[Biopython] clustalW output format

[Stefanie Lück]

Hello!

 

I’m using ClustalW2 for my alignments and would like to have the aln1 output
format (http://www.ebi.ac.uk/Tools/msa/clustalw2/help/). This should show
the line numbers. Actually this should be the default but it’s not. 

 

I tried to add aln1 in \Bio\Align\Applications\_Clustalw.py in line 100+

 

Option(["-output", "-OUTPUT", "OUTPUT", "output"],

["input"],

lambda x: x in ["GCG", "GDE", "PHYLIP", "PIR", "NEXUS",”ALN1”

                         "gcg", "gde", "phylip", "pir", "nexus", “aln1”]

 

but it doesn’t work.

Any ideas?

 

Thanks in advance!

Stefanie