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Sequence Removal

Based on a list of IDs, you can remove sequences in a collection of alignments. This feature is the opposite of segul extract feature. It is faster than segul extract if you remove less than a half of the sequences.

Remove sequences based on a list of IDs​

You can remove sequences based on a list of IDs. The list of IDs should be a text file with one ID per line. The IDs should be the same as the IDs in the alignment files. The IDs are case-sensitive.

segul sequence remove --dir [alignment-dir] -f [sequence-format-keyword] --id [list-of-id]

Example:

segul sequence remove --dir ./data/ -f fasta --id ./data/id.txt

Remove sequences based on a regular expression​

Using regular expression:

segul sequence remove --dir [alignment-dir] -f [sequence-format-keyword] --re=["regex"]

Example:

Command below will remove all sequences whose IDs with the name started with Homo.

segul sequence remove --dir ./data/ -f fasta --re="^Homo"