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