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Peter Ernst > Bio-Emboss- > Bio::Emboss



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Bio::Emboss - Write EMBOSS programs in Perl


  use Bio::Emboss qw(:all);

  embInitPerl("seqret", \@ARGV); 
  $seqall = ajAcdGetSeqall("sequence"); 
  $seqout = ajAcdGetSeqoutall("outseq"); 
  while ($seqall->ajSeqallNext($seq)) {
      $seqout->ajSeqAllWrite ($seq);


This module allows Perl programmers to access functions of the EMBOSS (European Molecular Biology Open Software Suite) package.


You can use this module in an object oriented way or not. I.e. the EMBOSS function

  AjBool       ajSeqallNext (AjPSeqall seqall, AjPSeq* retseq);

can be used from Perl in the following ways:

  $ok = $seqall->ajSeqallNext ($retseq);


  $ok = Bio::Emboss::ajSeqallNext ($seqall, $retseq);


  # --- with use Bio::Emboss ":all"
  $ok = ajSeqallNext ($seqall, $retseq);

AjPxxx types are translated into Perl references, blessed into the package Bio::Emboss::xxx. This allows the object oriented notation seen above.

Functions expecting pointers to variables, because the function changes the value of this variable don't need pointers/references from Perl. I.e.

  (AjPSeqall seqall, AjPSeq* retseq);

translates to

  ($seqall, $retseq)

Known problem: Some C prototypes are ambiguous for Perl: (int*) can mean a pointer to an integer value (because the functions changes the value), OR it can be an array of integers. Depending on the meaning a different translation into Perl needs to be done.

(In PerlXS, in the first case "&" instead of "*" is used for the prototype of the function. In the second case, the "&" must not be used. See "The & Unary Operator" in perlxs)


Because Perl provides the command-line in $0 and @ARGV (and not argc and argv like in C), two convenience functions have been implemented to start an EMBOSS application from Perl.

embInitPerl($program_name, \@ARGV)

Can be used instead of embInit(char *pgm, ajint argc, char *argv[])

ajGraphInitPerl($program_name, \@ARGV)

Can be used instead of ajGraphInit(char *pgm, ajint argc, char *argv[])


None by default.

Available export tags are:


With this export tag, all available functions in this module are copied into the callers namespace.


Export ajAcdGet... functions only.


perldoc Bio::Emboss::Ajax (if installed)

Examples in the t/ subdirectory of the Bio::Emboss source tree.


Peter Ernst, <>


Copyright 2003-2006 by Peter Ernst

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

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