements--noclobber
log behaviour (issue #79)--rerender
code (issue #85)genbank_get_genomes_by_taxon.py
to account for NCBI FTP location changescodecov.io
, landscape.io
and Travis-CI
rpy2
bin/
subdirectory