karyotype_mapping

Mapping from the known karyotype result to this species.

Parameters

Parameters	Standards and instructions
blast_reverse	Type: bool | Default: false The first two columns of the blast result swap positions.
score	Type: int | Default: 100 Score value in blast result.
evalue	Type: float | Default: 1e-5 Evalue value in blast result.
repeat_number	Type: int | Default: 10 The maximum number of homologous genes is allowed to remove more than part of the population.
ancestor_left	Type: file | Default: none Ancestor location file (Only one of (‘left’, ‘top’) can be reserved)
ancestor_top	Type: file | Default: none Ancestor location file (Only one of (‘left’, ‘top’) can be reserved)
blockinfo	Type: file | Default: - blockinfo.csv filtered according to certain conditions ‘-c’
the_other_lens	Type: file | Default: - The lens file for the species for which you want to generate ancestor files.
limit_length	Type: int | Default: 5 Show the minimum length of blocks.
the_other_ancestor_file	Type: file | Default: * .csv The resulting file.

Use command to enter the folder wgdi -km ? >> total.conf Take out the parameter file.

[karyotype_mapping]
blast = blast file
blast_reverse = false
gff1 = gff1 file
gff2 = gff2 file
score = 100
evalue = 1e-5
repeat_number = 5
ancestor_left = ancestor location file (Only one of ('left', 'top') can be reserved)
ancestor_top = ancestor location file
the_other_lens = the other lens file
blockinfo = block information (*.csv)
blockinfo_reverse = false
limit_length = 5
the_other_ancestor_file =  result file

Quick start

The original results are easily accessible at wgdi-example