NAME

Parse BLAST report and compute statistics on taxonomic affiliation.

USAGE

blastx-taxonomic-parsing.pl <infiles> --outfile [optional arguments]

REQUIRED ARGUMENTS

<infiles>

Path to input BLAST file [repeatable argument]. File must be structured like this if organism has assembly accession : assembly_accession.blastx. Unless, use --taxa option.

--outfile=<string>

Path to output file.

OPTIONS

--taxdir=<string>

Path to local mirror of the NCBI Taxonomy database. [default: string.default].

--contam-list=<string>

List of taxa to use to classify and compute stat [default: string.default].

--fasta-dir=<string>

Path to the fasta directory [default: string.default]. Fasta file must have same basename than infile.

--taxa=<string>

Taxa of organism. Use this option if organism do not have an assembly accession. Specified taxa must be in the --contam-list file.

--tax-min-len=<string>

minmal length of alignment to be considered for define bistcore [default: string.default].

--tax-min-ident=<string>

minimal percentage of identity of alignment to be considered for define bistcore [default: string.default].

--tax-min-score=<string>

minimal bitscore value [default: string.default].

--tax-score-mul=<string>

minimal percentage of bitscore for a hit to be considered for LCA [default: string.default].

--tax-min-hits=<string>

minimal number of hit for a read to compute LCA [default: string.default].

--tax-max-hits=<string>

maximal number of hit for a read to compute LCA [default: string.default].

--lca

Write a .lca report file [default: no].

--cleaning-fasta

Clean fasta file [default: no].