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GT-CHSEQIDS(1) GenomeTools Manual GT-CHSEQIDS(1)

NAME

gt-chseqids - Change sequence ids by the mapping given in a mapping file.

SYNOPSIS

gt chseqids [option ...] mapping_file [GFF3_file]

DESCRIPTION

-sort [yes|no]

sort the GFF3 features after changing the sequence ids (memory consumption is proportional to the input file size) (default: no)

-v [yes|no]

be verbose (default: no)

-o [filename]

redirect output to specified file (default: undefined)

-gzip [yes|no]

write gzip compressed output file (default: no)

-bzip2 [yes|no]

write bzip2 compressed output file (default: no)

-force [yes|no]

force writing to output file (default: no)

-help

display help and exit

-version

display version information and exit

File format for mapping_file:

The supplied mapping file defines a mapping table named “chseqids”. It maps the sequence-region entries given in the GFF3_file to other names. It can be defined as follows:

chseqids = {


  chr1  = "seq1",


  chr2  = "seq2"
}

When this example is used, all sequence ids “chr1” will be changed to “seq1” and all sequence ids “chr2” to “seq2”.

REPORTING BUGS

Report bugs to https://github.com/genometools/genometools/issues.

04/27/2024 GenomeTools 1.6.5