sequence-formats: A package with basic parsing utilities for several Bioinformatic data formats.

[ bioinformatics, gpl, library ] [ Propose Tags ]

Contains utilities to parse and write Eigenstrat, Fasta, FreqSum, VCF and other file formats used in population genetics analyses.


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Versions [faq] 1.1.4.1
Change log Changelog.md
Dependencies attoparsec (>=0.13.2.2 && <0.14), base (>=4.7 && <5), bytestring (>=0.10.8.2 && <0.11), containers (>=0.5.10.2 && <0.6), data-memocombinators (>=0.5.1 && <0.6), errors (>=2.2.2 && <2.3), exceptions (>=0.8.3 && <0.9), foldl (>=1.3.7 && <1.4), hslogger (>=1.2.10 && <1.3), lens-family (>=1.2.2 && <1.3), MissingH (>=1.4.0.1 && <1.5), pipes (>=4.3.7 && <4.4), pipes-attoparsec (>=0.5.1.5 && <0.6), pipes-bytestring (>=2.1.6 && <2.2), pipes-safe (>=2.2.6 && <2.3), pipes-text (>=0.0.2.5 && <0.1), split (>=0.2.3.3 && <0.3), text (>=1.2.2.2 && <1.3), transformers (>=0.5.2.0 && <0.6), turtle (>=1.4.5 && <1.5), vector (>=0.12.0.1 && <0.13) [details]
License GPL-3.0-only
Author Stephan Schiffels
Maintainer stephan.schiffels@mac.com
Category Bioinformatics
Uploaded by stephan_schiffels at Tue Mar 5 14:09:46 UTC 2019
Distributions NixOS:1.1.4.1
Downloads 45 total (21 in the last 30 days)
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Status Hackage Matrix CI
Docs not available [build log]
All reported builds failed as of 2019-03-05 [all 2 reports]

Modules

  • SequenceFormats
    • SequenceFormats.Eigenstrat
    • SequenceFormats.Fasta
    • SequenceFormats.FreqSum
    • SequenceFormats.RareAlleleHistogram
    • SequenceFormats.Utils
    • SequenceFormats.VCF

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Readme for sequence-formats-1.1.4.1

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Sequence-Formats is a Haskell package to provide file parsers and writers for some commonly, and less commonly used file formats in Bioinformatics, speficially population genetics.

The library makes heavy use of the pipes library to provide Producers and Consumers for reading and writing files.