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gt-chseqids - Online in the Cloud

Run gt-chseqids in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command gt-chseqids that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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 <[email protected]>.

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