readtagger 0.2.0 2017-02-21 ✔ PY2 ✔ PY3

readtagger on PyPI  

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


AuthorMarius van den Beek
LicenseMIT
Keywords Bioinformatics

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