repo stringclasses 454
values | file_path stringlengths 5 201 | extension stringclasses 1
value | content stringlengths 8 509k | num_lines int64 3 16.9k | size_bytes int64 8 511k |
|---|---|---|---|---|---|
scikit-bio | skbio/stats/distance/_anosim.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 229 | 9,216 |
scikit-bio | skbio/stats/distance/tests/test_permdisp.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 424 | 18,339 |
scikit-bio | skbio/stats/distance/tests/test_anosim.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 134 | 5,641 |
scikit-bio | skbio/stats/distance/tests/test_permanova.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 514 | 23,967 |
scikit-bio | skbio/stats/distance/tests/test_util.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 147 | 4,409 |
scikit-bio | skbio/stats/distance/tests/test_base.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 2,239 | 80,274 |
scikit-bio | skbio/stats/distance/tests/test_bioenv.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 267 | 11,667 |
scikit-bio | skbio/stats/distance/tests/test_mantel.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 1,204 | 48,490 |
scikit-bio | skbio/stats/evolve/__init__.py | .py | """Evolutionary statistics (:mod:`skbio.stats.evolve`)
===================================================
.. currentmodule:: skbio.stats.evolve
This package contains statistics pertaining to phylogenies and evolution.
Cophylogenetic methods
----------------------
These functions test for correlation between phylog... | 35 | 948 |
scikit-bio | skbio/stats/evolve/_hommola.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 275 | 11,227 |
scikit-bio | skbio/stats/evolve/tests/test_hommola.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 180 | 7,846 |
scikit-bio | skbio/stats/composition/_utils.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 310 | 9,028 |
scikit-bio | skbio/stats/composition/_base.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 1,769 | 56,281 |
scikit-bio | skbio/stats/composition/__init__.py | .py | r"""Composition Statistics (:mod:`skbio.stats.composition`)
=======================================================
.. currentmodule:: skbio.stats.composition
This module provides functions for compositional data analysis.
Many omics datasets are inherently compositional -- meaning that they are best
interpreted as ... | 207 | 5,171 |
scikit-bio | skbio/stats/composition/_ancom.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 427 | 16,081 |
scikit-bio | skbio/stats/composition/_dirmult.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 725 | 30,933 |
scikit-bio | skbio/stats/composition/_ancombc.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 1,126 | 46,702 |
scikit-bio | skbio/stats/composition/tests/test_ancom.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 672 | 30,454 |
scikit-bio | skbio/stats/composition/tests/test_ancombc.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 355 | 14,468 |
scikit-bio | skbio/stats/composition/tests/test_dirmult.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 505 | 23,818 |
scikit-bio | skbio/stats/composition/tests/test_base.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 1,483 | 56,402 |
scikit-bio | skbio/stats/composition/tests/test_utils.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 324 | 12,346 |
scikit-bio | skbio/stats/ordination/_utils.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 290 | 9,969 |
scikit-bio | skbio/stats/ordination/_canonical_correspondence_analysis.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 261 | 9,175 |
scikit-bio | skbio/stats/ordination/_principal_component_analysis.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 258 | 10,438 |
scikit-bio | skbio/stats/ordination/_correspondence_analysis.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 204 | 7,719 |
scikit-bio | skbio/stats/ordination/__init__.py | .py | r"""Ordination methods (:mod:`skbio.stats.ordination`)
==================================================
.. currentmodule:: skbio.stats.ordination
This module provides functions for ordination -- a category of methods that aim at
arranging data so that similar data points are proximate to each other. Ordination can
... | 210 | 5,418 |
scikit-bio | skbio/stats/ordination/_principal_coordinate_analysis.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 719 | 28,953 |
scikit-bio | skbio/stats/ordination/_redundancy_analysis.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 271 | 10,452 |
scikit-bio | skbio/stats/ordination/_mmvec.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 1,731 | 61,682 |
scikit-bio | skbio/stats/ordination/_ordination_results.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 690 | 25,836 |
scikit-bio | skbio/stats/ordination/tests/test_mmvec.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 949 | 35,315 |
scikit-bio | skbio/stats/ordination/tests/test_redundancy_analysis.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 258 | 10,446 |
scikit-bio | skbio/stats/ordination/tests/test_principal_component_analysis.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 234 | 9,339 |
scikit-bio | skbio/stats/ordination/tests/test_correspondence_analysis.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 462 | 15,955 |
scikit-bio | skbio/stats/ordination/tests/test_util.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 128 | 4,845 |
scikit-bio | skbio/stats/ordination/tests/test_principal_coordinate_analysis.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 536 | 23,065 |
scikit-bio | skbio/stats/ordination/tests/test_ordination_results.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 705 | 30,252 |
scikit-bio | skbio/stats/ordination/tests/test_canonical_correspondence_analysis.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 178 | 6,724 |
scikit-bio | skbio/stats/tests/test_misc.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 58 | 1,784 |
scikit-bio | skbio/stats/tests/test_subsample.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 219 | 8,940 |
scikit-bio | skbio/stats/tests/test_power.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 514 | 22,129 |
scikit-bio | skbio/stats/tests/test_gradient.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 1,048 | 55,450 |
scikit-bio | skbio/embedding/__init__.py | .py | r"""Biological Embeddings (:mod:`skbio.embedding`)
=================================================
.. currentmodule:: skbio.embedding
This module provides support for storing embeddings for biological objects, such
as protein embeddings outputted from protein language models (pLMs).
