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 AD, AR, BD and BR tags, where
the AD tag has detail mapping information for the current read, while
the BD tag has the information for the mate. AR and BR 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
---------------------
0.3.8 (2017-03-14)
---------------------
* Fix multithreaded blast runs and do not fail on empty Blast output
---------------------
0.3.7 (2017-03-14)
---------------------
* Add reference_fasta for blast functionality in findcluster galaxy wrapper
* Cleanup BlastProcessor object at the end of a run
* New test fixture for downloading reference fasta
* Implement first draft of blasting cluster contigs
* Limit clusterfinding to reads with `AD` or `BD` tag
---------------------
0.3.6 (2017-03-09)
---------------------
* Use query_alignment_sequence instead of query_sequence for compatibility with BWA MEMs -Y option
* Keep suppl. reads without primary reads by default
---------------------
0.3.5 (2017-03-08)
---------------------
* Install blast in travis environemnt and use conda-compatible virtualenv
* Add tools to extract supplementary alignments and tool to update MAPQ scores of supplementary alignments
* Add blast module
* Move to click as commandline argument parser for find cluster and write_supplementary_fastq
* Refactor code organization in project.
* Update ROADMAP.rst
---------------------
0.3.4 (2017-03-02)
---------------------
* Speed up assembly steps using multithreading
* Implement a cache for the Cluster.can_join method
---------------------
0.3.3 (2017-03-02)
---------------------
* Fix a crash when writing GFF for a cluster of hardclipped reads
* Change confusing variable names and copypasted docstring
---------------------
0.3.2 (2017-03-02)
---------------------
* Fix another crash when tuple starts with 1,2,7 or 8
---------------------
0.3.1 (2017-03-02)
---------------------
* Fix a crash when a mismatch is the last item in a cigartuple
---------------------
0.3.0 (2017-03-02)
---------------------
* Add a galaxy tool for the findcluster script
* Add new script that finds clusters of reads and outputs GFF or BAM files with these clusters.
* Implement writing clusters as GFF files
* Implement writing out reads with cluster number annotated in CD tag.
* Implement merging of clusters based on whether reads contribute to common contigs
* Use cached-property where it makes sense
* Add module to find, join and annotate clusters of reads
* Represent cigartuple as namedtuple
* Add a Roadmap file
* Add more logic for finding ends of insertions and
* Manipulate cluster of reads to find TSDs
* Add module for cap3 assembly and manipulation of assembled reads
* Fix conda recipe script entrypoints
---------------------
0.2.0 (2017-02-21)
---------------------
* Reformat help text in galaxy wrappers
* Add add_matesequence script to add the sequence of the mate of the current read as a tag
* Add option to discard alternative tag if read is a proper pair
* Stitch cigars that are separated by I or D events
* Add a tag tuple that knows how to format itself
* Update README.rst example with current default tag prefix
* Test with and without discarding verified reads
* Symlink test-files that are shared with the galaxy test, add testcase for allow_dovetailing script
* Fix HISTORY.rst formatting
---------------------
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 AD, AR, BD and BR tags, where
the AD tag has detail mapping information for the current read, while
the BD tag has the information for the mate. AR and BR 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
---------------------
0.3.8 (2017-03-14)
---------------------
* Fix multithreaded blast runs and do not fail on empty Blast output
---------------------
0.3.7 (2017-03-14)
---------------------
* Add reference_fasta for blast functionality in findcluster galaxy wrapper
* Cleanup BlastProcessor object at the end of a run
* New test fixture for downloading reference fasta
* Implement first draft of blasting cluster contigs
* Limit clusterfinding to reads with `AD` or `BD` tag
---------------------
0.3.6 (2017-03-09)
---------------------
* Use query_alignment_sequence instead of query_sequence for compatibility with BWA MEMs -Y option
* Keep suppl. reads without primary reads by default
---------------------
0.3.5 (2017-03-08)
---------------------
* Install blast in travis environemnt and use conda-compatible virtualenv
* Add tools to extract supplementary alignments and tool to update MAPQ scores of supplementary alignments
* Add blast module
* Move to click as commandline argument parser for find cluster and write_supplementary_fastq
* Refactor code organization in project.
* Update ROADMAP.rst
---------------------
0.3.4 (2017-03-02)
---------------------
* Speed up assembly steps using multithreading
* Implement a cache for the Cluster.can_join method
---------------------
0.3.3 (2017-03-02)
---------------------
* Fix a crash when writing GFF for a cluster of hardclipped reads
* Change confusing variable names and copypasted docstring
---------------------
0.3.2 (2017-03-02)
---------------------
* Fix another crash when tuple starts with 1,2,7 or 8
---------------------
0.3.1 (2017-03-02)
---------------------
* Fix a crash when a mismatch is the last item in a cigartuple
---------------------
0.3.0 (2017-03-02)
---------------------
* Add a galaxy tool for the findcluster script
* Add new script that finds clusters of reads and outputs GFF or BAM files with these clusters.
* Implement writing clusters as GFF files
* Implement writing out reads with cluster number annotated in CD tag.
* Implement merging of clusters based on whether reads contribute to common contigs
* Use cached-property where it makes sense
* Add module to find, join and annotate clusters of reads
* Represent cigartuple as namedtuple
* Add a Roadmap file
* Add more logic for finding ends of insertions and
* Manipulate cluster of reads to find TSDs
* Add module for cap3 assembly and manipulation of assembled reads
* Fix conda recipe script entrypoints
---------------------
0.2.0 (2017-02-21)
---------------------
* Reformat help text in galaxy wrappers
* Add add_matesequence script to add the sequence of the mate of the current read as a tag
* Add option to discard alternative tag if read is a proper pair
* Stitch cigars that are separated by I or D events
* Add a tag tuple that knows how to format itself
* Update README.rst example with current default tag prefix
* Test with and without discarding verified reads
* Symlink test-files that are shared with the galaxy test, add testcase for allow_dovetailing script
* Fix HISTORY.rst formatting
---------------------
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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