Changelogs » Caspredict

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Caspredict

0.5.4

Add argument to handle circular topology

0.5.2

Fix bug with sequences containing only CRISPRs

0.5.1

Add xgboost repeat classifier training script
  Fix some minor bugs

0.5.0

Restructure typing of small operons

0.4.5

Bump up version to fix pypi error

0.4.4

Fix pandas version problem
  Optimize typing

0.4.3

Update plotting features
  Do not plot putative CRISPR-Cas anymore

0.4.2

Fix small bugs with sequences having no operons
  Add plotting features

0.4.1

Fix bug with orderings of gene names in plot

0.4.0

Added plotting feature, to automatically draw maps of CRISPR-Cas loci

0.3.6

* Fix bug with deleting of CRISPR file if there was only one CRISPR
  * Lower thresholds to become more sensitive

0.3.5

* Solve hybrid systems: Write in output if an operon seems to a combination of two or more subtypes
  * Put putative CRISPR-Cas in separate file
  * Split spacers in a file per CRISPR array
  * Do not print empty files
  * Ensure correct parts are re-run with `--redo_typing`

0.3.4

Include some defensive checks for edge cases

0.3.3


        

0.3.2

Add repeat typing script

0.3.1

* Add consensus subtyping based on both Cas operons and CRISPR repeats
  * Fix multiprocess problem for macOS

0.3.0

Add minced for CRISPR prediction, and add xgboost for prediction of subtype based on repeat sequence.

0.2.1

Extra checks of input

0.2.0

Complete makeover of scripts into a python module

0.1.6

Add arguments.
  Fix coverage calculation. The first fix create new problems with overlapping alignments, which is fixed in this version.

0.1.3

Update argument structure.

0.1.2

Fix problem with ORF-HMM alignments which were split across multiple lines in the HMMER output. Prior to this version only the best match was chosen, now coverage is summed across the domain alignments, solving problems with detection of fusion proteins

0.1.1

Input can now be a prodigal-formatted protein fasta, by adding the `--aa` argument

0.1.0

Alpha version