Report¶
It aggregates sequence alignment results, and calculates their respective TAAI, AAI and other metrics. It can optionally output the algorithm selected best hits, as well as a graphical report. It can take as input results from either coast search or coast compare. The latter requires the use of the –reciprocal flag.
usage: coast report [-h] [-o OUT] [-f [OUTFMT ...]] [-k KEYWORDS] [--aai AAI]
[--id ID] [--cov COV] [--rbh] [--quiet] [--verbose]
[--filter_hypothetical]
results queries [queries ...]
Positional Arguments¶
- results
Path to the align results from the original coast run.
- queries
Produce the similarity matrices from a single or different GenBanks and FASTAs files. Each represents an organism. Must be the same used in the coast search/ coast compare query.
Named Arguments¶
- -o, --out
The directory where the output will be delivered.
Default: “/home/docs/checkouts/readthedocs.org/user_builds/coast-tools/checkouts/latest/docs”
- -f, --outfmt
Choose the output format that will be used for the produced data. It can either be the tabular, human readable text file or full workspace with intermediary files and extra results.
Default: [‘b’, ‘a’, ‘r’]
- -k, --keywords
This option is only taken into account when a GenBank File is provided, in such cases, it identifies the annotation keywords used to identify proteins, default is only using CDS.
Default: “CDS”
- --aai
Minimum Average Amino Acid Identity, for reporting purposes
Default: 10
- --id
Minimum Amino Acid Identity, for hit selection for AAIbd calculation
Default: 40
- --cov
Minimum coverage, for hit selection for AAIbd calculation
Default: 50
- --rbh
Analysis for reciprocal best hits.This should be used for ‘coast compare’ results
Default: False
- --quiet
Deactivate verbose terminal output along the created files.This is already the default behaviour.
Default: False
- --verbose
Activate verbose terminal output along the created files.
Default: False
- --filter_hypothetical
Filters proteins with ‘hypothetical’ in their description, use with caution.
Default: False