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|
%global _empty_manifest_terminate_build 0
Name: python-biocommons.seqrepo
Version: 0.6.5
Release: 1
Summary: Non-redundant, compressed, journalled, file-based storage for biological sequences
License: Apache Software License
URL: https://github.com/biocommons/biocommons.seqrepo
Source0: https://mirrors.nju.edu.cn/pypi/web/packages/f1/55/7bff2f7bd3971925d18bdfb9e666b6d0bb1abd7f28da7a82a19fc5a6529f/biocommons.seqrepo-0.6.5.tar.gz
BuildArch: noarch
Requires: python3-bioutils
Requires: python3-coloredlogs
Requires: python3-ipython
Requires: python3-pysam
Requires: python3-requests
Requires: python3-requests-html
Requires: python3-six
Requires: python3-tqdm
Requires: python3-yoyo-migrations
Requires: python3-tox
%description
biocommons.seqrepo
!!!!!!!!!!!!!!!!!!
Python package for writing and reading a local collection of
biological sequences. The repository is non-redundant, compressed,
and journalled, making it efficient to store and transfer multiple
snapshots.
Clients refer to sequences and metadata using familiar identifiers,
such as NM_000551.3 or GRCh38:1, or any of several hash-based
identifiers. The interface supports fast slicing of arbitrary regions
of large sequences.
A "fully-qualified" identifier includes a namespace to disambiguate
accessions (e.g., "1" in GRCh37 and GRCh38). If the namespace is
provided, seqrepo uses it as-is. If the namespace is not provided and
the unqualified identifier refers to a unique sequence, it is
returned; otherwise, ambiguous identifiers will raise an error.
SeqRepo favors identifiers from [identifiers.org](identifiers.org)
whenever available. Examples include
[refseq](https://registry.identifiers.org/registry/refseq) and
[ensembl](https://registry.identifiers.org/registry/ensembl).
`seqrepo-rest-service
<https://github.com/biocommons/seqrepo-rest-service>`__ provides a
REST interface and docker image.
Released under the Apache License, 2.0.
|ci_rel| | |cov| | |pypi_rel| | `ChangeLog <https://github.com/biocommons/biocommons.seqrepo/tree/master/docs/changelog/0.5>`_
Citation
!!!!!!!!
| Hart RK, Prlić A (2020)
| SeqRepo: A system for managing local collections of biological sequences.
| PLoS ONE 15(12): e0239883. https://doi.org/10.1371/journal.pone.0239883
Features
!!!!!!!!
* Timestamped, read-only snapshots.
* Space-efficient storage of sequences within a single snapshot and
across snapshots.
* Bandwidth-efficient transfer incremental updates.
* Fast fetching of sequence slices on chromosome-scale sequences.
* Precomputed digests that may be used as sequence aliases.
* Mappings of external aliases (i.e., accessions or identifiers like
NM_013305.4) to sequences.
Deployments Scenarios
!!!!!!!!!!!!!!!!!!!!!
* Local read-only archive, mirrored from public site,
accessed via Python API (see `Mirroring documentation <docs/mirror.rst>`__)
* Local read-write archive, maintained with command
line utility and/or API (see `Command Line Interface documentation
<docs/cli.rst>`__).
* Docker data-only container that may be linked to application container.
* SeqRepo and refget REST API for local or remote access (see `seqrepo-rest-service <https://github.com/biocommons/seqrepo-rest-service>`__)
Technical Quick Peek
!!!!!!!!!!!!!!!!!!!!
Within a single snapshot, sequences are stored *non-redundantly* and
*compressed* in an add-only journalled filesystem structure. A
truncated SHA-512 hash is used to assess uniquness and as an
internal id. (The digest is truncated for space efficiency.)
Sequences are compressed using the Block GZipped Format (`BGZF
<https://samtools.github.io/hts-specs/SAMv1.pdf>`__)), which enables
pysam to provide fast random access to compressed sequences. (Variable
compression typically makes random access impossible.)
Sequence files are immutable, thereby enabling the use of hardlinks
across snapshots and eliminating redundant transfers (e.g., with
rsync).
