Sequence ID Extraction

Often, we need to know what the taxa in our dataset are. The most straightforward command would be:

segul sequence id -i [input-path]

or using directory input:

segul sequence id -d alignment_dir

SEGUL will generate the unique ID across all input alignments. The output is a text file containing a list of the IDs in alphabetical order. By default, the output directory is SEGUL-ID. The file will be saved as id.txt in the output directory. For example, if all your alignments contain three samples, the output file will look like this:

sequence_1
sequence_2
sequence_3

To change the output directory, use the -o or --output option:

segul sequence id -i alignments/ -o my_alignment_id

To change the output file name, use the --prefix option:

segul sequence id -i alignments/ --prefix my_alignment_id

info

Before version 0.19.0, the SEGUL CLI outputs the sequence IDs in the current working directory. The output option will only change the file name.