Embedding types
--------------... | 80 | 1,733 |
scikit-bio | skbio/embedding/_embedding.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 377 | 10,976 |
scikit-bio | skbio/embedding/_protein.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 191 | 5,448 |
scikit-bio | skbio/embedding/tests/test_embedding.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 267 | 9,781 |
scikit-bio | skbio/embedding/tests/test_protein.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 160 | 5,914 |
scikit-bio | skbio/io/_warning.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 20 | 604 |
scikit-bio | skbio/io/descriptors.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 173 | 5,567 |
scikit-bio | skbio/io/_iosources.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 256 | 6,734 |
scikit-bio | skbio/io/util.py | .py | r"""I/O utilities (:mod:`skbio.io.util`)
====================================
.. currentmodule:: skbio.io.util
This module provides utility functions to deal with files and I/O in general.
Functions
---------
.. autosummary::
:toctree:
open
open_file
open_files
""" # noqa: D205, D415
# -------------... | 297 | 11,076 |
scikit-bio | skbio/io/__init__.py | .py | r"""Input and Output (:mod:`skbio.io`)
==================================
.. currentmodule:: skbio.io
This module provides input/output (I/O) functionality for scikit-bio.
In bioinformatics there are many different file formats, and in scikit-bio there are
many different classes which can read and write these format... | 395 | 12,141 |
scikit-bio | skbio/io/registry.py | .py | r"""I/O Registry (:mod:`skbio.io.registry`)
=======================================
.. currentmodule:: skbio.io.registry
Classes
-------
.. autosummary::
:toctree:
IORegistry
Format
Functions
---------
.. autosummary::
:toctree:
create_format
Exceptions
----------
.. autosummary::
DuplicateR... | 1,089 | 39,939 |
scikit-bio | skbio/io/_exception.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 145 | 3,122 |
scikit-bio | skbio/io/_fileobject.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 85 | 2,578 |
scikit-bio | skbio/io/format/sample_metadata.py | .py | """Sample Metadata object ported over from qiime2.
===============================================
.. currentmodule:: skbio.io.format.sample_metadata
This implements the Sample_Metadata format which is identical to the
Metadata format implemented in qiime2.
(see: https://docs.qiime2.org/2024.2/tutorials/metadata/)
... | 368 | 14,021 |
scikit-bio | skbio/io/format/binary_dm.py | .py | """Simple binary dissimilarity matrix format (:mod:`skbio.io.format.binary_dm`)
============================================================================
.. currentmodule:: skbio.io.format.binary_dm
The Binary DisSimilarity Matrix format (``binary_dm``) encodes a binary
representation for dissimilarity and distanc... | 227 | 7,104 |
scikit-bio | skbio/io/format/embl.py | .py | """EMBL format (:mod:`skbio.io.format.embl`)
=========================================
.. currentmodule:: skbio.io.format.embl
EMBL format stores sequence and its annotation together. The start of the
annotation section is marked by a line beginning with the word "ID". The start
of sequence section is marked by a lin... | 1,620 | 54,567 |
scikit-bio | skbio/io/format/embed.py | .py | r"""Embedding format (:mod:`skbio.io.format.embed`).
====================================================
.. currentmodule:: skbio.io.format.embed
This module provides support for reading and writing embedding files that
are outputted by sequential language models such as protein language models
(pLMs).
