Releases | Open Source Science

parsnp - v2.1.4

Use mauve format for partitioning mode and add VCF header for bcftools compatibility (#169 #177)
Fix logged sequence lengths #173
Use python3 in shebang line instead of python

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Published by bkille 11 months ago

parsnp - v2.1.3

Parsnp now outputs accurate CHROM and POS in the VCF output for multi-fasta references (they were previously being treated as a single concatenated sequence in terms of coordinates).

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Published by bkille about 1 year ago

parsnp - v2.1.2

Parsnp XMFA output now follows the Mauve format and has the appropriate header #FormatVersion Mauve so that HarvestTools parses it correctly. Fixes #169.
Adds warning for multifasta reference VCF coordinates.

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Published by bkille over 1 year ago

This release corrects the start location of reverse complement alignment records in the MAF output and also adds the ##maf version=1 program=parsnp header to the MAF output. The MAF output is now compliant with the UCSC format specification.

For more details, please see #167.

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Published by bkille over 1 year ago

parsnp - v2.1.0

The recombination filter has been fixed for partition workflows. Recombination filtering can now be enabled via --recomb-filter as well as the original -x, --xtrafast flags. Fixes #157.
The --no-recruit has been fixed and replaced by --skip-ani-filter. Fixes #164.
"Recruitment" in general has been renamed to "Filtering" to be consistent with other methods.
Crashes gracefully when a partition's genomes are too divergent. Fixes #165.
Inputs with duplicate filenames no longer allowed, i.e. /path1/genome.fna and /path2/genome.fna cannot both be provided. This is because the .xmfa and .maf output files use the file stem as the "sample" name. Fixes #166.

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Published by bkille over 1 year ago

parsnp - Parsnp v2.0.6

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

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Published by bkille over 1 year ago

parsnp - Release v2.0.5

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.

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Published by bkille almost 2 years ago

parsnp - Release v2.0.4

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

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Published by bkille about 2 years ago

parsnp - Release v2.0.3

Replaces internal commands which were incompatible with MacOS.

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Published by bkille about 2 years ago

parsnp - v2.0.2

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

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Published by bkille about 2 years ago

parsnp - Parsnp v2.0.1

Output is now deterministic, even in partition mode
time is now only prepended to commands if it exists on the system

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Published by bkille about 2 years ago

parsnp - Parsnp v2.0.0

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 100).
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.

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Published by bkille over 2 years ago

parsnp - Release v1.7.4

abpoa and muscle have been replaced by mafft for inter-LCB alignment.

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Published by bkille over 3 years ago

parsnp - Release v1.7.3

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.

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Published by bkille almost 4 years ago