Thanks Andres. On Fri, Dec 19, 2008 at 3:45 PM, Andres Pinzon <[email protected]>wrote:
> Hi Magdy, > This is Andres, please dont blame peter!!! for the script I wrote it :-) > > On Fri, Dec 19, 2008 at 3:58 PM, Magdy Alabady <[email protected]> wrote: > > 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: > > lets say you have 1 multiple fasta file whith 3 entries. > It will create 7 files. 3 single fasta files (one for every multiple > fasta enty). 3 ".bt", > one for each single fasta file and 1 file which concatenates this > ".bt" files. (thjis is the way it works in my machine). Please take > into account that if you run it several times on the same place it > will multiply your files. > > > > 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" > > nop, this option says seqret how to name the output files. So the > first entry in the multiple fasta file will correspond to the 1.fasta > file, the second one will correspond to 2.fasta and so on. > I hope this helps, > > Please don hesitate to contact me. > > Best, > > 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 > > ------------------------------------------------------------- > > > > > > > > -- > 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
