Extracting sequences in alignments

segul can extract sequences in a collection of alignments based on the sequence ID. You can input the sequence ID in three ways:

1. Using the standard input (stdin) via terminal
2. By inputing a list of IDs in a text file
3. Using regular expression

By default, segul will write the results in a nexus format and use the name from the original input. More details below.

Extracting sequences using stdin

This method is useful if you only need to extract a few sequences across all your alignmetns. To input the list of ID, use --id option. It allow as many sequence ID as you can type in your terminal. For a long list, however, we recommend to input the ID in a text file.

segul <input-option> [alignment-dir] --input-format [seq-format] --id [list-of-sequence-id]

For example, using the command below, we will extract seq_1, seq_2, and seq_3 from our alignments stored in alignments/ directory:

segul --dir alignments/ --input-format nexus --id seq_1 seq_2 seq_3

Extracting sequences using an input file

With a long list of IDs, it will be more convenient to input the list of the IDs instead. segul --file option is available for this task. You only need to list all the IDs in a text file with each ID in a new line as below:

seq_1
seq_2
seq_3
seq_4
seq_5

The command will be:

segul extract --dir alignments/ --input-format nexus --file id.txt

For lots of ID, you can generate all the ID first using unique ID finder function on segul (see above). Open the text file using your text editor and remove the sequence IDs that you don't need. Use this file as an input for segul extract.

NOTES: segul can parse input file written both on Unix-like OS (Linux, WSL, and MacOS) and Windows with carriage return.

Extracting sequences using regular expression

This is the most flexible option to extract sequence from a collection of alignments. segul use the Rust regex library to parse regular expression syntax. The syntax is similar to Perl-style regex syntax (details here). You can use this website to test your syntax.

To use regular expression, use the option --re= and put the syntax in either a single or double quatation. For example, our sequence id is named this way genus_species_voucherNo. We want to extract the sequences from the same genus: Mus. We could write a regular expression that search for sequence ID that starts with Mus as below:

segul extract --dir alignments/ --input-format nexus --re="^Mus"

We could also search it with case insentive match:

segul extract --dir alignments/ --input-format nexus --re="^(?i)mus"

All the matched sequences found in each alignment will be written to the output files. The name of the alignment will be maintain as the original.

Specifying output directory and format

By default, the output files will be written into SEGUL-Extract directory. To change the directory name, use the --ouput or -o option. For the output files, the matched sequences will be written in nexus format using the alignment original name. You can change the output format using --output-format (or -F in short version) option. For example, below we will change both the output directory and the output format of the resulting files.

segul extract --dir alignments/ --input-format nexus --re="^Mus" output Mus-alignment/ --output-format Fasta