[Biopython-dev] Clustal alignment format header line

[Cymon Cox]

Both Muscle (-clw) and Probcons (-clustalw)  output a programme specific
header line for the clustal format alignment:

"MUSCLE (3.7) multiple sequence alignment


AK1H_ECOLI/1-378      CPDSINAALICRGEKMSIAIMAGVLEAR etc"

"PROBCONS version 1.12 multiple sequence alignment

AK1H_ECOLI/1-378    CPDSINAALICRGEKMSIAIMA

"

Bio.AlignIO will not read these alignments
Bio/AlignIO/ClustalIO.py:94
 if line[:7] != 'CLUSTAL':
       raise ValueError("Did not find CLUSTAL header")

Muscle does have a -clwstrict flag but ProbCons doesnt.

Would it be a good idea to relax the header parsing?

C.
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