Each sequence id is associated with a namespaced alias in a sqlite
database. Such as ``<seguid,rvvuhY0FxFLNwf10FXFIrSQ7AvQ>``,
``<NCBI,NP_004009.1>``, ``<gi,5032303>``,
``<ensembl-75ENSP00000354464>``, ``<ensembl-85,ENSP00000354464.4>``.
The sqlite database is mutable across releases.
For calibration, recent releases that include 3 human genome
assemblies (including patches), and full RefSeq sets (NM, NR, NP, NT,
XM, and XP) consumes approximately 8GB. The minimum marginal size for
additional snapshots is approximately 2GB (for the sqlite database,
which is not hardlinked).
For more information, see `<docs/design.rst>`__.
Requirements
!!!!!!!!!!!!
Reading a sequence repository requires several Python packages, all of
which are available from pypi. Installation should be as simple as
`pip install biocommons.seqrepo`.
*Writing* sequence files also requires ``bgzip``, which provided in
the `htslib <https://github.com/samtools/htslib>`__ repo. Ubuntu users
should install the ``tabix`` package with ``sudo apt install tabix``.
Development and deployments are on Ubuntu. Other systems may work but
are not tested. Patches to get other systems working would be
welcomed.
**Mac Developers** If you get "xcrun: error: invalid active developer
path", you need to install XCode. See this `StackOverflow answer
<https://apple.stackexchange.com/questions/254380/why-am-i-getting-an-invalid-active-developer-path-when-attempting-to-use-git-a>`__.
Quick Start
!!!!!!!!!!!
On Ubuntu 16.04::
$ sudo apt install -y python3-dev gcc zlib1g-dev tabix
$ pip install seqrepo
$ sudo mkdir /usr/local/share/seqrepo
$ sudo chown $USER /usr/local/share/seqrepo
$ seqrepo pull -i 2018-11-26
$ seqrepo show-status -i 2018-11-26
seqrepo 0.2.3.post3.dev8+nb8298bd62283
root directory: /usr/local/share/seqrepo/2018-11-26, 7.9 GB
backends: fastadir (schema 1), seqaliasdb (schema 1)
sequences: 773587 sequences, 93051609959 residues, 192 files
aliases: 5579572 aliases, 5480085 current, 26 namespaces, 773587 sequences
# Simple Pythonic interface to sequences
>> from biocommons.seqrepo import SeqRepo
>> sr = SeqRepo("/usr/local/share/seqrepo/latest")
>> sr["NC_000001.11"][780000:780020]
'TGGTGGCACGCGCTTGTAGT'
# Or, use the seqrepo shell for even easier access
$ seqrepo start-shell -i 2018-11-26
In [1]: sr["NC_000001.11"][780000:780020]
Out[1]: 'TGGTGGCACGCGCTTGTAGT'
# N.B. The following output is edited for simplicity
$ seqrepo export -i 2018-11-26 | head -n100
>SHA1:9a2acba3dd7603f... SEGUID:mirLo912A/MppLuS1cUyFMduLUQ Ensembl-85:GENSCAN00000003538 ...
MDSPLREDDSQTCARLWEAEVKRHSLEGLTVFGTAVQIHNVQRRAIRAKGTQEAQAELLCRGPRLLDRFLEDACILKEGRGTDTGQHCRGDARISSHLEA
SGTHIQLLALFLVSSSDTPPSLLRFCHALEHDIRYNSSFDSYYPLSPHSRHNDDLQTPSSHLGYIITVPDPTLPLTFASLYLGMAPCTSMGSSSMGIFQS
QRIHAFMKGKNKWDEYEGRKESWKIRSNSQTGEPTF
>SHA1:ca996b263102b1... SEGUID:yplrJjECsVqQufeYy0HkDD16z58 NCBI:XR_001733142.1 gi:1034683989
TTTACGTCTTTCTGGGAATTTATACTGGAAGTATACTTACCTCTGTGCAAAATTGCAAATATATAAGGTAATTCATTCCAGCATTGCTTATATTAGGTTG
AACTATGTAACATTGACATTGATGTGAATCAAAAATGGTTGAAGGCTGGCAGTTTCATATGATTCAGCCTATAATAGCAAAAGATTGAAAAAATCCATTA
ATACAGTGTGGTTCAAAAAAATTTGTTGTATCAAGGTAAAATAATAGCCTGAATATAATTAAGATAGTCTGTGTATACATCGATGAAAACATTGCCAATA
See `Installation <docs/installation.rst>`__ and `Mirroring
<docs/mirror.rst>`__ for more information.
Environment Variables
!!!!!!!!!!!!!!!!!!!!!
SEQREPO_LRU_CACHE_MAXSIZE sets the lru_cache maxsize for the sqlite query response caching. It defaults to 1 million but can also be set to "none" to be unlimited.
Developing
!!!!!!!!!!
Here's how to get started developing::
python3.6 -m venv
source venv/bin/activate
pip install -U setuptools pip
make develop
.. |pypi_rel| image:: https://badge.fury.io/py/biocommons.seqrepo.png
:target: https://pypi.org/pypi?name=biocommons.seqrepo
:align: middle
.. |ci_rel| image:: https://travis-ci.org/biocommons/biocommons.seqrepo.svg?branch=master
:target: https://travis-ci.org/biocommons/biocommons.seqrepo
:align: middle
.. |cov| image:: https://coveralls.io/repos/github/biocommons/biocommons.seqrepo/badge.svg?branch=
:target: https://coveralls.io/github/biocommons/biocommons.seqrepo?branch=
%package -n python3-biocommons.seqrepo
Summary: Non-redundant, compressed, journalled, file-based storage for biological sequences
Provides: python-biocommons.seqrepo
BuildRequires: python3-devel
BuildRequires: python3-setuptools
BuildRequires: python3-pip
%description -n python3-biocommons.seqrepo
biocommons.seqrepo
!!!!!!!!!!!!!!!!!!
Python package for writing and reading a local collection of
biological sequences. The repository is non-redundant, compressed,
and journalled, making it efficient to store and transfer multiple
snapshots.
Clients refer to sequences and metadata using familiar identifiers,
such as NM_000551.3 or GRCh38:1, or any of several hash-based
identifiers. The interface supports fast slicing of arbitrary regions
of large sequences.
A "fully-qualified" identifier includes a namespace to disambiguate
accessions (e.g., "1" in GRCh37 and GRCh38). If the namespace is
provided, seqrepo uses it as-is. If the namespace is not provided and
the unqualified identifier refers to a unique sequence, it is
returned; otherwise, ambiguous identifiers will raise an error.
SeqRepo favors identifiers from [identifiers.org](identifiers.org)
whenever available. Examples include
[refseq](https://registry.identifiers.org/registry/refseq) and
[ensembl](https://registry.identifiers.org/registry/ensembl).
`seqrepo-rest-service
<https://github.com/biocommons/seqrepo-rest-service>`__ provides a
REST interface and docker image.
Released under the Apache License, 2.0.
|ci_rel| | |cov| | |pypi_rel| | `ChangeLog <https://github.com/biocommons/biocommons.seqrepo/tree/master/docs/changelog/0.5>`_
Citation
!!!!!!!!
| Hart RK, Prlić A (2020)
| SeqRepo: A system for managing local collections of biological sequences.
| PLoS ONE 15(12): e0239883. https://doi.org/10.1371/journal.pone.0239883
Features
!!!!!!!!
* Timestamped, read-only snapshots.
* Space-efficient storage of sequences within a single snapshot and
across snapshots.
* Bandwidth-efficient transfer incremental updates.
* Fast fetching of sequence slices on chromosome-scale sequences.
* Precomputed digests that may be used as sequence aliases.
* Mappings of external aliases (i.e., accessions or identifiers like
NM_013305.4) to sequences.
Deployments Scenarios
!!!!!!!!!!!!!!!!!!!!!
* Local read-only archive, mirrored from public site,
accessed via Python API (see `Mirroring documentation <docs/mirror.rst>`__)
* Local read-write archive, maintained with command
line utility and/or API (see `Command Line Interface documentation
<docs/cli.rst>`__).
* Docker data-only container that may be linked to application container.
* SeqRepo and refget REST API for local or remote access (see `seqrepo-rest-service <https://github.com/biocommons/seqrepo-rest-service>`__)
Technical Quick Peek
!!!!!!!!!!!!!!!!!!!!
Within a single snapshot, sequences are stored *non-redundantly* and
*compressed* in an add-only journalled filesystem structure. A
truncated SHA-512 hash is used to assess uniquness and as an
internal id. (The digest is truncated for space efficiency.)
Sequences are compressed using the Block GZipped Format (`BGZF
<https://samtools.github.io/hts-specs/SAMv1.pdf>`__)), which enables
pysam to provide fast random access to compressed sequences. (Variable
compression typically makes random access impossible.)
Sequence files are immutable, thereby enabling the use of hardlinks
across snapshots and eliminating redundant transfers (e.g., with
rsync).
Each sequence id is associated with a namespaced alias in a sqlite
database. Such as ``<seguid,rvvuhY0FxFLNwf10FXFIrSQ7AvQ>``,
``<NCBI,NP_004009.1>``, ``<gi,5032303>``,
``<ensembl-75ENSP00000354464>``, ``<ensembl-85,ENSP00000354464.4>``.
The sqlite database is mutable across releases.
For calibration, recent releases that include 3 human genome
assemblies (including patches), and full RefSeq sets (NM, NR, NP, NT,
XM, and XP) consumes approximately 8GB. The minimum marginal size for
additional snapshots is approximately 2GB (for the sqlite database,
which is not hardlinked).
For more information, see `<docs/design.rst>`__.
Requirements
!!!!!!!!!!!!
Reading a sequence repository requires several Python packages, all of
which are available from pypi. Installation should be as simple as
`pip install biocommons.seqrepo`.
*Writing* sequence files also requires ``bgzip``, which provided in
the `htslib <https://github.com/samtools/htslib>`__ repo. Ubuntu users
should install the ``tabix`` package with ``sudo apt install tabix``.
Development and deployments are on Ubuntu. Other systems may work but
are not tested. Patches to get other systems working would be
welcomed.
**Mac Developers** If you get "xcrun: error: invalid active developer
path", you need to install XCode. See this `StackOverflow answer
<https://apple.stackexchange.com/questions/254380/why-am-i-getting-an-invalid-active-developer-path-when-attempting-to-use-git-a>`__.
Quick Start
!!!!!!!!!!!
On Ubuntu 16.04::
$ sudo apt install -y python3-dev gcc zlib1g-dev tabix
$ pip install seqrepo
$ sudo mkdir /usr/local/share/seqrepo
$ sudo chown $USER /usr/local/share/seqrepo
$ seqrepo pull -i 2018-11-26
$ seqrepo show-status -i 2018-11-26
seqrepo 0.2.3.post3.dev8+nb8298bd62283
root directory: /usr/local/share/seqrepo/2018-11-26, 7.9 GB
backends: fastadir (schema 1), seqaliasdb (schema 1)
sequences: 773587 sequences, 93051609959 residues, 192 files
aliases: 5579572 aliases, 5480085 current, 26 namespaces, 773587 sequences
# Simple Pythonic interface to sequences
>> from biocommons.seqrepo import SeqRepo
>> sr = SeqRepo("/usr/local/share/seqrepo/latest")
>> sr["NC_000001.11"][780000:780020]
'TGGTGGCACGCGCTTGTAGT'
# Or, use the seqrepo shell for even easier access
$ seqrepo start-shell -i 2018-11-26
In [1]: sr["NC_000001.11"][780000:780020]
Out[1]: 'TGGTGGCACGCGCTTGTAGT'
# N.B. The following output is edited for simplicity
$ seqrepo export -i 2018-11-26 | head -n100
>SHA1:9a2acba3dd7603f... SEGUID:mirLo912A/MppLuS1cUyFMduLUQ Ensembl-85:GENSCAN00000003538 ...
MDSPLREDDSQTCARLWEAEVKRHSLEGLTVFGTAVQIHNVQRRAIRAKGTQEAQAELLCRGPRLLDRFLEDACILKEGRGTDTGQHCRGDARISSHLEA
SGTHIQLLALFLVSSSDTPPSLLRFCHALEHDIRYNSSFDSYYPLSPHSRHNDDLQTPSSHLGYIITVPDPTLPLTFASLYLGMAPCTSMGSSSMGIFQS
QRIHAFMKGKNKWDEYEGRKESWKIRSNSQTGEPTF
>SHA1:ca996b263102b1... SEGUID:yplrJjECsVqQufeYy0HkDD16z58 NCBI:XR_001733142.1 gi:1034683989
TTTACGTCTTTCTGGGAATTTATACTGGAAGTATACTTACCTCTGTGCAAAATTGCAAATATATAAGGTAATTCATTCCAGCATTGCTTATATTAGGTTG
AACTATGTAACATTGACATTGATGTGAATCAAAAATGGTTGAAGGCTGGCAGTTTCATATGATTCAGCCTATAATAGCAAAAGATTGAAAAAATCCATTA
ATACAGTGTGGTTCAAAAAAATTTGTTGTATCAAGGTAAAATAATAGCCTGAATATAATTAAGATAGTCTGTGTATACATCGATGAAAACATTGCCAATA
See `Installation <docs/installation.rst>`__ and `Mirroring
<docs/mirror.rst>`__ for more information.
Environment Variables
!!!!!!!!!!!!!!!!!!!!!
SEQREPO_LRU_CACHE_MAXSIZE sets the lru_cache maxsize for the sqlite query response caching. It defaults to 1 million but can also be set to "none" to be unlimited.
Developing
!!!!!!!!!!
Here's how to get started developing::
python3.6 -m venv
source venv/bin/activate
pip install -U setuptools pip
make develop
.. |pypi_rel| image:: https://badge.fury.io/py/biocommons.seqrepo.png
:target: https://pypi.org/pypi?name=biocommons.seqrepo
:align: middle
.. |ci_rel| image:: https://travis-ci.org/biocommons/biocommons.seqrepo.svg?branch=master
:target: https://travis-ci.org/biocommons/biocommons.seqrepo
:align: middle
.. |cov| image:: https://coveralls.io/repos/github/biocommons/biocommons.seqrepo/badge.svg?branch=
:target: https://coveralls.io/github/biocommons/biocommons.seqrepo?branch=
%package help
Summary: Development documents and examples for biocommons.seqrepo
Provides: python3-biocommons.seqrepo-doc
%description help
biocommons.seqrepo
!!!!!!!!!!!!!!!!!!
Python package for writing and reading a local collection of
biological sequences. The repository is non-redundant, compressed,
and journalled, making it efficient to store and transfer multiple
snapshots.
Clients refer to sequences and metadata using familiar identifiers,
such as NM_000551.3 or GRCh38:1, or any of several hash-based
identifiers. The interface supports fast slicing of arbitrary regions
of large sequences.
A "fully-qualified" identifier includes a namespace to disambiguate
accessions (e.g., "1" in GRCh37 and GRCh38). If the namespace is
provided, seqrepo uses it as-is. If the namespace is not provided and
the unqualified identifier refers to a unique sequence, it is
returned; otherwise, ambiguous identifiers will raise an error.
SeqRepo favors identifiers from [identifiers.org](identifiers.org)
whenever available. Examples include
[refseq](https://registry.identifiers.org/registry/refseq) and
[ensembl](https://registry.identifiers.org/registry/ensembl).
`seqrepo-rest-service
<https://github.com/biocommons/seqrepo-rest-service>`__ provides a
REST interface and docker image.
Released under the Apache License, 2.0.
|ci_rel| | |cov| | |pypi_rel| | `ChangeLog <https://github.com/biocommons/biocommons.seqrepo/tree/master/docs/changelog/0.5>`_
Citation
!!!!!!!!
| Hart RK, Prlić A (2020)
| SeqRepo: A system for managing local collections of biological sequences.
| PLoS ONE 15(12): e0239883. https://doi.org/10.1371/journal.pone.0239883
Features
!!!!!!!!
