act

NAME

act - Artemis comparison tool for genome sequences

SYNOPSIS

act [options] SEQUENCE_1 COMPARISON_1_2 SEQUENCE_2 ...

OPTIONS

SEQUENCE An EMBL, GenBank, FASTA, or GFF3 file
FEATURE An Artemis TAB file, or GFF file
COMPARISON A BLAST comparison file in tabular format
-options FILE Read a text file of options from FILE
-chado Connect to a Chado database (using PGHOST, PGPORT, PGDATABASE, PGUSER environment variables)
-Dblack_belt_mode=? Keep warning messages to a minimum [true,false]
-DuserplotX=FILE[,FILE2] For sequence 'X' open one or more userplots
-DloguserplotX=FILE[,FILE2] For sequence 'X' open one or more userplots, take log(data)
-DbamX=FILE[,FILE2,...] For sequence 'X' open one or more BAM, CRAM, VCF, or BCF files
-Dchado="h:p/d?u" Get ACT to open this CHADO database
-Dread_only Open CHADO database read-only

EXAMPLES

% act
% act af063097.embl af063097_v_b132222.crunch b132222.embl
% act -Dblack_belt_mode=true -Dbam1=MAL_0h.bam -Dbam2=MAL_7h.bam,var.raw.new.bcf
% act -Duserplot2=/pathToFile/userPlot

SEE ALSO

https://sanger-pathogens.github.io/Artemis/ACT/ art(1), dnaplotter(1)