[EMBOSS] backtranseq

[Magdy Alabady]

Thanks Andres.

On Fri, Dec 19, 2008 at 3:45 PM, Andres Pinzon <andrespinzon at gmail.com>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 <malabady at gmail.com> 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 <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
> > ------------------------------------------------------
> > 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
-------------------------------------------------------------