FAQ and miscellanea¶
Can I change colour theme / Can I use my configuration?¶
To change colour theme use the -c/--config
command line option or the
interactive command setConfig
. To make your own theme and set it as default,
use as template one of the files in the repository directory config, edit
it as desired and save it as ~/.asciigenome_config
.
Examples:
ASCIIGenome -c metal ... <- Use the "metal" built-in them
ASCIIGenome -c mytheme.conf <- Read configuration from this file
ASCIIGenome ... <- No args to -c: Read file ~/.asciigenome_config or use default theme
For available colour names see the help in colorTrack
or this cheat sheet.
Can I turn off case sensitivity?¶
For command that do not explicitly enable turning on or off case sensitivity,
you can prepend (?i)
to your regex to match in case insensitve
mode, e.g. (?i)bam
will capture foo.bam
and foo.BAM
. This is standard regular expression
syntax unrelated to ASCIIGenome.
Note that the command seqRegex
by default is case insensitive, unless
the flag -c
is set.
Why reads and coverage in bam tracks sometimes disappear?¶
When displaying bam files, ASCIIGenome is configured to disable the coverage and read tracks if the window size is >100,000 bp. This is to prevent the browsing to become too slow. To display such large windows consider bigWig or tdf file format.
Can I execute multiple commands inside -x/--exec
or at the command prompt?¶
Use the &&
to concatenate commands (similar to Unix syntax). E.g.
colorTrack red && goto chr1:150000 && zo
.
How can I print the header of a VCF file?¶
Assuming bcftools
is available, use the sys
command, for example:
sys bcftools view -H my_variants.vcf.gz | less
Of course you can further parse the header by piping to standard Unix tools. For
example, to exclude the contig
lines use:
sys bcftools view -h mutect/WW00282.vcf.gz | grep -v '##contig' | less