==========
genomicspy
==========
.. image:: https://img.shields.io/pypi/v/genomicspy.svg
:target: https://pypi.python.org/pypi/genomicspy
.. image:: https://img.shields.io/travis/vivianleung/genomicspy.svg
:target: https://travis-ci.com/vivianleung/genomicspy
.. image:: https://readthedocs.org/projects/genomicspy/badge/?version=latest
:target: https://genomicspy.readthedocs.io/en/latest/?version=latest
:alt: Documentation Status
Tools for manipulating vcfs doing genomics work
Features
=========
Classes:
---------
* ``Chunk``: for handling chunks of vcfpy.Record objects
* ``Saver``: to save Chunks and vcfpy.Record objects
Types:
-------
* ``SeqType``
Methods and constants:
-----------------------
allele_msa: multiple sequence alignments operations
* ``find_read_msas``
* ``gen_variants_df``
* ``parse_alignments``
alleles: manipulating and filling in alleles and variants
* ``combine_ivrs_variants``
* ``calc_circular``
* ``calc_end_pos``
* ``gen_ivrs``
* ``check_overlap``
* ``gen_alleles_for_chrom_vcf``
* ``gen_alleles_from_variants_df``
alleles2fastas: converting allele data to fasta sequences
* ``check_fasta_seq_coverage``
* ``get_seqlen``
* ``infer_entry_name``
* ``read_alleles_gts_from_variants``
* ``read_alleles_gts_from_vcf``
* ``write_fasta_seq``
regions: reading and parsing GFF3 and region-feature info
* ``consolidate_gff3``
* ``parse_gff3``
* ``select_regions``
* ``GFF3_COLS``
trim: trim alleles or sequences
* ``trim_alleles``
* ``trim_allele_seqs``
vcf: read VCFs
* ``get_entry_data``
* ``parse_records_generator``
* ``VCF_COLS``
* ``VCF_DEFAULT_DICT``
* Free software: MIT license
* Documentation: https://genomicspy.readthedocs.io.
Credits
--------
This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
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