Format Suppo... | 348 | 12,611 |
scikit-bio | skbio/io/format/_base.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 240 | 7,599 |
scikit-bio | skbio/io/format/newick.py | .py | r"""Newick format (:mod:`skbio.io.format.newick`)
=============================================
.. currentmodule:: skbio.io.format.newick
Newick format (``newick``) stores spanning-trees with weighted edges and node
names in a minimal file format [1]_. This is useful for representing
phylogenetic trees and taxonomies... | 491 | 20,416 |
scikit-bio | skbio/io/format/fasta.py | .py | r"""FASTA/QUAL format (:mod:`skbio.io.format.fasta`)
================================================
.. currentmodule:: skbio.io.format.fasta
The FASTA file format (``fasta``) stores biological (i.e., nucleotide or
protein) sequences in a simple plain text format that is both human-readable
and easy to parse. The fi... | 1,086 | 38,059 |
scikit-bio | skbio/io/format/phylip_dm.py | .py | """PHYLIP distance matrix format (:mod:`skbio.io.format.phylip_dm`)
================================================================
.. currentmodule:: skbio.io.format.phylip_dm
.. versionadded:: 0.7.2
The PHYLIP file format stores pairwise distance matrices. This format is commonly
used in phylogenetic analysis and... | 543 | 18,110 |
scikit-bio | skbio/io/format/fastq.py | .py | r"""FASTQ format (:mod:`skbio.io.format.fastq`)
===========================================
.. currentmodule:: skbio.io.format.fastq
The FASTQ file format (``fastq``) stores biological (e.g., nucleotide)
sequences and their quality scores in a simple plain text format that is both
human-readable and easy to parse. Th... | 674 | 22,405 |
scikit-bio | skbio/io/format/qseq.py | .py | r"""QSeq format (:mod:`skbio.io.format.qseq`)
=========================================
.. currentmodule:: skbio.io.format.qseq
The QSeq format (`qseq`) is a record-based, plain text output format produced
by some DNA sequencers for storing biological sequence data, quality scores,
per-sequence filtering information,... | 369 | 10,482 |
scikit-bio | skbio/io/format/_sequence_feature_vocabulary.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 395 | 12,177 |
scikit-bio | skbio/io/format/emptyfile.py | .py | r"""Empty Files (:mod:`skbio.io.format.emptyfile`)
==============================================
.. currentmodule:: skbio.io.format.emptyfile
This format exists to make debugging simpler, often an empty file is a mistake
which can take an embarrassing amount of time to notice. This format has only
a sniffer and no r... | 40 | 1,179 |
scikit-bio | skbio/io/format/stockholm.py | .py | """Stockholm format (:mod:`skbio.io.format.stockholm`)
===================================================
.. currentmodule:: skbio.io.format.stockholm
The Stockholm format is a multiple sequence alignment format (MSA) that
optionally supports storing arbitrary alignment features (metadata). Features
can be placed in... | 818 | 29,028 |
scikit-bio | skbio/io/format/biom.py | .py | r"""BIOM-Format (:mod:`skbio.io.format.biom`)
============================================
.. currentmodule:: skbio.io.format.biom
The BIOM-Format (format v2.1.0) is an HDF5-based format to represent sample/feature
counts or relative abundances. It is designed specifically for sparse data.
Internally, it stores the d... | 140 | 4,279 |
scikit-bio | skbio/io/format/blast7.py | .py | """BLAST+7 format (:mod:`skbio.io.format.blast7`)
==============================================
.. currentmodule:: skbio.io.format.blast7
The BLAST+7 format (``blast+7``) stores the results of a BLAST [1]_ database
search. This format is produced by both BLAST+ output
format 7 and legacy BLAST output format 9. The r... | 406 | 14,690 |
scikit-bio | skbio/io/format/clustal.py | .py | r"""Clustal format (:mod:`skbio.io.format.clustal`)
===============================================
.. currentmodule:: skbio.io.format.clustal
Clustal format (``clustal``) stores multiple sequence alignments. This format
was originally introduced in the Clustal package [1]_.
