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Popcorn is a tool for predicting whether prokaryotic genomic sequences are coding or noncoding.
EXAMPLE USAGE: python Popcorn.py -s ACGTACGTACGT
EXAMPLE USAGE: python Popcorn.py -f *.fa
EXAMPLE USAGE: python Popcorn.py -s ACGTACGTACGT -g genome_dir
EXAMPLE USAGE: python Popcorn.py -f *.fa -g genome_dir
***** Required argument *****
-s STRING Genomic sequence, e.g., ACGTACGTACGT
Either -s or -f flag is required but not both
Use -s to make a prediction for a single
sequence provided on the command line
-f STRING File of genomic sequences either in FASTA format
or with each sequence separated by a blank line
Either -s or -f flag is required but not both
Use -f to make predictions for one or more
sequences in a provided file
***** Optional argument (RECOMMENDED) *****
-g STRING Path to directory containing two files:
- *.fna (genome in FASTA format)
- *.gff (list of genes in GFF format)
Files may be gzipped or not
***** Optional arguments *****
-o STRING File to which results should be output
(default is standard out)
-m STRING File containing the trained ML model
(default is DataFiles/model.pickle with -g flag)
(default is DataFiles/model.all.pickle without -g flag)
-z STRING File containing genome statistics when -g flag is not used
(default is DataFiles/genome.all.pickle)
-h print USAGE and DESCRIPTION, ignore all other flags
-help print USAGE and DESCRIPTION, ignore all other flags