genial: GENome Interactive Annotation Library

This library provides InteractiveAnnotation, a high level representation of genome annotations, allowing users to easily extract information, manipulate and reformat commonly used annotation files such as BED and GFF.

The package is currently in alpha stage and only runs on python3.

Supported formats

• Input: BED, GFF3, GTF
• Output: BED

Scripts

For convenience, we provide two CLI utilities: annotParser.py and annotMergeSmallGap.py.

$ annotParser.py -h
usage: annotParser.py [-h] [-i INPUT] [-o OUTPUT] [-f {gff3,gtf,bed}]
                      [-t {extb,bed}] [-n MIN_EXON_COUNT]
                      [-igs IGNORE_GAPS_SMALLER_THAN]
                      [-igb IGNORE_GAPS_BIGGER_THAN] [-v]

Parse, filter and convert annotation files

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        input file. to read from pipe, use the argument
                        'stdin'
  -o OUTPUT, --output OUTPUT
                        output file
  -f {gff3,gtf,bed}, --input_format {gff3,gtf,bed}
                        input file format
  -t {extb,bed}, --output_format {extb,bed}
                        output file format
  -n MIN_EXON_COUNT, --min_exon_count MIN_EXON_COUNT
                        min number of exons
  -igs IGNORE_GAPS_SMALLER_THAN, --ignore_gaps_smaller_than IGNORE_GAPS_SMALLER_THAN
  -igb IGNORE_GAPS_BIGGER_THAN, --ignore_gaps_bigger_than IGNORE_GAPS_BIGGER_THAN
  -v, --invert_match    select non matching annotations (similar to grep -v)

$ annotMergeSmallGaps.py -h
usage: annotMergeSmallGaps.py [-h] [-i INPUT] [-o OUTPUT] [-f {gff3,bed,gtf}]
                              [-t {extb,bed}] [-s SMALL_GAP_SIZE]

Merge exons separated by small gaps. Can also be used to convert different
kinds of annotations.

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        input file. to read from pipe, use the argument
                        'stdin'
  -o OUTPUT, --output OUTPUT
                        output file
  -f {gff3,bed,gtf}, --input_format {gff3,bed,gtf}
                        input file format
  -t {extb,bed}, --output_format {extb,bed}
                        output file format
  -s SMALL_GAP_SIZE, --small_gap_size SMALL_GAP_SIZE
                        gap size.

Both the scripts above can also be used to convert from different kinds of annotation files. A more advanced usage can be achieved importing the library.

Instalation instructions

for a systemwide instalation on ubuntu:

sudo apt-get install python3-pip
sudo pip3 install genial

Acknowledgements

I'd like to thank my friends, Lucas Silva and David Pires, for all the help and encouragement to learn python and software development. Without them, I'd hardly have found so much fun coding and this project would never came to be. I also thank Marcelo Reis for the help naming this library :D