[Bioperl-guts-l] [BioPerl - Bug #3299] AlignIO MSF writing

[redmine at redmine.open-bio.org]

Issue #3299 has been updated by Chris Fields.

Category set to Core Components
Assignee set to Bioperl Guts


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Bug #3299: AlignIO MSF writing
https://redmine.open-bio.org/issues/3299

Author: Bernd W
Status: New
Priority: Normal
Assignee: Bioperl Guts
Category: Core Components
Target version: 
URL: 


Hi

Bioperl describes the MSF format: http://www.bioperl.org/wiki/MSF_multiple_alignment_format
I found that writing MSF (version 1.5.2 to 1.61 and bioperl-live is different from this description. 
I am not sure what is all allowed in MSF, but the header is written like this:
	$self->_print (sprintf("\n%s   MSF: %d  Type: %s  %s  Check: 00 ..\n\n",
			       $name,  $aln->num_sequences, $type, $date));

This means that  we get lines like this:
NoName   MSF: 3  Type: P  Tue Oct  4 21:34:51 2011  Check: 00 ..

However, after MSF there should be the length, as in the Len: field.
In other descriptions I do find the alignment name preceding the MSF: and sometimes also column numbering as is written by BioPerl:


                      1                                                   50
CYS1_DICDI/1-343      -----MKVIL LFVLAVFTVF VSS------- --------RG IPPEEQ---- 
ALEU_HORVU/1-362      MAHARVLLLA LAVLATAAVA VASSSSFADS NPIRPVTDRA ASTLESAVLG 
CATH_HUMAN/1-335      ------MWAT LPLLCAGAWL LGV------- -PVCGAAELS VNSLEK---- 


However, most format description i see do not have numbers and alignment names.
See e.g.
http://www.ebi.ac.uk/help/formats.html#MSF
but also http://tcoffee.vital-it.ch/Doc/doc3.html
and http://bmerc-www.bu.edu/examples/output/seqlist.msf.html

In any case it seems that  $aln->num_sequences, is wrong and should be $aln->length




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