Help - how to execute multiple lot of file to blast

[Leandro de Mattos]

Dear colleagues,

I have lot of files with one protein each and I going to want execute a blast of each file againts an database (Eukaryotes).
Is there a way for to do it automatically?


Thanks for any help.

Leandro

[Matthew]

Check out Find::File and File::Recursive. You can use these modules to open all or multiple files in a folder using a regex to select the particular files, or also to open particular folders and pick a file from the folder.

Matthew

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[Keith Bradnam]

If:

1. You want to search all sequences against the same database
2. Each entry ends with a newline after the last amino acid character
3. You are not particularly interested in the order in which you search the sequences 

Then you could just combine all sequences into one file to start with. You then have to process the multiple results, but they will be in one output file.

E.g. cat *.fasta > all_sequences_combined.fasta

If condition 2 is not met, then you will end up with problem FASTA records that might look like this (where the 2nd record gets mistakenly combined on to the end of the first record):

>AT1G15970.1 | Symbols:  | methyladenine glycosylase family protein | chr1:5486538-5488488 REVERSE

MSVPPRFRSVNSDEREFRSVLGPTGNKLQRKPPGMKLEKPMMEKTIIDSKDEKAKKPTTP

ASPRTTLKQCSSLCSSILRKNSASMTASYSSDASSSCESSPLSVASSSSCKKVVRRSGSV

SSTRKLSVGKEEEKVSGDCFADGRKRCAWITPKADPCYVAFHDEEWGVPVHDDKKLFELL

CLSGALAELSWTDILSRRHILREVFMDFDPVAVAELNDKKLTAPGTAAISLLSEVKIRSI

LDNSRHVRKIIAECGSLKKYMWNFVNNKPTQSQFRYQRQVPVKTSKAEFISKDLVRRGFR

SVSPTVIYSFMQAAGLTNDHLIGCFRYQDCCVDAETTTTTKAKKKNERESDK*>AT1G73440.1 | Symbols:  | calmodulin-related | chr1:27615079-27615843 FORWARD

MARGESEGESSGSERESSSSSSGNESEPTKGTISKYEKQRLSRIAENKARLDALGISKAA

KALLSPSPVSKKRRVKRNSGEEDDDYTPVIADGDGDEDDDEVEEIDEDEEFLCKRKNKSS

ASKRKVSSRKILNTSVSLGEDDDDLDKAIALSLQGSVAGSDKEAATMKKKRPELMSKTQM

TQDELVMYFCQFDEGGKGFITLRDVAKMATVHDFTWTEEELQDMIRCFDMDKDGKLSLDE

FRKIVSRCRMLKGS*

[Alex Van Dam]

ls -1 *my_file_handle | awk '{ print "blastp -options -db etc. -query "$1" -o "$1"_blastp_out &" }' | less > commands_for_multi_blast.sh

sh commands_for_multi_blast.sh

there are many flavors of this depending on your system but this is basically how it's done you might not want the "&" at the end and add other code to the end or have nothing depending on your system, but the "&" basically lets you run multiple jobs at the same time, there are other ways to do this i'm sure but this is a "one-liner" way.

Cheers,

Alex

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Mr. Alex Van Dam, Ph.D. 
NSF Postdoctoral Researcher

Frandsen Lab
Denmark Technical University
Department of Systems Biology
Søltofts plads, Building 223
2800 Kgs. Lyngby
Denmark