The visualize subcommand

You can use this subcommand to visualize a GenBank format file. Read the help below to learn about the meanings for each track.

$ mitoz visualize -h
usage: mitoz visualize [-h] [--circos <str>] --gb <file> [--gc {yes,no}]
                       [--win <str>] [--gc_fill <str>] [--depth_file <file>]
                       [--run_map {yes,no}] [--fq1 <file>] [--fq2 <file>]
                       [--bwa <str>] [--thread <int>] [--samtools <str>]
                       [--opts_samtools <str>] [--depth_fill <str>]
                       [--cds_color <str>] [--trna_color <str>]
                       [--rrna_color <str>] [--label_color <str>]
                       [--locus_color <str>] [--base {yes,no}] [--bgc <str>]
                       [--outdir <str>]

Visualize input GenBank file.

optional arguments:
  -h, --help            show this help message and exit
  --circos <str>        absolute path of circos executable. otherwise,
                        `circos` must be in your `PATH` variable [circos]
  --gb <file>           Your input Genbank file [required]

GC content track (the innermost one)
        In the resulting GC track (the innermost one),
        the red line means 0.5, while each black lines mean 0.05. :
  --gc {yes,no}         whether draw GC content track. [no]
  --win <str>           windows size for calculating GC content [50]
  --gc_fill <str>       color for filling the GC track [128,177,211]

Abundance track (the middle one)
        This reveals the depth distribution, with dark green for the outline.
        If the depth lower than the minimum value (default 20), it turns red,
        whereas if the depth larger than upper quartile,
        it turns dark green as same with the outline:
  --depth_file <file>   A file of tab-separated table with three columns:
                        reference name, position, and coverage depth, which is
                        generated by 'samtools depth' command. Or you can set
                        '--run_map yes' and '--fq1' and '--fq2' to get this
                        information
  --run_map {yes,no}    If you do NOT have the '--depth_file', setting '--
                        run_map yes' as well as '--fq1' and '--fq2' to map
                        reads to references to get the '--depth_file' [no]
  --fq1 <file>          fastq 1 file. Do NOT forget to set '--run_map yes'
  --fq2 <file>          fastq 2 file. Do NOT forget to set '--run_map yes'
  --bwa <str>           absolute path of bwa executable, otherwise, `bwa` must
                        be in your `PATH` variable [bwa]
  --thread <int>        BWA thread number [2]
  --samtools <str>      absolute path of samtools executable, otherwise,
                        `samtools` must be in your `PATH` variable [samtools]
  --opts_samtools <str>
                        optional arguments for samtools [-a -a]
  --depth_fill <str>    color for filling the abundance track [190,186,218]

Color setting (the outermost one):
  --cds_color <str>     PCG color [141,211,199]
  --trna_color <str>    tRNA color [251,128,114]
  --rrna_color <str>    rRNA color [253,192,134]
  --label_color <str>   gene name label color [black]
  --locus_color <str>   locus name's clolor showed on center of circle [black]

Base track:
  --base {yes,no}       whether draw base track [no]

Outfile setting:
  --bgc <str>           background color or the path to a user-defined image
                        file (as the background of the resulting file!)
                        [white]
  --outdir <str>        output directory [./outdir]