Sequence Removal
Based on a list of IDs, you can remove sequences in a collection of alignments. This feature is the opposite of the segul extract
feature. Removing less than half of the sequences is faster than segul extract
.
Remove sequences based on a list of IDs
You can remove sequences based on a list of sequence IDs. Input a list of IDs as a string separated by semi-colons.
segul sequence remove --dir [alignment-dir] -f [sequence-format-keyword] --id="[list-of-id]"
Example:
segul sequence remove --dir ./data/ -f fasta --id="seq_1;seq_2;seq_3"
warning
To input a list of IDs, you must use the equal sign "=" and quotation marks "
.
Remove sequences based on a regular expression
Using regular expression:
segul sequence remove --dir [alignment-dir] -f [sequence-format-keyword] --re=["regex"]
Example:
The command below will remove all sequences whose IDs with the name started with Mus
.
segul sequence remove --dir ./data/ -f fasta --re="^Mus"