makeblastdb on custom databases?

[tseemann]

The -u (update) option does two things:

1. DOWNLOAD
2. FORMAT (makeblastdb)

Could you please add an option to (re)-format the BLAST databases (CDS and Prot) as provided by the --db option?

It seems manualyl running the commands is the only way to do it otherwise?

Perhaps also doing a check of the dates at runtime and warning if AMRProt has a modified date newer than AMRProt.p?? etc?

[evolarjun]

Hi Torsten,

You make a good point. Now that there are several different makeblastdb commands (nucleotide and protein) it would be nice to enable just running that portion of the update.

Arjun

[evolarjun]

So it occurred to me that I have the same problem. I make modifications to the database, and I use a Makefile. I know it's not as good as a built-in function, but if you're hacking at something it could be useful. Here are the relevant parts in case it'll be helpful to you.

blastp = AMRProt.phr  AMRProt.pin  AMRProt.psq
blastn = AMR_DNA-Campylobacter.nin AMR_DNA-Salmonella.nin AMR_DNA-Escherichia.nin AMR_DNA-Staphylococcus_aureus.nin
blastdb = *.nin *.nhr *.nsq *.ndb *.not *.nto *.ntf *.pin *.phr *.psq *.pot *.pto *.ptf
HMMdb = AMR.LIB.h3f AMR.LIB.h3i AMR.LIB.h3m AMR.LIB.h3p

all:    $(HMMdb) $(blastp) $(blastn)

$(HMMdb): AMR.LIB
	hmmpress -f AMR.LIB

$(blastp): AMRProt
	makeblastdb -in AMRProt -dbtype prot -out AMRProt

%.nin: $(basename %.nin)
	makeblastdb -in $< -dbtype nucl

clean:
	-rm $(blastdb) $(HMMdb)