Entering edit mode
2.7 years ago
Priya
▴
20
i have a task and i am having difficulty in getting the key values out of my key-value file , at the replacement. i have tried several versions of this seqkit replacement command but not able to get the right result. my key-value file:
WP_000014594.1 WP_000014594.1#0001
WP_000025662.1 WP_000025662.1#0001
so the column1 has accession numbers/ids that will find in my fasta file header and i need to replace these with values given in column2.
but im either getting blank space there (command a.)or partial ids like this >_000014594
(command b.)
command a.
$ seqkit replace -p "^(\w+)_(\d+).(\d+)" --replacement "{kv}" -k accesskey_idsvalue1 GCF_000016305.1_ASM1630v1_protein.faa
command b.
$ seqkit replace -p "^(\w+)_(\d+).(\d+)" --replacement '{kv}_${2}' -k accesskey_idsvalue1 GCF_000016305.1_ASM1630v1_protein.faa
if fasta has only OP strings, you can use
^(\w+\.\w)
or^(\w+\.\d)
pattern.