[Bioperl-l] Parsing needle/water output

uludag at ebi.ac.uk uludag at ebi.ac.uk
Fri May 15 17:09:16 EDT 2009

Hi Shalab,

> is there any way i can get the full id of the sequence from the water

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


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