create
usage: blobtools create -i FASTA [-y FASTATYPE] [-o PREFIX] [--title TITLE]
[-b BAM...] [-s SAM...] [-a CAS...] [-c COV...]
[--nodes <NODES>] [--names <NAMES>] [--db <NODESDB>]
[-t HITS...] [-x TAXRULE...] [-m FLOAT] [-d FLOAT] [--tax_collision_random]
[-h|--help]
Options:
-h --help show this
-i, --infile FASTA FASTA file of assembly. Headers are split at whitespaces.
-y, --type FASTATYPE Assembly program used to create FASTA. If specified,
coverage will be parsed from FASTA header.
(Parsing supported for 'spades', 'velvet', 'platanus')
-t, --hitsfile HITS... Hits file in format (qseqid\ttaxid\tbitscore)
(e.g. BLAST output "--outfmt '6 qseqid staxids bitscore'")
Can be specified multiple times
-x, --taxrule <TAXRULE>... Taxrule determines how taxonomy of blobs
is computed (by default both are calculated)
"bestsum" : sum bitscore across all
hits for each taxonomic rank
"bestsumorder" : sum bitscore across all
hits for each taxonomic rank.
- If first <TAX> file supplies hits, bestsum is calculated.
- If no hit is found, the next <TAX> file is used.
-m, --min_score <FLOAT> Minimal score necessary to be considered for taxonomy calculaton, otherwise set to 'no-hit'
[default: 0.0]
-d, --min_diff <FLOAT> Minimal score difference between highest scoring
taxonomies (otherwise "unresolved") [default: 0.0]
--tax_collision_random Random allocation of taxonomy if highest scoring
taxonomies have equal scores (otherwise "unresolved") [default: False]
--nodes <NODES> NCBI nodes.dmp file. Not required if '--db'
--names <NAMES> NCBI names.dmp file. Not required if '--db'
--db <NODESDB> NodesDB file (default: $BLOBTOOLS/data/nodesDB.txt).
-b, --bam <BAM>... BAM file(s), can be specified multiple times
-s, --sam <SAM>... SAM file(s), can be specified multiple times
-a, --cas <CAS>... CAS file(s) (requires clc_mapping_info in $PATH), can be specified multiple times
-c, --cov <COV>... COV file(s), can be specified multiple times
-o, --out <PREFIX> BlobDB output prefix
--title TITLE Title of BlobDB [default: output prefix)
Comments
- Input files
- one assembly file, e.g. example/assembly.fna
- one (or more) coverage file(s), e.g. example/mapping_1.bam
- one (or more) hits file(s), e.g. example/blast.out
Updated about 7 years ago