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Commit e7be21bd authored by Martin Larralde's avatar Martin Larralde
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Update documentation index to show related packages [ci skip]

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docs/_static/js/custom-icon.js
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docs/guide/index.rst
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User Guide
==========
This section contains guides and documents about some aspects of PyHMMER,
including the rationale behind the parallelization strategy implemented
in `pyhmmer.hmmer`.
.. toctree::
:maxdepth: 1
:caption: Getting Started
......@@ -9,7 +13,6 @@ User Guide
Publications <publications>
Performance <performance>
.. toctree::
:maxdepth: 1
:caption: Resources
......
docs/index.rst
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......@@ -77,22 +77,23 @@ language, that provides bindings to HMMER3. It directly interacts with the
HMMER internals, which has the following advantages over CLI wrappers:
.. grid:: 1 2 3 3
:gutter: 1
.. grid-item-card:: :fas:`battery-full` Batteries-included
Just install ``pyhmmer`` as a ``pip`` or ``conda`` dependency, no need
for the HMMER binaries or any other dependency.
Just add ``pyhmmer`` as a ``pip`` or ``conda`` dependency, no need
for the HMMER binaries or any external dependency.
.. grid-item-card:: :fas:`screwdriver-wrench` Flexible
Create input `~pyhmmer.easel.Sequence` and `~pyhmmer.plan7.HMM` objects
Create input `~pyhmmer.easel.Sequence` and `~pyhmmer.plan7.HMM` objects
with the :doc:`API <api/index>`, or load them from a file.
.. grid-item-card:: :fas:`gears` Practical
Retrieve nested results as dedicated `~pyhmmer.plan7.TopHits` objects,
write them to a file, or use them for further Python analysis.
.. grid-item-card:: :fas:`gauge-high` Fast
Run `hmmsearch` in parallel using an efficient threading model, which
......@@ -100,15 +101,10 @@ HMMER internals, which has the following advantages over CLI wrappers:
.. grid-item-card:: :fas:`dolly` Shareable
:doc:`Distribute <examples/embed_hmms> and load` `~pyhmmer.plan7.HMM`
from inside a Python package to facilitate sharing analyses.
:doc:`Distribute and load <examples/embed_hmms>` `~pyhmmer.plan7.HMM`
objects from inside a Python package to facilitate sharing analyses.
.. grid-item-card:: :fas:`dolly` Distributable
:doc`Distribute <examples/embed_hmms>` and load `HMM` next
in Python package to facilitate sharing and improve reproducibility.
.. grip-item-card:: :fas:`eye` Inspectable
.. grid-item-card:: :fas:`eye` Transparent
Access the internals of a `~pyhmmer.plan7.HMM`, inspect the attributes
and manually edit transitions or emissions scores.
......@@ -137,22 +133,107 @@ Library
:maxdepth: 2
User Guide <guide/index>
.. Examples <examples/index>
Examples <examples/index>
API Reference <api/index>
Related Projects
----------------
Building a HMM from scratch? Then you may be interested in the `PyFAMSA <https://pypi.org/project/pyfamsa/>`_
package, providing bindings to `FAMSA <https://github.com/refresh-bio/FAMSA>`_,
a very fast multiple sequence aligner. In addition, you may want to trim alignments:
in that case, consider `PytrimAl <https://pypi.org/project/pytrimal>`_, which
wraps `trimAl 2.0 <https://github.com/inab/trimal/tree/2.0_RC>`_.
The following Python libraries may be of interest for bioinformaticians.
.. grid:: 1 3 5 5
:gutter: 1
.. grid-item-card:: :fas:`fire` Pyrodigal
:link: https://pyrodigal.readthedocs.io
Gene Finding (with Prodigal).
.. grid-item-card:: :fas:`virus-covid` Pyrodigal-gv
:link: https://github.com/althonos/pyrodigal-gv
Pyrodigal for Giant Viruses.
.. grid-item-card:: :fas:`align-center` PyFAMSA
:link: https://pyfamsa.readthedocs.io
Multiple Sequence Alignment (with FAMSA).
.. grid-item-card:: :fas:`scissors` PytrimAl
:link: https://pytrimal.readthedocs.io
Alignment Trimming (with trimAl).
.. grid-item-card:: :fas:`music` LightMotif
:link: https://lightmotif.readthedocs.io
Platform-accelerated motif scoring.
.. grid-item-card:: :fas:`knife;fa-custom` Diced
:link: https://diced.readthedocs.io
CRISPR Detection (with MinCED).
.. grid-item-card:: :fas:`table-cells` Scoring Matrices
:link: https://scoring-matrices.readthedocs.io
Common scoring matrices for Cython.
.. grid-item-card:: :fas:`chain` Pyskani
:link: https://pyskani.readthedocs.io
Average Nucleotide Identity (with skani).
.. grid-item-card:: :fas:`forward-fast` PyFastANI
:link: https://pyfastani.readthedocs.io
Average Nucleotide Identity (with FastANI).
.. grid-item-card:: :fas:`magnifying-glass` PyJess
:link: https://pyjess.readthedocs.io
Geometric Template Matching (with Jess).
.. grid-item-card:: :fas:`repeat` PyTantan
:link: https://pytantan.readthedocs.io
Tandem Repeat Masking (with Tantan).
.. grid-item-card:: :fas:`gem` PyOpal
:link: https://pyopal.readthedocs.io
Query/Database Aligner (with Opal).
.. grid-item-card:: :fas:`sword;fa-custom` PySWRD
:link: https://pyswrd.readthedocs.io
Database Heuristic Filtering (with SWORD).
.. grid-item-card:: :fas:`rocket` Mini3di
:link: https://github.com/althonos/mini3di
Protein structure to 3di (with FoldSeek).
.. grid-item-card:: :fas:`calculator` ``peptides.py``
:link: https://peptides.readthedocs.io
Peptide descriptors.
.. grid-item-card:: :fas:`diagram-project` Pronto
:link: https://pronto.readthedocs.io
Open Biomedical Ontologies in Python.
.. grid-item-card:: :fas:`box` NAFcodec
:link: https://nafcodec.readthedocs.io
Nucleotide Archival Format in Python.
.. grid-item-card:: :fas:`bank` ``gb-io.py``
:link: https://gb-io.readthedocs.io
If despite of all the advantages listed earlier, you would rather use HMMER
through its CLI, this package will not be of great help. You can instead check
the `hmmer-py <https://github.com/EBI-Metagenomics/hmmer-py>`_ package developed
by `Danilo Horta <https://github.com/horta>`_ at the `EMBL-EBI <https://www.ebi.ac.uk>`_.
Fast GenBank parser written in Rust.
License
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