seq-tools


Nameseq-tools JSON
Version 1.0.9 PyPI version JSON
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home_pagehttps://github.com/jason-weirather/py-seq-tools
SummaryPython tools for working with biological sequence data
upload_time2017-09-17 23:58:52
maintainer
docs_urlNone
authorJason L Weirather
requires_python
licenseApache License, Version 2.0
keywords bioinformatics sequence alignment
VCS
bugtrack_url
requirements No requirements were recorded.
Travis-CI No Travis.
coveralls test coverage No coveralls.
            # py-seq-tools
Free python libraries for working with biological sequences, alignments, and formats. These libraries are part of Au-public scripts, I haven't documented them well yet.  The goal here is to put them into a package and get them better documented.

Longer term, these were written in python 2, but it would be nice to either support python3 full compatability or to completely migrate them over to python3.

The command line utilities of this package serve a dual purpose. 1) is to provide useful utilities you can run through the commandline, and 2) is to provide examples on how to make use the of the libraries included in this package.

Access to the command line utilities can be found with

`$ seq-tools <cli command>`

Where cli command is the name of a cli module.

To use the libraries in this distribution please consult the [API documentation](https://github.com/jason-weirather/py-seq-tools/blob/master/manual.pdf)

You can install seq-tools with pip

>From within the source directory you can try

`$ pip install .`

This should make the `seq-tools` command available as well as the `seqtools` library for import.

This library includes the following modules:

* seqtools
  * align
  * errors
  * format
    * bamindex
    * bed
    * bgzf
    * fasta
    * fastq
    * pacbio
    * psl
    * sam
  * graph
  * range
  * sequence
  * simulation
    * emitter
    * permute
    * randomsource
  * statistics
  * stream
  * structure

Again, details are available in the [API documentation](https://github.com/jason-weirather/py-seq-tools/blob/master/manual.pdf).



            

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    "description": "# py-seq-tools\nFree python libraries for working with biological sequences, alignments, and formats. These libraries are part of Au-public scripts, I haven't documented them well yet.  The goal here is to put them into a package and get them better documented.\n\nLonger term, these were written in python 2, but it would be nice to either support python3 full compatability or to completely migrate them over to python3.\n\nThe command line utilities of this package serve a dual purpose. 1) is to provide useful utilities you can run through the commandline, and 2) is to provide examples on how to make use the of the libraries included in this package.\n\nAccess to the command line utilities can be found with\n\n`$ seq-tools <cli command>`\n\nWhere cli command is the name of a cli module.\n\nTo use the libraries in this distribution please consult the [API documentation](https://github.com/jason-weirather/py-seq-tools/blob/master/manual.pdf)\n\nYou can install seq-tools with pip\n\n>From within the source directory you can try\n\n`$ pip install .`\n\nThis should make the `seq-tools` command available as well as the `seqtools` library for import.\n\nThis library includes the following modules:\n\n* seqtools\n  * align\n  * errors\n  * format\n    * bamindex\n    * bed\n    * bgzf\n    * fasta\n    * fastq\n    * pacbio\n    * psl\n    * sam\n  * graph\n  * range\n  * sequence\n  * simulation\n    * emitter\n    * permute\n    * randomsource\n  * statistics\n  * stream\n  * structure\n\nAgain, details are available in the [API documentation](https://github.com/jason-weirather/py-seq-tools/blob/master/manual.pdf).\n\n\n", 
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