Application and Python module for average nucleotide identity analyses of microbes.
MIT License
Minor update to increment version number in the code.
Published by widdowquinn 3 months ago
This release fixes a deprecated matplotlib
call, and deprecated pandas
calls.
Published by baileythegreen about 2 years ago
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.'
Published by widdowquinn over 3 years ago
This release fixes issues due to pandas
API changes.
pyani
are now found in pandas.errors
not pandas.io.common
Published by widdowquinn over 4 years ago
This release fixes the bug reported in issue #178 that affected graphical output if all input filenames could be interpreted as floating point numbers.
Published by widdowquinn over 5 years ago
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!
Published by widdowquinn over 5 years ago
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 schedulersPublished by widdowquinn about 7 years ago
Published by widdowquinn about 7 years ago
This release fixes a PyPI installation problem, resulting from a badly-built .whl
wheel.
Published by widdowquinn about 7 years ago
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)Published by widdowquinn over 7 years ago
genbank_get_genomes_by_taxon.py
to account for NCBI FTP location changescodecov.io
, landscape.io
and Travis-CI
rpy2
bin/
subdirectoryv0.2.1
introduces minor changes with respect to v0.2.0
:
genbank_get_genomes_by_taxon.py
uses the new NCBI FTP locations, and will attempt to identify and inform the user about failed downloads.seaborn
output can now handle larger (>500 genomes) datasetsThere are also several bugfixes (see CHANGES.md
for more details)
Version 0.2.0 introduces a number of changes with respect to the v0.1 series of releases. Notably:
--fragsize
option is fixedBLAST
/nucmer
results are now written to a subdirectory of the output folder, and are compressed to save disk space