Utilities to collapse reads in bam files to their 5' end.
Installing
Get the source using git clone git@gitlab.pasteur.fr:bli/bam25prime.git, cd into it and run python3 -m pip install .
It might also work directly:
python3 -m pip install git+ssh://git@gitlab.pasteur.fr/bli/bam25prime.gitTroubleshooting
Compilation may fail if the version of gcc is too old.
On a cluster with environment modules, a workaround might be something like running module load gcc/7.2.0.
You may encounter the following error:
ImportError: liblzma.so.5: cannot open shared object file: No such file or directoryYou need to locate this liblzma.so.5 file. If you find it, then set the
LD_LIBRARY_PATH environment variable so that it points to the directory
containing it. For instance:
export LD_LIBRARY_PATH="/local/gensoft2/exe/xz/5.2.2/lib"Usage
This package provides a bam25prime script.
Its help can be obtained using option -h or --help.
$ bam25prime --help
usage: bam25prime [-h] -b BAMFILE -o OUT_BED
When executed, this module collapses reads in a bam file to their 5-prime end
(reducing them to length 1) and writes the result in bed format.
optional arguments:
-h, --help show this help message and exit
-b BAMFILE, --bamfile BAMFILE
Sorted and indexed bam file containing the aligned
reads. (default: None)
-o OUT_BED, --out_bed OUT_BED
Bed file in which the results should be written.
(default: None)