[Bioperl-l] Parsing needle/water output

[uludag at ebi.ac.uk]

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