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API

Introduction

This section describes application programming interface (API) for the fuc package.

Below is the list of submodules available in the fuc API:

  • common : The common submodule is used by other fuc submodules such as pyvcf and pybed. It also provides many day-to-day actions used in the field of bioinformatics.
  • pybam : The pybam submodule is designed for working with sequence alignment files (SAM/BAM/CRAM). It essentially wraps the pysam package to allow fast computation and easy manipulation. If you are mainly interested in working with depth of coverage data, please check out the pycov submodule which is specifically designed for the task.
  • pybed : The pybed submodule is designed for working with BED files. It implements pybed.BedFrame which stores BED data as pandas.DataFrame via the pyranges package to allow fast computation and easy manipulation. The submodule strictly adheres to the standard BED specification.
  • pychip : The pychip submodule is designed for working with annotation or manifest files from the Axiom (Thermo Fisher Scientific) and Infinium (Illumina) array platforms.
  • pycov : The pycov submodule is designed for working with depth of coverage data from sequence alingment files (SAM/BAM/CRAM). It implements pycov.CovFrame which stores read depth data as pandas.DataFrame via the pysam package to allow fast computation and easy manipulation. The pycov.CovFrame class also contains many useful plotting methods such as CovFrame.plot_region and CovFrame.plot_uniformity.
  • pyfq : The pyfq submodule is designed for working with FASTQ files. It implements pyfq.FqFrame which stores FASTQ data as pandas.DataFrame to allow fast computation and easy manipulation.
  • pygff : The pygff submodule is designed for working with GFF/GTF files. It implements pygff.GffFrame which stores GFF/GTF data as pandas.DataFrame to allow fast computation and easy manipulation. The submodule strictly adheres to the standard GFF specification.
  • pykallisto : The pykallisto submodule is designed for working with RNAseq quantification data from Kallisto. It implements pykallisto.KallistoFrame which stores Kallisto's output data as pandas.DataFrame to allow fast computation and easy manipulation. The pykallisto.KallistoFrame class also contains many useful plotting methods such as KallistoFrame.plot_differential_abundance.
  • pymaf : The pymaf submodule is designed for working with MAF files. It implements pymaf.MafFrame which stores MAF data as pandas.DataFrame to allow fast computation and easy manipulation. The pymaf.MafFrame class also contains many useful plotting methods such as MafFrame.plot_oncoplot and MafFrame.plot_summary. The submodule strictly adheres to the standard MAF specification.
  • pysnpeff : The pysnpeff submodule is designed for parsing VCF annotation data from the SnpEff program. It should be used with pyvcf.VcfFrame.
  • pyvcf : The pyvcf submodule is designed for working with VCF files. It implements pyvcf.VcfFrame which stores VCF data as pandas.DataFrame to allow fast computation and easy manipulation. The pyvcf.VcfFrame class also contains many useful plotting methods such as VcfFrame.plot_comparison and VcfFrame.plot_tmb. The submodule strictly adheres to the standard VCF specification.
  • pyvep : The pyvep submodule is designed for parsing VCF annotation data from the Ensembl VEP program. It should be used with pyvcf.VcfFrame.

For getting help on a specific submodule (e.g. pyvcf):

from fuc import pyvcf
help(pyvcf)

fuc.common

.. automodule:: fuc.api.common
   :members:

fuc.pybam

.. automodule:: fuc.api.pybam
   :members:

fuc.pybed

.. automodule:: fuc.api.pybed
   :members:

fuc.pychip

.. automodule:: fuc.api.pychip
   :members:

fuc.pycov

.. automodule:: fuc.api.pycov
   :members:

fuc.pyfq

.. automodule:: fuc.api.pyfq
   :members:

fuc.pygff

.. automodule:: fuc.api.pygff
   :members:

fuc.pykallisto

.. automodule:: fuc.api.pykallisto
   :members:

fuc.pymaf

.. automodule:: fuc.api.pymaf
   :members:

fuc.pysnpeff

.. automodule:: fuc.api.pysnpeff
   :members:

fuc.pyvcf

.. automodule:: fuc.api.pyvcf
   :members:

fuc.pyvep

.. automodule:: fuc.api.pyvep
   :members: