Tags reads in a BAM file based on other BAM files.
Project description
Readtagger
----------
.. image:: https://travis-ci.org/bardin-lab/readtagger.svg?branch=master
:target: https://travis-ci.org/bardin-lab/readtagger
.. image:: https://coveralls.io/repos/github/bardin-lab/readtagger/badge.svg?branch=master
:target: https://coveralls.io/github/bardin-lab/readtagger?branch=master
.. image:: https://badge.fury.io/py/readtagger.svg
:target: https://badge.fury.io/py/readtagger
.. image:: https://anaconda.org/mvdbeek/readtagger/badges/version.svg
:target: https://anaconda.org/mvdbeek/readtagger
Tags reads in a BAM file based on other BAM files.
Installation
------------
::
pip install readtagger
Usage
------
To tag reads in file ``a.bam`` with file ``b.bam`` and output to path
output.bam, type
::
readtagger --tag_file a.bam --annotate_with b.bam ----output_file output.bam
This will by default tag reads with the RD, RR, MD and MR tags, where
the RD tag has detail mapping information for the current read, while
the MD tag has the information for the mate. RR and MR contain the
aligned reference (i.e chromosome). The first letter can be changed on a
per-file basis by appending ":first\_letter\_read:first\_letter\_mate"
to the file path. To change the above example into X for the read and Y
for the mate, run:
::
readtagger --tag_file a.bam --annotate_with b.bam:X:Z ----output_file output.bam
To tag one bam file using multiple alignment files, run:
::
readtagger --tag_file a.bam --annotate_with b.bam:A:B c.bam:C:D ----output_file output.bam
Now reads that align in file ``b.bam`` will be tagged with AR, AD and
BR, BD, while reads aligned in file ``c.bam`` are marked with CR, CD and
DR, DD.
Advanced usage
--------------
To see the advanced options, type:
::
readtagger -h
Testing
-------
If you modify readtagger, you can run all tests by running tox:
::
pip install tox
tox
History
-------
.. to_doc
---------------------
0.1.13(2017-02-17)
---------------------
* Add instructions for development
* Install planemo in deployment step
---------------------
0.1.12(2017-02-17)
---------------------
* Test deployment again
---------------------
0.1.11 (2017-02-17)
---------------------
* Test deployment
---------------------
0.1.10 (2017-02-17)
---------------------
* Fix toolshed deployment
---------------------
0.1.9 (2017-02-17)
---------------------
* Add automated deployment to Galaxy Toolshed
* Add instructions for development and release process
---------------------
0.1.8 (2017-02-17)
---------------------
* Minor release to test release process
---------------------
0.1.7 (2017-02-17)
---------------------
* Extend testing with coverage testing
* Automate deployment to pypi and conda
* Register project with pyup.io
---------------------
0.1.6 (2017-02-16)
---------------------
* Rename to readtagger
* Fix bug with stdin closing file descriptor too early, leading to corrupt
BAM files
* Extend testing
---------------------
0.1.5 (2017-02-12)
---------------------
* Add option (-wd) to write suboptimal tag into separate BAM file
* Add option (-wv) to write verified tags into separate BAM file
* Performance improvments by letting sambamba handle BAM reading
and writing. Also elimininate regualr expression to parse cigarstring
---------------------
0.1.4 (2017-02-10)
---------------------
* Add option (-k) to keep alternative tags if they do not
explain the softclipped read any better.
Default is to discard them.
---------------------
0.1.3.2 (2017-02-08)
---------------------
* Fix dovetailing script
---------------------
0.1.3 (2017-02-07)
---------------------
* Add option to allow dovetailing in alignment files when tagging reads
* Add separate entrypoint for standalone script
---------------------
0.1.2 (2017-02-05)
---------------------
* Add conda recipe
* Python3 string fix
---------------------
0.1.0 (2017-02-05)
---------------------
* Initial version
----------
.. image:: https://travis-ci.org/bardin-lab/readtagger.svg?branch=master
:target: https://travis-ci.org/bardin-lab/readtagger
.. image:: https://coveralls.io/repos/github/bardin-lab/readtagger/badge.svg?branch=master
:target: https://coveralls.io/github/bardin-lab/readtagger?branch=master
.. image:: https://badge.fury.io/py/readtagger.svg
:target: https://badge.fury.io/py/readtagger
.. image:: https://anaconda.org/mvdbeek/readtagger/badges/version.svg
:target: https://anaconda.org/mvdbeek/readtagger
Tags reads in a BAM file based on other BAM files.
Installation
------------
::
pip install readtagger
Usage
------
To tag reads in file ``a.bam`` with file ``b.bam`` and output to path
output.bam, type
::
readtagger --tag_file a.bam --annotate_with b.bam ----output_file output.bam
This will by default tag reads with the RD, RR, MD and MR tags, where
the RD tag has detail mapping information for the current read, while
the MD tag has the information for the mate. RR and MR contain the
aligned reference (i.e chromosome). The first letter can be changed on a
per-file basis by appending ":first\_letter\_read:first\_letter\_mate"
to the file path. To change the above example into X for the read and Y
for the mate, run:
::
readtagger --tag_file a.bam --annotate_with b.bam:X:Z ----output_file output.bam
To tag one bam file using multiple alignment files, run:
::
readtagger --tag_file a.bam --annotate_with b.bam:A:B c.bam:C:D ----output_file output.bam
Now reads that align in file ``b.bam`` will be tagged with AR, AD and
BR, BD, while reads aligned in file ``c.bam`` are marked with CR, CD and
DR, DD.
Advanced usage
--------------
To see the advanced options, type:
::
readtagger -h
Testing
-------
If you modify readtagger, you can run all tests by running tox:
::
pip install tox
tox
History
-------
.. to_doc
---------------------
0.1.13(2017-02-17)
---------------------
* Add instructions for development
* Install planemo in deployment step
---------------------
0.1.12(2017-02-17)
---------------------
* Test deployment again
---------------------
0.1.11 (2017-02-17)
---------------------
* Test deployment
---------------------
0.1.10 (2017-02-17)
---------------------
* Fix toolshed deployment
---------------------
0.1.9 (2017-02-17)
---------------------
* Add automated deployment to Galaxy Toolshed
* Add instructions for development and release process
---------------------
0.1.8 (2017-02-17)
---------------------
* Minor release to test release process
---------------------
0.1.7 (2017-02-17)
---------------------
* Extend testing with coverage testing
* Automate deployment to pypi and conda
* Register project with pyup.io
---------------------
0.1.6 (2017-02-16)
---------------------
* Rename to readtagger
* Fix bug with stdin closing file descriptor too early, leading to corrupt
BAM files
* Extend testing
---------------------
0.1.5 (2017-02-12)
---------------------
* Add option (-wd) to write suboptimal tag into separate BAM file
* Add option (-wv) to write verified tags into separate BAM file
* Performance improvments by letting sambamba handle BAM reading
and writing. Also elimininate regualr expression to parse cigarstring
---------------------
0.1.4 (2017-02-10)
---------------------
* Add option (-k) to keep alternative tags if they do not
explain the softclipped read any better.
Default is to discard them.
---------------------
0.1.3.2 (2017-02-08)
---------------------
* Fix dovetailing script
---------------------
0.1.3 (2017-02-07)
---------------------
* Add option to allow dovetailing in alignment files when tagging reads
* Add separate entrypoint for standalone script
---------------------
0.1.2 (2017-02-05)
---------------------
* Add conda recipe
* Python3 string fix
---------------------
0.1.0 (2017-02-05)
---------------------
* Initial version
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