[ensembl-dev] Problem in Running Ensembl Core API

Urjaswita Yadav urjaswita at gmail.com
Mon Nov 15 22:12:54 GMT 2010


Hello Andreas,

Thanks for your reply.

Yes I specified the inputfile name as mentioned by you. I used
perl IDmapper.pl -s human -f idmapper.in and
 IDmapper.pl --species=human < ./inputfile

But still it does not print anything. I am not sure what's wrong.

Thanks again.

Best Regards,
Urjaswita

On Mon, Nov 15, 2010 at 10:43 AM, Andreas Kahari <ak at ebi.ac.uk> wrote:

> Hi Urjaswita,
>
> How did you run the program?
>
> The ID mapper code needs to be run with --species=human (for human, for
> example), and with the input file either piped into standard input:
>
>  IDmapper.pl --species=human < ./inputfile
>
> or
>
>  cat inputfile | IDmapper.pl --species=human
>
> or by specifying with --file=inputfile what file to read:
>
>  IDmapper.pl --species=human --file=inputfile
>
> If only the species is specified, the program will not print anything
> and will wait for input on standard input.
>
> Note that I'm utterly unfamiliar with Windows, so I can not give any
> Windows-specific help.
>
>
> Andreas
>
> On Sat, Nov 13, 2010 at 04:51:41PM +0100, Urjaswita Yadav wrote:
> > Dear List Members,
> >
> > This maybe a bit naive question since i am using Ensembl API for the
> first
> > time. While trying to setup the Ensembl API, I followed the instructions
> and
> > I guess it installed correctly. I also have Bioperl and DBI installed.
> >
> > But when I am trying to use any script e.g. Idmapper.pl (
> > ftp://ftp.ensembl.org/pub/misc-scripts/ID_mapper_1.0/) it does not do
> > anything. It neither prints any output nor any error message. I tried
> some
> > other scripts too but the response is same: no error and no output, it
> just
> > remains executing. It even does not prints a statement that I write at
> the
> > top of program.
> >
> > This might be a problem with proxy but I am not sure as I am able to ping
> > Ensembl database but am not able to connect to it using a database client
> > like SQLyog. However I am able to download files from internet using
> > LWP::Simple. While browsing the internet using mozilla I select "No
> proxy"
> > or "autodetect proxy" for the network.
> >
> > I am using Windows XP. It would be a great help if anyone could suggest
> > anything. The programs I tried are attached.
> >
> > Thanks in anticipation.
> >
> > Best Regards,
> > Urjaswita
>
>
>
>
> > _______________________________________________
> > Dev mailing list
> > Dev at ensembl.org
> > http://lists.ensembl.org/mailman/listinfo/dev
>
>
> --
> Andreas Kähäri, Ensembl Software Developer
> European Bioinformatics Institute (EMBL-EBI)
> Wellcome Trust Genome Campus
> Hinxton, Cambridge CB10 1SD, United Kingdom
>
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