[Bioperl-l] Parsing needle/water output

shalabh sharma shalabh.sharma7 at gmail.com
Mon May 18 10:29:40 EDT 2009

Thanks for your valuable suggestions.


On Fri, May 15, 2009 at 5:09 PM, <uludag at ebi.ac.uk> wrote:

> Hi Shalab,
> > is there any way i can get the full id of the sequence from the water
> output.
> I checked emboss website and have a quick look into the relevant source
> file but cannot find an option to adjust length of the sequence
> identifiers written in alignment reports. For example prettyplot has
> 'maxnamelen' option for a similar purpose, a similar option seems to be
> reasonable for alignment reports.
> For now, as a workaround you can read sequence identifiers from your input
> bioperl sequence objects. It seems EMBOSS doesn't change the order of
> sequences.
> Regards,
> Mahmut

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