karyotype_mapping ----------------- Mapping from the known karyotype result to this species. .. rubric:: Parameters .. tabularcolumns:: column spec ========================= ======================================================================== 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 in this conf file, and the other should be deleted) ------------------------- ------------------------------------------------------------------------ ancestor_top Type: **file** | Default: **none** Ancestor location file (Only one of ('left', 'top') can be reserved in this conf file, and the other should be deleted) ------------------------- ------------------------------------------------------------------------ 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. .. code-block:: python [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 .. rubric:: Quick start The original results are easily accessible at `wgdi-example `_