Sequence ID Mapping
To map the distribution of your samples across your dataset, you only need to pass --map flag in the finding unique IDs command:
segul sequence id -i [input-path] --map
It will generate two files, saved to SEGUL-ID by default. The first file is the list of unique IDs in your dataset (named default to id.txt). This file is similar to generating unique IDs. The second file is a csv file (named default to id_map.txt) containing the distribution of your samples presented in TRUE/FALSE values across your alignments. The content of the file will look like as below:
| Alignments | sequence_1 | sequence_2 | sequence_3 |
|---|---|---|---|
| locus_1 | TRUE | FALSE | TRUE |
| locus_2 | TRUE | TRUE | TRUE |
| locus_3 | FALSE | FALSE | TRUE |
To change the output directory, use the -o or --output option:
segul sequence id -i alignments/ --map -o my_alignment_id
To change the output file name, use the --prefix option:
segul sequence id -i alignments/ --map --prefix my_alignment_id