[Bioperl-l] fasta-formatted alignment used in SearchIO

[Vladimir Babenko]

  Hello all,
  I'm trying to use SearchIO module with
fasta-formatted output of alignment in a form:
>id1
gccgccgcc---ccc
>id2
gccgccgccggg---
>id3
gccgccgcc---ccc

  While invocationg SeqIO object:
my $format='fasta';
my $in = new Bio::SearchIO(-file   => $report,
			   -format => $format);
and trying to read alignment:
while( my $r = $in->next_result ) {
...}

  I'm getting a warning:
--------------------------------------
MSG: unrecognized FASTA Family report file!
--------------------------------------
  Is it OK to use the abovementioned format or
direct alignment output should be used as fasta?
    Thank you,
   Vladimir

  


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