Changes

Version 1.6.0

  • swarm updated to version 2.1.12;
  • Now the mergepairs command allows merging staggered reads by default. With the new option -n/--nostagger the command produces the same results of the previous versions (<=1.5);
  • classify and tabletotax commands now strip the D_X__ prefix from the Silva taxonomy files;
  • Documentation updated;
  • Fix: remove duplicate file closing in micca.api.merge().

Version 1.5.0

  • Now the NAST algorithm trims candidate sequences to that which is bound by the beginning and end points of the alignment span; with the new option --nast-notrim in micca msa produces the same results of the previous version (<=1.4.0);
  • Y-scale in micca tablebar when --raw fixed;
  • “text file busy error” in micca msa (nast) fixed;
  • pandas deprecation warnings fixed;
  • documentation updated.

Version 1.4.0

  • No-filter option added to micca.api.msa.nast() (do not remove positions which are gaps in every sequenceces) and to the msa command (--nast-nofilter option);
  • documentation improved.

Version 1.3.0

  • Swarm clustering algorithm added to micca otu;
  • micca.api.otu.denovo_swarm() function added;
  • micca v1.3.0 includes: VSEARCH v1.9.5, MUSCLE v3.8.31, FastTree v2.1.8, swarm v2.1.8;
  • documentation updated.

Version 1.2.2

  • Mow micca can generate plots with matplotlib when the DISPLAY environment variable is undefined;
  • MANIFEST.in, Dockerfile updated.

Version 1.2.1

  • Dockerfile added;
  • Documentation improved.

Version 1.2.0

  • Hits output file option added to micca.api.msa.nast() (hits_fn option) and to the msa command (--nast-hits option);
  • setup.py improved.

Version 1.1.0

  • Strand option added in classify (consensus-based classifier), msa (NAST) and otu (closed-reference and open reference OTU picking protolcols) commands. Now these commands search both strand (default) instead the plus strand only.

Version 1.0.0

  • micca 1.0.0 includes: VSEARCH v1.9.5, MUSCLE v3.8.31, FastTree v2.1.8.