[BioC] bgafun - file format.

[Lavinia Gordon]

   Dear all,
   I have recently tried the package bgafun and am having problems with the
   sequence file format.
   I have a file in CLUSTAL format (*.aln).  I have checked the read.alignment
   details and the file fulfills the criteria.
   I am using the commands:
   >LDH <- read.alignment(file = "clustalw.aln", format = "clustal")
   >class(LDH)
   [1] "alignment"
   this command:
   >LDH.amino = convert_aln_amino(LDH)
   is slow, and echoes the content of the file back to me.  Scrolling through
   the screen, I can see a couple of error messages:
   [4871]       "-"                        "-"                        "-"
   "-"
   [1]    "Error    for    position   "   "1673"                  "in   "
   "-"                   "-"
   [6]        "-"                         "-"                         "-"
   "-"                   "-"
   The aligned file (*.aln) looks like this:
   CLUSTAL W (1.81) multiple sequence alignment
   MDH9402143      ------------------------------------------------------------
   MDH1933634      ------------------------------------------------------------
   MDH4407328      ------------------------------------------------------------
   ...
   MDH9402143      -----MAEAPPRRLGLGPPPGDAPRAELVALTAVQSEQGEAGGG---GSPRRLGLLGSPL
   MDH1933634      -----MAEAPPRRLGLGPPPGDAPRAELVALTAVQSEQGEAGGG---GSPRRLGLLGSPL
   MDH4407328      -----MAEAPPRRLGLGPPPGDAPRAELVALTAVQSEQGEAGGG---GSPRRLGLLGSPL
   I have saved the output directly from CLUSTAL in .aln format, and it is
   accepted by other sequence programs, e.g. MEGA.  If anyone can shed any
   light  onto  what I am doing wrong with the alignment, I would greatly
   appreciate it.
   With thanks for your time,
   Lavinia Gordon.

   -------------------------------------------------------
   Bioinformatics Department
   Rm SW916, 9th Floor
   Murdoch Children's Research Institute
   Royal Children's Hospital
   Flemington Road, Parkville
   Victoria 3052
   Australia
   Tel: (+613) 8341 6221
   -------------------------------------------------------