Thanks Peter, it works well except it produces so many files. the number of files is 4 or 5 times more than the number of sequences x2. for example, if I have 10 sequences, I would expected 21 files produced: 10 protein sequences, 10 backtranslation files, and one concatenated file. Is this correct: one other thing, forgive me if it bad question, in the first line of the script isn't the "-outseq 1.fasta" should be "-outseq $1.fasta"
thanks On Fri, Dec 19, 2008 at 10:56 AM, Andres Pinzon <[email protected]>wrote: > This is a not too elegant solution to your problem: > paste the following code in a file called "script.sh": > ====================================== > > > #!/bin/bash > > seqret -ossingle -sequence $1 -outseq 1.fasta > > > for i in $( ls ); do > if [ "$i" != "script.sh" ]; then > echo Processing: $i > backtranseq -sequence $i -outfile $i.bt > fi > done > > cat *.bt > $1.backtranslated.fasta > > ================================================= > > and run the script as this: > ================================================== > ./script.sh ../yourMultipleFastaFile > ================================================== > > > This script will take your multiple fasta file, will create single > files from it. will run backtranslate on each of them and will create > an output file with your results called: > yourMultipleFastaFile_backtranslated.fasta > > > Hope it helps. > > regards, > > > > On Thu, Dec 18, 2008 at 6:20 PM, Peter Rice <[email protected]> wrote: > > Magdy Alabady wrote: > >> > >> Hello all, > >> > >> Can backtranseq run input file contains several 100's of protein > sequences > >> in Fasta format? can it make bulk back translation? please tell me how > to > >> do > >> so if it is possible > > > > Backtranseq only processes a single sequence. You have several choices: > > > > 1. make a new version of backtranseq that can process multiple sequences > > (easy to do ... but you need to learn a little EMBOSS programming first > :-) > > > > 2. put your sequence file in a directory and name it with anything other > > than a .fasta extension. > > > > use seqret -ossingle to convert your file into 100s of single sequence > files > > > > run backtranseq on each of the individual files. > > > > > > I wonder ... do you really want 100s of backtranslations in a single > file? > > > > regards, > > > > Peter Rice > > _______________________________________________ > > EMBOSS mailing list > > [email protected] > > http://lists.open-bio.org/mailman/listinfo/emboss > > > > > > -- > Andrés Pinzón > http://bioinf.ibun.unal.edu.co/~apinzon/<http://bioinf.ibun.unal.edu.co/%7Eapinzon/> > Bioinformatics Center, Colombia EMBnet node > http://bioinf.ibun.unal.edu.co > Tel +57 3165000 ext 16961 Fax +571 3165415 > Micology and Phytopathology Laboratory - Los Andes University. > http://bioinf.uniandes.edu.co > Tel +571 3394949 ext. 2768 > -- Magdy S. Alabady, PhD ------------------------------------------------------ If A is a success in life, then A equals x plus y plus z. Work is x; y is play; and z is keeping your mouth shut. .....Albert Einstein ------------------------------------------------------------- _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
