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PIrANHA version 0.4-alpha

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@justincbagley justincbagley released this 13 Apr 16:46
· 522 commits to master since this release
v0.4a
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Scripts for file processing and analysis in phylogenomics & phylogeography

This is PIrANHA v0.4a, a software package that provides a number of utility functions and pipelines for file processing and analysis in standard phylogenetics, phylogenomics, and phylogeography. PIrANHA stands for "Phylogenetics and Phylogeography," and v0.4a (=v0.4-alpha) is a new development pre-release, or 'minor version' that is greatly improved and ready for alpha testing! Please feel free to download this release and try it out, as most of the scripts have been verified; however, realize that PIrANHA is still under active development. Please email all suggestions and bug fix requests to Justin directly at bagleyj (at) umsl (dot) edu (also see Contact page of the wiki).

See full description in the PIrANHA README and wiki pages.

What's new?

v0.4a (v0.4-alpha)

This update builds on the previous pre-release, v0.3-alpha.2, by updating the main prianha script including improvements to how arguments are passed and fixes to debug mode, updates to all functions (improved syntax, bug fixes, and help texts), as well as the addition of new functions. The most recent changes include:

PIrANHA v0.4a (official minor pre-release version 0.4-alpha) - April 13, 2020

  • April 12, 2020: Various minor updates to piranha bin/ functions, and important update to options in main piranha script now allows arguments to be passed to the program directly after the function call (after -f flag), without -a|--args flag. This fixes a problem where the previous implementation's reliance on --args='<args>' format (arguments passed in quotes) meant that Bash completion would not work while writing out the arguments.
  • April 6-7, 2020: Major piranha package update, including edits to main script, all functions, dir structure, and other files (e.g. test files). Bug fixes for errors when no arguments and failed rm calls, check and update debug code, plus updates to READMEs and help texts.
  • April 2-3, 2020: Multiple updates. Added new FASTAsummary function that automates summarizing characteristics of one or multiple FASTA files in current working directory, and I also modified calcAlignmentPIS to integrate with this new function, and now both functions work well when run separately or together (the function to calculate PIS is now called within FASTAsummary. Also updated PHYLIPsummary function. Also added new splitFASTA function that splits each tip taxon (individual sequence) in a FASTA file into a separate FASTA file. This set of updates also includes a new piranha script with updated -f list function accommodating new functions, and with an attempt at adding debugging code (but this needs additional testing and fixing (How to best implement debugging?)).
  • March 30, 2020: Multiple updates. Added new nQuireRunner function that automates running nQuire to estimate ploidy levels for samples based on mapped NGS reads (BAM files); updated FASTA2PHYLIP function to have new options (-f and -i) allowing analysis of a single input FASTA or multiple FASTAs (prev. only did multiple FASTAs in cwd); updated MAGNET with minor fixes to v1.1.1 (updated versioning in README as well); and updated piranha function to have complete list function output. Also added test FASTA file 'test.fasta' to test/ subfolder of repository containing test input files.
  • December 12, 2019: Added new BEAST_logThinner function script that downsizes, or 'thins', BEAST2 .log files to every nth line. Tested and working interactively. Outputs new log file in current working directory, without replacement.
  • October 23, 2019: Added new PHYLIPsummary function script that summarizes no. taxa and no. characters for one or multiple PHYLIP DNA sequence alignments in current directory.
  • October 22, 2019: Made minor edits (e.g. fixing versioning) and bug fixes (fixing sed code that caused failures when user had GNU SED installed instead of BSD SED) to all of the following function scripts: PhyloMapperNullProc, PHYLIPsubsampler, PHYLIPcleaner, PHYLIP2PFSubsets, MLEResultsProc, getBootTrees, fastSTRUCTURE, dropRandomHap, dadiUncertainty, dadiRunner, dadiPostProc, calcAlignmentPIS, BEASTRunner, BEAST_PSPrepper, RAxMLRunChecker, RAxMLRunner, SNAPPRunner, SpeciesIdentifier, AnouraNEXUSPrepper, concatenateSeqs, concatSeqsPartitions, FASTA2VCF, getTaxonNames, makePartitions, MrBayesPostProc, phyNcharSumm, pyRAD2PartitionFinder, pyRADLocusVarSites, renameForStarBeast2, renameTaxa, renameTaxa_v1, splitPHYLIP, taxonCompFilter, treeThinner, vcfSubsampler, completeSeqs, RYcoder, RogueNaRokRunner, PHYLIP2NEXUS, PHYLIP2Mega, NEXUS2PHYLIP, NEXUS2MultiPHYLIP, Mega2PHYLIP, BEASTReset, FASTA2PHYLIP, completeConcatSeqs
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