Hm, I should update my blastdb...
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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.
How about parsing the output of blastdbcmd -info and take the total residues from 2. line:
$blastdbcmd -info -db ~/blastdb/swissprot
Database: Non-redundant UniProtKB/SwissProt sequences
455,621 sequences; 169,969,125 total residues
Date: Jul 29, 2013 6:13 AM Longest sequence: 41,943 residues
[...]
Hm, I should update my blastdb...
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