=========
SeqPandas
=========
Import genomic data to get a custom Pandas & Biopython hybrid class object with fancy shortcuts to make Machine Learning preprocessing easy!
* Free software: MIT license
* Documentation: https://seqpandas.readthedocs.io.
Installation
------------
.. code:: bash
pip install seqpandas
Usage
-----
.. code:: python
import seqpandas as spd
# Direct File Path
df = spd.read_seq('file.fasta', format='fasta')
df = spd.read_seq('file.sam', format='sam')
df = spd.read_vcf('file.vcf', format='vcf')
df = spd.read_bed('file.bed', format='bed')
# Just need BioPython Seqs? No problem!
seqrecords = spd.read('file.fasta', format='fasta')
# Already Opened BioPython Handle
from Bio import SeqIO
seqrecords = SeqIO.parse('file.fasta', format='fasta')
df = spd.BioDataFrame.from_seqrecords(seqrecords)
Tutorial
--------
For a complete walkthrough and to use it for a machine learning pipeline please follow the `tutorial notebook <https://github.com/tmsincomb/SeqPandas/blob/master/tutorial.ipynb>`_.
Credits
-------
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.
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"description": "=========\nSeqPandas\n=========\nImport genomic data to get a custom Pandas & Biopython hybrid class object with fancy shortcuts to make Machine Learning preprocessing easy!\n\n* Free software: MIT license\n* Documentation: https://seqpandas.readthedocs.io.\n\n\nInstallation\n------------\n\n.. code:: bash\n\n pip install seqpandas\n\n\nUsage\n-----\n\n.. code:: python\n\n import seqpandas as spd\n\n # Direct File Path\n df = spd.read_seq('file.fasta', format='fasta')\n df = spd.read_seq('file.sam', format='sam')\n df = spd.read_vcf('file.vcf', format='vcf')\n df = spd.read_bed('file.bed', format='bed')\n\n # Just need BioPython Seqs? No problem!\n seqrecords = spd.read('file.fasta', format='fasta')\n\n # Already Opened BioPython Handle\n from Bio import SeqIO\n seqrecords = SeqIO.parse('file.fasta', format='fasta')\n df = spd.BioDataFrame.from_seqrecords(seqrecords)\n\n\nTutorial\n--------\nFor a complete walkthrough and to use it for a machine learning pipeline please follow the `tutorial notebook <https://github.com/tmsincomb/SeqPandas/blob/master/tutorial.ipynb>`_.\n\n\nCredits\n-------\n\nThis package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.\n",
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