franskloet / inverse-gff

script that creates non-coding regions (=other than gene ranges) from an existing gff file

inverse-gff

python script to create ranges that are not related to any gene

required packages (automatically installed)

pandas
numpy

usage

usage: inverse_gtf.py [-h] [-t] [-k KEY] [-c] [-m MAXT] gff out

positional arguments:
    gff                   The input gff file
    out                   The output gff file

optional arguments:
    -h, --help            show this help message and exit
    -t, --type            Look in the type column (default info column)
    -k KEY, --key KEY     The key to look for
    -c, --case            Do a case sensitive key match (default case insensitive)
    -m MAXT, --maxt MAXT  Set the maximum number of threads (default 1)
    -l LIM, --lim LIM     Set the memory limit (default 0.8)

To prevent unexpected system exceptions the memory limit is set to 80% of the available system memory. If the memory limit is reached/exceeded the script generates memory errors indicating that too many threads were specified for the system. It then tries to run the large blocks in a single thread. If memory errors still occur the script is quit. Either increase memory by increasing the memory limit (max=1) or shutting down running applications.

examples:

case sensitive search in the info column for the word gene

python inverse-gff.py Mus_musculus.GRCm39.111.gff3 out.gff3 --key gene --case

example 2, case insensitive search in the type (3rd) column for the word gene

python inverse_gtf.py Mus_musculus.GRCm39.111.gff3 test.111.gene.gff3 --key gene --type

example 3, case insentive search for transcript in the info column using 10 cores

python inverse_gtf.py Mus_musculus.GRCm39.111.gff3 test.111.gene.gff3 -m 10