index.rst

Welcome to sequencing_tools's documentation!

This is Douglas's repo for useful bioinformatics stuff.

.. toctree::
   :maxdepth: 2
   :caption: Contents:

Installation

Installation can be done via conda:

$ conda config --add channels bioconda
$ conda create -q -n test-environment python=3.6 \
    cython numpy networkx seaborn pyBigwig six pysam ujson pytest scipy   \
    matplotlib samtools future pytest-cov codecov
$ git clone https://github.com/wckdouglas/sequencing_tools.git
$ cd sequencing_tools
$ pip install .

fastq_tools

This module contains functions to interact with fastq files

.. autoclass:: sequencing_tools.fastq_tools._fastq_tools.fastqRecord
    :members:

.. automodule:: sequencing_tools.fastq_tools._fastq_tools
    :members:

.. autoclass:: sequencing_tools.fastq_tools.pe_align.ConsensusBuilder
    :members:

.. autoclass:: sequencing_tools.fastq_tools.function_clip.ReadTrimmer
    :members:

fasta_tools

This module contains functions to interact with fasta files

.. automodule:: sequencing_tools.fasta_tools
    :members:

.. autoclass:: sequencing_tools.fasta_tools.IUPAC
    :members:

.. autoclass:: sequencing_tools.fasta_tools.MultiAlignments
    :members:

bam_tools

This module contains functions to interact with bam files and bed files

.. automodule:: sequencing_tools.bam_tools._bam_tools
    :members:

consensus_tools

.. autoclass:: sequencing_tools.consensus_tools._consensus_tools.ErrorCorrection
    :members:

gene_tools

This module contains functions to interact with bed files, refflat, and gtf files.

.. autoclass:: sequencing_tools.gene_tools.Bed12Record
    :members:

.. autoclass:: sequencing_tools.gene_tools.GTFRecord
    :members:

.. autoclass:: sequencing_tools.gene_tools.transcriptome.Transcriptome
    :members:

.. autoclass:: sequencing_tools.gene_tools.transcriptome.Transcript
    :members:

.. autoclass:: sequencing_tools.gene_tools.transcriptome.Exon
    :members:

viz_tools

This module contains some functions that work with figures

.. automodule:: sequencing_tools.viz_tools
    :members:

stats_tools

This module contains some math functions

.. automodule:: sequencing_tools.stats_tools._stats_tools
    :members:

.. autoclass:: sequencing_tools.stats_tools._stats_tools.Bootstrap
    :members:

.. autoclass:: sequencing_tools.stats_tools.regression.GradientDescent
    :members:

utils

.. automodule:: sequencing_tools.utils
    :members:

Indices and tables

• :ref:`genindex`
• :ref:`modindex`
• :ref:`search`