Format Support
--------------
**Has Sniff... | 354 | 12,348 |
scikit-bio | skbio/io/format/lsmat.py | .py | r"""Labeled square matrix format (:mod:`skbio.io.format.lsmat`)
===========================================================
.. currentmodule:: skbio.io.format.lsmat
The labeled square matrix file format (``lsmat``) stores numeric square
matrix data relating a set of objects along each axis. The format also stores
ide... | 281 | 10,157 |
scikit-bio | skbio/io/format/blast6.py | .py | r"""BLAST+6 format (:mod:`skbio.io.format.blast6`)
==============================================
.. currentmodule:: skbio.io.format.blast6
The BLAST+6 format (``blast+6``) stores the results of a BLAST [1]_ database
search. The results are stored in a simple tabular format with no column
headers. Values are separate... | 289 | 12,714 |
scikit-bio | skbio/io/format/taxdump.py | .py | r"""Taxdump format (:mod:`skbio.io.format.taxdump`)
===============================================
.. currentmodule:: skbio.io.format.taxdump
The NCBI Taxonomy database dump (``taxdump``) format stores information of
organism names, classifications and other properties. It is a tabular format
with a delimiter: ``<ta... | 327 | 13,154 |
scikit-bio | skbio/io/format/_blast.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 96 | 2,301 |
scikit-bio | skbio/io/format/phylip.py | .py | """PHYLIP multiple sequence alignment format (:mod:`skbio.io.format.phylip`)
=========================================================================
.. currentmodule:: skbio.io.format.phylip
The PHYLIP file format stores a multiple sequence alignment. The format was
originally defined and used in Joe Felsenstein's ... | 406 | 15,495 |
scikit-bio | skbio/io/format/genbank.py | .py | """GenBank format (:mod:`skbio.io.format.genbank`)
===============================================
.. currentmodule:: skbio.io.format.genbank
GenBank format (GenBank Flat File Format) stores sequence and its
annotation together. The start of the annotation section is marked by
a line beginning with the word "LOCUS". ... | 763 | 26,375 |
scikit-bio | skbio/io/format/ordination.py | .py | r"""Ordination results format (:mod:`skbio.io.format.ordination`)
=============================================================
.. currentmodule:: skbio.io.format.ordination
The ordination results file format (``ordination``) stores the results of an
ordination method in a human-readable, text-based format. The forma... | 447 | 14,876 |
scikit-bio | skbio/io/format/gff3.py | .py | """GFF3 format (:mod:`skbio.io.format.gff3`)
=========================================
.. currentmodule:: skbio.io.format.gff3
GFF3 (Generic Feature Format version 3) is a standard file format for
describing features for biological sequences. It contains lines of
text, each consisting of 9 tab-delimited columns [1]_.... | 558 | 18,798 |
scikit-bio | skbio/io/format/tests/test_emptyfile.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 37 | 1,097 |
scikit-bio | skbio/io/format/tests/test_clustal.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 292 | 11,715 |
scikit-bio | skbio/io/format/tests/test_lsmat.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 337 | 12,432 |
scikit-bio | skbio/io/format/tests/test_newick.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 370 | 12,594 |
scikit-bio | skbio/io/format/tests/test_fastq.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 676 | 28,821 |
scikit-bio | skbio/io/format/tests/test_sequence_feature_vocabulary.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 121 | 4,598 |
scikit-bio | skbio/io/format/tests/test_phylip.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 286 | 11,028 |
scikit-bio | skbio/io/format/tests/test_biom.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 67 | 2,371 |
scikit-bio | skbio/io/format/tests/test_embl.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 889 | 36,313 |
scikit-bio | skbio/io/format/tests/test_embed.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 226 | 8,940 |
scikit-bio | skbio/io/format/tests/test_taxdump.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 174 | 8,055 |
scikit-bio | skbio/io/format/tests/test_blast7.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 211 | 9,968 |
scikit-bio | skbio/io/format/tests/test_ordination.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 318 | 15,071 |
scikit-bio | skbio/io/format/tests/test_base.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 326 | 13,438 |
scikit-bio | skbio/io/format/tests/test_blast6.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 124 | 6,399 |
scikit-bio | skbio/io/format/tests/test_genbank.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 408 | 15,587 |
scikit-bio | skbio/io/format/tests/test_sample_metadata.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 82 | 2,763 |
scikit-bio | skbio/io/format/tests/test_stockholm.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 915 | 42,679 |
scikit-bio | skbio/io/format/tests/test_qseq.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 353 | 13,189 |
scikit-bio | skbio/io/format/tests/test_gff3.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 349 | 13,406 |
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