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Releases: marbl/parsnp

Parsnp v2.0.6

28 Sep 19:05
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  • Previously we were importing the extension module even if the user didn't need it. This required the pyspoa module and was causing issues. Now, users can run parsnp w/out pyspoa by using the --no-partition flag.
  • Removes log redirects for harvest which cause crashes
  • Uses regex strings for the parsers #153
  • Adds back the gingr support for phipack results

Release v2.0.5

12 Apr 02:54
8e0d41c
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  • Parsnp now outputs a MAF file in addition to the typical XMFA file (can turn this off with (--no-maf).
  • Parsnp now uses the partition mode by default when there are more than 100 input sequences.

Release v2.0.4

14 Mar 23:50
f0392eb
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  • fasttree output is now moved to the correct spot for downstream processing (fixes #147)
  • --min-ref-cov arg is now an inclusive lower bound instead of exclusive

Release v2.0.3

29 Jan 15:51
1d3fbcc
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  • Replaces internal commands which were incompatible with MacOS.

Release v2.0.2

19 Jan 18:05
2eeaa25
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  • The interval for each xmfa record is now inclusive, following the xmfa format. This only effects the internal coordinate representation, used by gingr. The s[seq_idx]:p[position] coordinates remain unchanged.
  • tqdm logging has been redirected to the Parsnp logger
  • The extension module now also uses SPOA. However, it is still experimental.
  • Extension is much more conservative than before, but still can produce less conserved alignments

Release v2.0.1

16 Jan 17:22
1b5b48b
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  • Output is now deterministic, even in partition mode
  • time is now only prepended to commands if it exists on the system

Parsnp v2.0.0

05 Jan 17:01
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What's Changed

  • You can now pass a newline-separated file of paths to query sequences to -d in addition to directories and command-line lists.
  • Adds --partition flag, which splits recruited genomes into partitions of size --partition-size (default 50).
  • Adds --no-recruit option which skips the recruitment step, but still drops genomes if their size differs substantially from the reference.
  • Fixes multiple bugs in the output:
    • Output can now be parsed by BioPython's AlignIO module with the "mauve" format
    • LCBs no longer overlap
    • Ambiguous base pairs and small contigs no longer lead to incorrect coordinates
    • VCF now contains the correct reference allele.
  • FastANI now guarantees at least 100 segments (unless it requires a fragment length < 500)
  • Adds --min-ref-cov option (default 90), which when used with --use-ani, removes query genomes that do not cover at least 90% of the reference.
  • Output folder has been reorganized to separate logs and config files from the main output.

Release v1.7.4

09 Jul 01:44
3a2ef47
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  • abpoa and muscle have been replaced by mafft for inter-LCB alignment.

Release v1.7.3

05 Jul 22:05
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The --extend-lcbs parameter now performs a gapped alignment using either muscle (>50nt) or abpoa (<=50nt) on inter-LCB regions. Alignments are trimmed back based on an ANI parameter that can also be provided by the user (i.e., cuts alignment off when it falls below 95% ANI). This parameter still only works w/ single contig genomes.

Also added better SeqIO validation. Throws out any genomes that can't be parsed.

Release v1.7.2

31 Mar 19:34
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  • Fix bug where Harvesttools is provided both a gbk and fasta reference.