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 Sequence-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 map.csv) containing the distribution of your samples presented in true/false values across your alignments. The content of the file will look like as below:

locus	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 -d alignments/ --map -o my_alignment_id

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

segul sequence id -d alignments/ --map --prefix my_alignment_id

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