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 Sequence-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 -d alignments/ -o my_alignment_id

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

segul sequence id -d alignments/ --prefix my_alignment_id

Note

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.

All options

Option	Description
-d, --dir	Directory with alignments
-i, --input	Alignment files. Allows wildcards
-f, --input-format	Input format: auto (default), fasta, nexus, or phylip
--datatype	Data type: dna (default), aa, or ignore
--map	Also write the presence of each ID in each alignment
-o, --output	Output directory. Default: Sequence-ID
-p, --prefix	Prefix of the output files
--force	Overwrite an existing output directory
--log	Log file path. Default: segul.log