* Timestamped, read-only snapshots.
* Space-efficient storage of sequences within a single snapshot and
across snapshots.
* Bandwidth-efficient transfer incremental updates.
* Fast fetching of sequence slices on chromosome-scale sequences.
* Precomputed digests that may be used as sequence aliases.
* Mappings of external aliases (i.e., accessions or identifiers like
NM_013305.4) to sequences.
Deployments Scenarios
!!!!!!!!!!!!!!!!!!!!!
* Local read-only archive, mirrored from public site,
accessed via Python API (see `Mirroring documentation <docs/mirror.rst>`__)
* Local read-write archive, maintained with command
line utility and/or API (see `Command Line Interface documentation
<docs/cli.rst>`__).
* Docker data-only container that may be linked to application container.
* SeqRepo and refget REST API for local or remote access (see `seqrepo-rest-service <https://github.com/biocommons/seqrepo-rest-service>`__)
Technical Quick Peek
!!!!!!!!!!!!!!!!!!!!
Within a single snapshot, sequences are stored *non-redundantly* and
*compressed* in an add-only journalled filesystem structure. A
truncated SHA-512 hash is used to assess uniquness and as an
internal id. (The digest is truncated for space efficiency.)
Sequences are compressed using the Block GZipped Format (`BGZF
<https://samtools.github.io/hts-specs/SAMv1.pdf>`__)), which enables
pysam to provide fast random access to compressed sequences. (Variable
compression typically makes random access impossible.)
Sequence files are immutable, thereby enabling the use of hardlinks
across snapshots and eliminating redundant transfers (e.g., with
rsync).
Each sequence id is associated with a namespaced alias in a sqlite
database. Such as ``<seguid,rvvuhY0FxFLNwf10FXFIrSQ7AvQ>``,
``<NCBI,NP_004009.1>``, ``<gi,5032303>``,
``<ensembl-75ENSP00000354464>``, ``<ensembl-85,ENSP00000354464.4>``.
The sqlite database is mutable across releases.
For calibration, recent releases that include 3 human genome
assemblies (including patches), and full RefSeq sets (NM, NR, NP, NT,
XM, and XP) consumes approximately 8GB. The minimum marginal size for
additional snapshots is approximately 2GB (for the sqlite database,
which is not hardlinked).
For more information, see `<docs/design.rst>`__.
Requirements
!!!!!!!!!!!!
Reading a sequence repository requires several Python packages, all of
which are available from pypi. Installation should be as simple as
`pip install biocommons.seqrepo`.
*Writing* sequence files also requires ``bgzip``, which provided in
the `htslib <https://github.com/samtools/htslib>`__ repo. Ubuntu users
should install the ``tabix`` package with ``sudo apt install tabix``.
Development and deployments are on Ubuntu. Other systems may work but
are not tested. Patches to get other systems working would be
welcomed.
**Mac Developers** If you get "xcrun: error: invalid active developer
path", you need to install XCode. See this `StackOverflow answer
<https://apple.stackexchange.com/questions/254380/why-am-i-getting-an-invalid-active-developer-path-when-attempting-to-use-git-a>`__.
Quick Start
!!!!!!!!!!!
On Ubuntu 16.04::
$ sudo apt install -y python3-dev gcc zlib1g-dev tabix
$ pip install seqrepo
$ sudo mkdir /usr/local/share/seqrepo
$ sudo chown $USER /usr/local/share/seqrepo
$ seqrepo pull -i 2018-11-26
$ seqrepo show-status -i 2018-11-26
seqrepo 0.2.3.post3.dev8+nb8298bd62283
root directory: /usr/local/share/seqrepo/2018-11-26, 7.9 GB
backends: fastadir (schema 1), seqaliasdb (schema 1)
sequences: 773587 sequences, 93051609959 residues, 192 files
aliases: 5579572 aliases, 5480085 current, 26 namespaces, 773587 sequences
# Simple Pythonic interface to sequences
>> from biocommons.seqrepo import SeqRepo
>> sr = SeqRepo("/usr/local/share/seqrepo/latest")
>> sr["NC_000001.11"][780000:780020]
'TGGTGGCACGCGCTTGTAGT'
# Or, use the seqrepo shell for even easier access
$ seqrepo start-shell -i 2018-11-26
In [1]: sr["NC_000001.11"][780000:780020]
Out[1]: 'TGGTGGCACGCGCTTGTAGT'
# N.B. The following output is edited for simplicity
$ seqrepo export -i 2018-11-26 | head -n100
>SHA1:9a2acba3dd7603f... SEGUID:mirLo912A/MppLuS1cUyFMduLUQ Ensembl-85:GENSCAN00000003538 ...
