Bioperl: Problem with 'toStream' and 'fromStream' in Sanger Embl.pm ???

[Gordon D. Pusch]

This is not strictly a question for this group, but I am hoping
someone in it will still be able to help me...

I am trying to use the Sanger EMBL modules I downloaded from
<ftp://ftp.sanger.ac.uk/pub/PerlModules/>, but I am running into
fatal erros on the first two executable lines of the example taken
nearly verbatim (modulo pound-bang line) from the documentation at
<http://www.sanger.ac.uk/Software/PerlModule/Embl.html>.


The lines causing the problems are (slightly reformatted for 72-column
readability --- full script appended below):

# open the stream
open(FH, "$emblFile") || die "oops - could not open $emblFile"; 

# read all of the embl entries from that stream.
$set = Read Embl(\*FH);          

# set is an EMBL:Set object.
$set->toStream(\*STDOUT);    # print the entries all out to stdout.


However, the 'Read Embl' line yields the error:

  In type EMBL::Parser, can't access fromStream - probably passed a wrong variable into Sequence   at /home/wit/Sanger/PerlModules/Embl.pm line 86


Likewise, the '$set->toStream()' line is yielding:

  Can't call method "toStream" on unblessed reference at ./scan_embl line 50.


As I said, this example is taken nearly verbatim from the documentation --- 
all I have added is the pound-bang line to tell it where perl5 is, a 
'use lib' statement to tell it where 'Embl.pm' is; I also replaced the
hardwired filename 'emblFile' in the 'open()' statement with a variable, 
so I can run it on any file. Can someone tell me what I am doing wrong ???

Thanks in advance,

--  Gordon D. Pusch   <pusch@mcs.anl.gov>

Disclaimer:  I'm a consultant collaborating with Argonne researchers;
I don't speak for ANL or the DOE --- and they *certainly* don't speak
for =ME= !!!

Claimer:  I report =ALL= SPAMvertisers to their ISP --- =NO= exceptions !!!

------------------------------------------------------------------------

#!/usr/local/bin/perl5
($] >= 5.004) || die "version is $] -- need perl 5.004 or greater";


use lib "/home/wit/Sanger/PerlModules";
use Embl;

if (defined $ENV{"VERBOSE"})
{
    foreach $symbol (sort keys %Embl::)
    {
	local *sym = $Embl::{$symbol};
	print "\$$symbol is ", (ref $sym), "\n"  if defined $sym;
	print "\@$symbol is ", (ref @sym), "\n"  if defined @sym;
	print "\%$symbol is ", (ref %sym), "\n"  if defined %sym;
    }
    print "\n";
}


( $emblFile = shift @ARGV )  ||  die "usage:  scan_embl embl.file > parsed.output";


# read in some embl files from a stream, and write them to stdout.
#
open(FH, "$emblFile") || die "oops - could not open $emblFile"; # open the stream
$set = Read Embl(\*FH);          # read all of the embl entries from that stream.
# die "\$set is a ", (ref $set);

# set is an EMBL:Set object.
$set->toStream(\*STDOUT);    # print the entries all out to stdout.

# read in an embl entry from efetch using the default parser
#
$myParser = Embl->defaultParser();
open(EFETCH, "efetch M31544 |") || die "Could not open the file";
$efetch = $myParser->setFromStream(\*EFETCH);
close EFETCH;

# now add this to the entries read from file handle earlier
$set->addSet($efetch);

# could print out again with $set->toEMBLStream

# get an array of all of the EMBL::Entry objects within $set,
# and print each one out to a different file
@entries = $set->entries();
while ($entry = pop @entries) 
{
    if( ! defined ($id = $entry->ID()) ) 
    {
        warn("Got no id for this entry. Skipping...\n");
    }
    open(OUT, ">$id.embl") || die "could not open this entry file";
    $entry->toStream(\*OUT);
    close OUT;
}    

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