I have piped unknown length sequences into makeblastdb
. Now I want to know total length of those sequences (BLAST database size).
Example:
# "cat" is used as an example
# My "real" sequences are piped from "make random length sequences" command
cat unknown_length_sequences>Seq1
AA --//-- TG>Seq2
GG --//-- TA>Seq3
AC --//-- CC
...
cat unknown_length_sequences |
makeblastdb \
-in - \
-dbtype 'nucl' \
-parse_seqids \
-out random_seq \
-title "random_seq"
Output files look like this:
random_seq.nhr
random_seq.nin
random_seq.nog
random_seq.nsd
random_seq.nsi
random_seq.nsq
My question is - How to get BLAST database size (length of all the sequences)?
Result should be the same as using: grep -v '>' INPUT | tr -d '\n' | wc
Edit
I want to achieve this without making intermediate files.