Tags reads in a BAM file based on other BAM files.
Project description
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
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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