Release v 0.3.4

Release v0.3.4

Changed so precomputed blast matrix is used for existing genomes, by default

All data can be re-computed by using :

--no-precomputed Don't use the precomputed blastn matrix

Release v0.3.3

Release v 0.3.3

Bug fix: Updated code to recognise the correct sheet in the VMR record now sheet 1 not 0.

Automatically looks for a sheet naming containing "VMR" rather than the new index sheet in the VMR file provided by ICTV

Full Changelog: 0.3.2...0.3.3

0.3.2

Release v0.3.2

Update:

• Speed increase by pre-calculation of similarity for all currently classified phages. Only similarity against the query genome have to be now computed. Option to use pre-calculated data or calculate all from scratch is available.

Full Changelog: 0.3.1...0.3.2

0.3.1

Release v0.3.1

Bug:

• Modification of the blast command in case the similarity module is used. It will sort the blast results first in case similar sequences are in the input file and the reference (that would be the case if reference is not used as the input file will be the reference in that case)

Full Changelog: 0.3.0...0.3.1

0.3.0

Release v0.3.0

Modification variables:

• Modification variable including Poor Mans to Clustering on Genomic Similarity or similarity depending on the context

Full Changelog: 0.2.9...0.3.0

0.2.9

Release v0.2.9

Bug:

• Because some genome have the version at the end of the accession in the Bacteriophage.fasta file, the reduction of the VMR remove them from the VMR even if exists in the MASH database. So I removed the version number from the accession to be ablel to not remove them from the VMR. (See issue #14)

Full Changelog: 0.2.8...0.2.9

0.2.8

Release v0.2.8

Improvement:

• Change the way the information are printed on the stdout
• Organised the Summary_file.txt to be more readable
• Added some functional test for some of the functions

Full Changelog: 0.2.7...0.2.8

0.2.7

Release v0.2.7

Bugs:

• Corrected the problem found in issue #10: Modified the script's behavior to consider all cases of differences in genus count between Viridic and ICTV genera.
• Corrected the problem found in issue #11. Now the font arial should be called normally
• Corrected the problem found in issue #13. The problem was coming from the old name for the similarity module not changed in the main.py

Improvement:

• Change the behaviour of taxmyphage to select the closest genome in case of multiple genus in the same viridic cluster. Resolving issue #12
• Added in the summary table the message of information that is printed on the terminal. Now the message in this table indicate if the taxonomic assignation if confident or not. Resolving issue #12

Full Changelog: 0.2.6...0.2.7

0.2.6

Release v0.2.6

Bugs:

• Some GenBank accession identifier of bacteriophage are not in the Bacteriophage.fasta. The reason is that they are bacteriophage without a proper Genbank ID (depends on the bacterial genome) (e.g. QUVN01000024 and AE006468 (2844298.2877981)).
• Correction: Reduce the VMR to only ID in the Bacteriophage.fasta database

0.2.5

Release v0.2.5

Improvement:

• Add an additional folder to have a better organisation of folder