MDSPLREDDSQTCARLWEAEVKRHSLEGLTVFGTAVQIHNVQRRAIRAKGTQEAQAELLCRGPRLLDRFLEDACILKEGRGTDTGQHCRGDARISSHLEA
SGTHIQLLALFLVSSSDTPPSLLRFCHALEHDIRYNSSFDSYYPLSPHSRHNDDLQTPSSHLGYIITVPDPTLPLTFASLYLGMAPCTSMGSSSMGIFQS
QRIHAFMKGKNKWDEYEGRKESWKIRSNSQTGEPTF
>SHA1:ca996b263102b1... SEGUID:yplrJjECsVqQufeYy0HkDD16z58 NCBI:XR_001733142.1 gi:1034683989
TTTACGTCTTTCTGGGAATTTATACTGGAAGTATACTTACCTCTGTGCAAAATTGCAAATATATAAGGTAATTCATTCCAGCATTGCTTATATTAGGTTG
AACTATGTAACATTGACATTGATGTGAATCAAAAATGGTTGAAGGCTGGCAGTTTCATATGATTCAGCCTATAATAGCAAAAGATTGAAAAAATCCATTA
ATACAGTGTGGTTCAAAAAAATTTGTTGTATCAAGGTAAAATAATAGCCTGAATATAATTAAGATAGTCTGTGTATACATCGATGAAAACATTGCCAATA
See `Installation <docs/installation.rst>`__ and `Mirroring
<docs/mirror.rst>`__ for more information.
Environment Variables
!!!!!!!!!!!!!!!!!!!!!
SEQREPO_LRU_CACHE_MAXSIZE sets the lru_cache maxsize for the sqlite query response caching. It defaults to 1 million but can also be set to "none" to be unlimited.
Developing
!!!!!!!!!!
Here's how to get started developing::
python3.6 -m venv
source venv/bin/activate
pip install -U setuptools pip
make develop
.. |pypi_rel| image:: https://badge.fury.io/py/biocommons.seqrepo.png
:target: https://pypi.org/pypi?name=biocommons.seqrepo
:align: middle
.. |ci_rel| image:: https://travis-ci.org/biocommons/biocommons.seqrepo.svg?branch=master
:target: https://travis-ci.org/biocommons/biocommons.seqrepo
:align: middle
.. |cov| image:: https://coveralls.io/repos/github/biocommons/biocommons.seqrepo/badge.svg?branch=
:target: https://coveralls.io/github/biocommons/biocommons.seqrepo?branch=
%prep
%autosetup -n biocommons.seqrepo-0.6.5
%build
%py3_build
%install
%py3_install
install -d -m755 %{buildroot}/%{_pkgdocdir}
if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi
if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi
if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi
if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi
pushd %{buildroot}
if [ -d usr/lib ]; then
find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/lib64 ]; then
find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/bin ]; then
find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/sbin ]; then
find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst
fi
touch doclist.lst
if [ -d usr/share/man ]; then
find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst
fi
popd
mv %{buildroot}/filelist.lst .
mv %{buildroot}/doclist.lst .
%files -n python3-biocommons.seqrepo -f filelist.lst
%dir %{python3_sitelib}/*
%files help -f doclist.lst
%{_docdir}/*
%changelog
* Tue Apr 11 2023 Python_Bot <Python_Bot@openeuler.org> - 0.6.5-1
- Package Spec generated
|
