[EMBOSS] backtranseq

[Magdy Alabady]

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 <andrespinzon at gmail.com>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 <pmr at ebi.ac.uk> 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
> > EMBOSS at lists.open-bio.org
> > 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
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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
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