- usage: sixgill_build [-h] [--minlength MINLENGTH]
- [--minqualscore MINQUALSCORE] [--metagenefile METAGENEFILE] [--minmetagenescore MINMETAGENESCORE] [--minorflength MINORFLENGTH] [--minlongesttryppeplen MINLONGESTTRYPPEPLEN] [--maxreads MAXREADS] [--minreadcount MINREADCOUNT] --out OUT [--outfasta OUTFASTA] [--debug] fastqfiles [fastqfiles ...]
Read in one or more fastq files. For each read, do a 6-frame translation and add all metapeptides that pass the specified filtering criteria. If --metagenefile is specified, start with the output of MetaGene Annotator instead of raw reads.
-h, --help | show this help message and exit |
--minlength MINLENGTH | |
min AA length of a metapeptide | |
--minqualscore MINQUALSCORE | |
min base-call phred score across any NT in a metapeptide | |
--metagenefile METAGENEFILE | |
input MetaGene Annotator output file. Records must be in same linear order as reads in fastqfiles | |
--minmetagenescore MINMETAGENESCORE | |
minimum MetaGene score | |
--minorflength MINORFLENGTH | |
min length of ORF-portion | |
--minlongesttryppeplen MINLONGESTTRYPPEPLEN | |
minimum length of the longest tryptic peptide | |
--maxreads MAXREADS | |
stop early if we hit this many reads | |
--minreadcount MINREADCOUNT | |
minimum read count | |
--out OUT | Output metapeptide database file |
--outfasta OUTFASTA | |
Output metapeptide fasta database file | |
--debug | Enable debug logging |