GOODORFS is a tool to classify open reading frames into coding and noncoding
It takes as input a fasta file representing the entire genome. It then finds all potential open reading frames, and then for each, calculates the Energy Density Profile from the amino acid frequency.
To install GOODORFS,
pip3 install goodorfs
or
git clone https://github.com/deprekate/goodorfs.git
cd goodorfs
python3 setup.py install
To run GOODORFS simply provide the path to a fasta file. The default output is the same format as Glimmers LONGORFS program, in order to serve as a drop in replacement.
The columns are: orf_id, start_location, stop_location, frame, a bunch of zeros as filler
$ goodorfs.py tests/NC_001416.fna
00001 191 736 +2 0.000
00002 711 2636 +3 0.000
00003 2633 2839 +2 0.000
00004 3270 2830 -1 0.000
00005 2836 4437 +1 0.000
00006 5095 4604 -2 0.000
00007 4283 5737 +2 0.000
...
Additionally GOODORFS can also output the nucleotide sequences in fasta format for use in other applications:
$ good-orfs.py -Y fna tests/NC_001416.fna | head
>NC_001416_orf1 [START=191] [STOP=736]
ATGGAAGTCAACAAAAAGCAGCTGGCTGACATTTTCGGTGCGAGTATCCGTACCATTCA...
>NC_001416_orf2 [START=711] [STOP=2636]
GTGAATATATCGAACAGTCAGGTTAACAGGCTGCGGCATTTTGTCCGCGCCGGGCTTCG...
>NC_001416_orf3 [START=2633] [STOP=2839]
ATGACGCGACAGGAAGAACTTGCCGCTGCCCGTGCGGCACTGCATGACCTGATGACAGG...
>NC_001416_orf4 [START=3270] [STOP=2830]
GTGCATGGCCACACCTTCCCGAATCATCATGGTAAACGTGCGTTTTCGCTCAACGTCAA...
...
We have started testing GOODORFS to run on metagenomes. All that is needed is to bin reads according to their GC content and then run the bins through GOODROFS in batches in order to predict gene fragments within the reads.
We have added a script to group the reads according to gc content. It prints out batches of 500 reads separated by the null terminator character, which allows commands to be chained to xargs. To run GOODORFS on the supplied sample metagenome (which is in FASTA file format), run the command:
python3 scripts/bin_reads.py tests/ERR5004783_part.fasta | xargs -0 -I {} sh -c "echo '{}' | ./goodorfs.py -Y fna"