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1.1.0 (2025-01-13)

  • Adds support for reorienting contigs where the gene of interest spands the contig ends - fixes this issue. Thanks @marade @oschwengers.
    • Specifically, this is done by rotating each contig in the input by half the genome length, then running MMseqs2 for both the original and rotated contigs. The MMseqs2 hit with the highest bitscore across the original and rotated contigs will be chosen as the top hit to rotate by, therefor enabling detection of partial hits (on the original contig) that span the contig ends.
  • This has only been implemented for dnaapler all (this should be the command used by 99% of users).

1.0.1 (2024-11-22)

  • Thanks to the inimitable @rrwick, v1.0.1 is a patch fixing a string-parsing bug.
  • If your contig headers were integers, dnaapler did not rotate the found BLAST/MMseqs2 hits. This was a pre-existing issue (not introduced by v1.0.0).

1.0.0 (2024-11-21)

  • BREAKING CHANGE - dnaapler now uses MMSeqs2 rather than BLAST. You will need to install MMSeqs if you upgrade (if you use conda, it should be handled for you)
  • There are 2 reasons for this:
    1. Users reported problems installing BLAST on MacOS with Apple Silicon (see e.g. here). MMseqs works on all platforms and is dilligently maintained.
    2. MMSeqs2 is much much faster than BLAST (what took BLAST a few minutes takes MMSeqs2 seconds). We should have written dnaapler with MMseqs2 to begin with.
  • The alignment resuls may not be identicial (i.e. they might find specifically different top hits), but the actual reorientation is likely to be identical (at least in my tests). Please reach out or make an issue if you notice any discrepancies.

For example - on my machine (Ubuntu 20.04, Intel i9 13th gen 13900 CPU with 32 threads), for a Staphylococcus aureus genome with 1 small plasmid, dnaapler -i staph.fasta -o staph_dnaapler -t 8 took ~129 seconds wallclock with v0.8.1 using BLAST, while it took ~3 seconds wallclock with v1.0.0 using MMseqs2.

0.8.1 (2024-09-16)

  • Minor release - adds --db dnaa,repa,cog1474 as an option for dnaapler all to allow for archaea orientation in hybracter

0.8.0 (2024-07-24)

  • Adds dnaapler archaea and adds archaeal reorientation functionality into dnaapler all
  • Specifically, this uses 403 COG1474 genes COG1474
  • Relaxes (to warning) where no BLAST hits are found - pipleine will still complete (requested in a number of issues #74 #76 #77)

0.7.0 (2024-02-05)

  • Adds -c/--custom_db with dnaapler all to allow specifying custom databases with dnaapler all.

0.6.0 (2024-01-31)

  • Fixes bug where if the starting gene (dnaA/terL/repA) was on the reverse strand and the top BLAST hit did not find the start codon, it would reorient the replicon to begin at the end of the starting gene, not the start. Thanks @susiegriggo

0.5.2 (2024-01-24)

  • Bumps version to include updated citation

0.5.1 (2024-01-09)

  • With dnaapler all, adds the reoriented gene to the header (thanks @ammaraziz #67)
  • Adds --db parameter to dnaapler all allowing specifying a subset of genes to make up the database. In particular, if you have bacteria and plasmids, --db dnaa,repa should speed up Dnaapler's runtime quite a bit (thanks @oschwengers #63)

0.5.0 (2023-12-03)

  • JOSS release with minor typos and bug fixes from v0.4

0.4.0 (2023-10-25)

  • Implemented a modification to the logic for all cases where the top blastx hit alignment does not begin with a start codon. In this case, dnaapler will find the CDS according the pyrodigal that has the most overlap with the top hit alignment. Thanks @simone-pignotti for this suggestion here.
  • Changes dnaapler all output FASTA to _reoriented.fasta instead of _all_reoriented.fasta for consistency with all other commands (except dnaapler bulk).
  • Adds -a or --autocomplete option with dnaapler all.
  • Adds dnaapler largest and -a largest as an option to orient your sequence beginning with the largest

0.3.2 (2023-09-20)

  • Changes Orffinder to Genefinder to support pyrodigal v3.
  • Updates dependency to pyrodigal >=v3.

0.3.1 (2023-09-01)

  • Minor release to fix an error with dnaapler all #38 thanks @samnooij

0.3.0 (2023-08-18)

  • dnaapler all subcommand added thanks @alexweisberg
  • dnaapler all implements --ignore to ignore some contigs

0.2.0 (2023-08-08)

  • dnaapler nearest subcommand added
  • dnaapler bulk subcommand added
  • dnaA database filtered to keep only bona-file dnaA genes (i.e. GN=dnaA)
  • Adds -e parameter to vary BLAST evalue if desired
  • Adds -a autocomplete parameter if user wants to reorient sequences with mystery or nearest methods in case the BLAST based method fails

0.1.0 (June 2023)

  • Completely overhauled
  • First stable released with pypi and conda
  • dnaapler chromosome added
  • dnaapler custom added
  • dnaapler mystery added
  • dnaapler phage added
  • dnaapler plasmid added

0.0.1 (2022-10-12)

  • First release (conda only conda install -c gbouras dnaapler)