Sequence ID Renaming
SEGUL provides an easy way to rename sequence IDs across all your alignments. To use this function, SEGUL requires a list of the original IDs and the names it needs to change. The input IDs can be written in a tabulated format as a comma-delimited file (.csv) or a tab-delimited file (.tsv).
The table must contain two columns with a header for each column. Both the header names and the IDs should contain no space. The name of the header does not matter. You'll be able to name it whichever makes sense for you. It is only there for record keeping. The order of the columns, however, is essential. The first column should be the original IDs, and the second should be the new ones. For example:
| Original_names | New_names |
|---|---|
| Genus_species1_random | Genus_species1_voucherID |
| Genus_species2_random | Genus_species2_voucherID |
If you need to rename a lot of sequence IDs, you can simplify the process by generating the unique IDs first. Then, copy the IDs you want to rename in the csv or tsv input. Use the -replace-id option to input this file. SEGUL will infer the file format based on its extension. The full command is structured as below:
segul sequence rename -d [alignment-dir] -f [sequence-format-keyword] --replace-id [file-path-to-IDs]
For example:
segul sequence rename -d alignments/ -f nexus --replace-id new_names.csv
You can use --dry-run option to check if the input names are parsed correctly:
segul sequence rename -d alignments/ -f nexus --replace-id new_names.csv --dry-run
By default, SEGUL will write the result in SEGUL-Rename directory. To change the output directory, use the --output or -o option.
segul sequence rename -d alignments/ --input-format nexus --replace-id new_names.csv --output new_seq_names/
Like other functions, SEGUL will not overwrite your original files. The output files will default to NEXUS. To change the output format, use the --output-format or -F function:
segul sequence rename -d alignments/ --input-format nexus --replace-id new_names.csv --output new_seq_names/ --output-format fasta
Other renaming options
Remove matching input text
You can remove a matching text from the sequence ID. This is useful if you have a common text in all your sequence IDs that you want to remove. For example, if all your sequence IDs have a common suffix _contigs, you can remove this suffix using the --remove or -r option:
segul sequence rename -d alignments/ --input-format nexus --remove _contigs
Remove matching regular expression
You can also remove a matching regular expression from the sequence ID. This is useful if you have a common pattern in all your sequence IDs that you want to remove. For example, if all your sequence IDs have a common prefix locus followed by a number, you can remove this pattern using the --remove-re:
segul sequence rename -d alignments/ --input-format nexus --remove-re="^locus[0-9]"
Suppose multiple patterns exist in a single sequence ID. The command above will only remove the first matching pattern. Then, it will continue to look for the same pattern in the following sequence ID.
You can also remove all the matches found in a single sequence ID by using the --remove-all option:
segul sequence rename -d alignments/ --input-format nexus --remove-re="^locus[0-9]" --remove-all
Find and replace a matching text
You can also replace a matching text from the sequence ID. For example, you can replace locus01 with locus1 using the --replace-from and --replace-to options:
segul sequence rename -d alignments/ --input-format nexus --replace-from locus01 --replace-to locus1
Find and replace a matching regular expression
You can also replace a regular expression matching the sequence ID. For example, if all your sequence IDs have a common prefix locus followed by a number, you can use the regular expression ^locus[0-9] to match the pattern. Use the --replace-from-re and --replace-to options to replace the matching prefix:
segul sequence rename -d alignments/ --input-format nexus --replace-from-re ^locus[0-9] --replace-to locus