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
0.4.2 (2017-12-13)
Fix passing of region specification to pileup engine
Point out typical useage of –reference_fasta and –reference_index
Fix cheetah bwa index variable for findcluster galaxy tool
0.4.1 (2017-11-20)
Add matplotlib and pandas to dependencies
Add a script that can plot coverage as an area plot between two bam files
Update dependencies
If either three_p or five_p of a tsd is unknown assign the available use the available side to test of a read belongs to the left or right side of an insertion
Fix crash for unaligned(?) reads
Change deprecacted alen, pos and mpos to current replacements
Tune clusterfinding for misaligned long reads
0.4.0 (2017-11-09)
Fixes for CRAM input and output
Adjust chunk-size in readtagger based on readlength (for pacbio/nanopore reads)
Cleanup temporary bwa indexes
Dependency updates
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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