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readtagger 0.3.25

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

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

0.3.25 (2017-06-21)

  • Refine cluster coordinates using an Assembly strategy
  • Fix GFF sorting on python 3
  • Improve BWA alignment settings (default to intractg plus -Y) and add align_contigs method to SimpleAligner
  • Add pysamtools_view command
  • Improve cluster-splitting
  • Add multiprocessing-logging recipe
  • Only output BWA stderr if the exit code is not zero
  • Add a function to sort gff files
  • Close open file descriptors
  • Make imprecise insertion sites more realistic
  • Fix read_index property
  • Adapt readtagger to higher coverage datasets
  • Fix readtagger crash when not producing discard tag file.
  • Add number of mates for left and right support to GFF
  • Split clusters that start with reverse reads conatining only BD tags

0.3.24 (2017-05-11)

  • Split cluster if there are multiple polarity switches between Forward and Reverse orientation
  • Manipulate copy of cigarlist to avoid numpy issue

0.3.23 (2017-05-09)

  • Expose reference fasta option in bam_readtagger.xml

0.3.22 (2017-05-09)

  • Move readtagger CLI form argparse to click
  • Index bamfile if neccesary
  • Replace multipocessing pool with ProcessPoolExecutor
  • Set the matesequence while tagging reads
  • Fix false positives in readtagger module
  • Do cap3 assembly in shared memory if passing –shm_dir or if SHM_DIR environment variable is defined
  • Parallelize findlcluster by splitting input bam
  • Add check_call.py script for rapidly verifying IGV screenshots

0.3.21 (2017-04-27)

  • Fix crash when determining reference name

0.3.20 (2017-04-27)

  • Guess the best TE match and write it into GFF Parent
  • Fix case where input files are already sorted
  • Remove blast from requirements

0.3.19 (2017-04-27)

  • Skip creating tempdirs in current working directory
  • Remove blast-specific files
  • Switch to using BWA for annotating detected insertions
  • Add more logging and default to not changing sort order unless specifically demanded
  • Do dovetailing on coordinate-sorted file

0.3.18 (2017-04-25)

  • Fix small outputs due to switching of -t and -a options

0.3.17 (2017-04-25)

  • Fix file seeking
  • Update dependencies

0.3.16 (2017-04-23)

  • Parallelize readtagger

0.3.15 (2017-04-20)

  • Do not count reads as support if both AD and BD tag contribute to an insertion
  • Remove sambamba support

0.3.14 (2017-04-19)

  • Perform readtagging on readname sorted files.
  • Catch possible errors
  • Add BWA alignment module to replace Blast

0.3.13 (2017-04-05)

  • Add possibility to output cluster contigs as fasta

0.3.12 (2017-03-31)

  • Fix and accelerate the calculation of nref (=non support evidence)
  • Update priors and genotype frequrencies to a more realistic model

0.3.11 (2017-03-28)

  • Add a testcase for genotyping module
  • Stream over full alignment file instead of fetching regions, pysam.AlignmentFile.fetch is too slow

0.3.10 (2017-03-26)

  • Revert local conda dependency resolution
  • Fix readtagger.add_mate to work also if one mate is unmapped

0.3.9 (2017-03-26)

  • Add a genotyping module
  • Keep tags for alternative alignments if mates are not in a proper pair

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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