[Bioperl-l] searchio scripts

Richard Rouse rrouse at biomail.ucsd.edu
Wed Feb 18 18:09:44 EST 2004

I tried Steve's suggestion by putting this right above:
  while ( my $blast = $in->next_result() ) {

Then putting another } at the end of the script.

Doing this and then running a large blast output file, I got:

Using SearchIO->new()

Report 1: Bio::Search::Result::BlastResult=HASH(0x87d7fb8)

Report 2: Bio::Search::Result::BlastResult=HASH(0x8dfea60)

------------- EXCEPTION  -------------
MSG: Trouble in ResultTableWriter::_set_row_data_func() eval:
------------- EXCEPTION  -------------
MSG: Can't get identical or conserved data: no data.
STACK Bio::Search::Hit::GenericHit::matches
STACK Bio::Search::Hit::GenericHit::frac_identical
STACK (eval) (eval 310):1
STACK Bio::SearchIO::Writer::ResultTableWriter::__ANON__
STACK Bio::SearchIO::Writer::HitTableWriter::to_string
STACK Bio::SearchIO::write_result ../..//Bio/SearchIO.pm:321
STACK Bio::SearchIO::blast::write_result ../..//Bio/SearchIO/blast.pm:1495
STACK toplevel new.mod.hitwriter.pl:106


STACK Bio::SearchIO::Writer::ResultTableWriter::__ANON__
STACK Bio::SearchIO::Writer::HitTableWriter::to_string
STACK Bio::SearchIO::write_result ../..//Bio/SearchIO.pm:321
STACK Bio::SearchIO::blast::write_result ../..//Bio/SearchIO/blast.pm:1495
STACK toplevel new.mod.hitwriter.pl:106

I tried Lincoln's suggestion as well. In this case I added:

my $in = Bio::SearchIO->new(-format=>'blast',-fh=>\*ARGV);


while ( my $blast = $in->next_result() ) {

This script just runs getting no result.

By the way I am running Suse linux 9.0, perl 5.8.1


-----Original Message-----
From: Steve Chervitz [mailto:steve_chervitz at affymetrix.com]
Sent: Wednesday, February 18, 2004 12:16 PM
To: Lincoln Stein
Cc: Richard Rouse; Bioperl
Subject: Re: [Bioperl-l] searchio scripts

Good tip, Lincoln. But regardless, the change in IO::_readline's
behavior means that any script that depended on its pre-1.303
default-to-STDIN behavior is now broken. This could be a lot since the
code in examples and scripts exploited this. I received three messages
about it yesterday, so I fear there could be many others out there
scratching their heads, especially considering that the
default-to-STDIN behavior has been around since the early days of
SeqIO. From the SeqIO docs:

>    $seqIO = Bio::SeqIO->new(-format => $format);
>   ....
> If neither a filehandle nor a filename is specified, then the module
> will read from the @ARGV array or STDIN, using the familiar <>
> semantics.

Relying on a default behavior of a dependent module (Root::IO) always
troubled me. It seems a better design to make it explicit in your
script where you expect your input to come from. Typing "-fh=>\*ARGV"
or putting an @ARGV loop around your script is extra work, but I think
it's a change for the better. (BTW, this situation also exposes a
weakness in the test code which didn't test the default _readline
behavior -- I guess doing this is difficult within the Perl test

The issue remains: What to do about backwards compatibility? Some

1. Fix all of the scripts, examples, POD docs, bptutorial etc. to not
rely on default STDIN/@ARGV reading behavior of _readline and release
these as part of bioperl-1.4.1.

2. Revert _readline to it's old behavior and add a new method in IO.pm
that has the new behavior (_readline2). Update any module/script that
needs the new _readline behaviour to use _readline2.

#2 is the backward-compatible route, but uglier from a software
engineering perspective. #1 breaks backward compatibility. Given the
legacy of the old _readline behaviour, I'm favoring #2. Just seems more
politic. We could still update the scripts and docs to discourage the
old _readline behaviour. Thoughts?


On Feb 18, 2004, at 4:57 AM, Lincoln Stein wrote:

> Hash: SHA1
> Or do this:
> 	my $in = Bio::SearchIO->new(-format=>'blast',-fh=>\*ARGV);
> 	while (my $result = $in->next_result()) {
> 		...
> 	}
> That might even be easier.
> Lincoln
> On Wednesday 18 February 2004 12:27 pm, Steve Chervitz wrote:
>> Looks like there was a change in the Root::IO.pm module that
>> affects the way these scripts process command-line arguments. As of
>> bioperl-1.303, the SearchIO::blast module appears to be unable to
>> read data from STDIN or files listed in @ARGV. This affects the
>> scripts in examples/searchio and scripts/searchio.
>> As a workaround, I'd recommend you iterate over @ARGV in your
>> script and initialize the SearchIO object using the -file option to
>> new(), as in:
>> while (my $file = shift @ARGV) {
>>      my $in = Bio::SearchIO->new( -format => 'blast',
>>                                   -file => $file
>>                                 );
>>      while ( my $result = $in->next_result() ) {
>>          # process result...
>>      }
>> }
>> As far as tracking down the cause, I've pinpointed the following
>> change in Bio::Root::IO::_readline():
>>      my $fh = $self->_fh or return;   # revision 1.50
>> (bioperl-1.303)
>> formerly this was:
>>      my $fh = $self->_fh || \*ARGV;   # revision 1.49
>> (bioperl-1.302)
>> This also appears to break SeqIO reading from STDIN. Try executing
>> this at the top-level distribution dir for the 1.302 and 1.303
>> releases:
>>      perl -I. ./scripts/seq/translate_seq.PLS -format fasta <
>> t/data/dna1.fa
>> According to Lincoln's commit log, the Root::IO::_readline() change
>> was necessary to get the GFF, SeqFeature, and Registry regression
>> tests working. I tested these tests with the 1.49 version of IO.pm
>> and the only one that was affected was SeqFeature.t. Specifically,
>> test #6 which calls SeqFeature::Generic::gff_string() hangs and
>> waits for input before proceeding. I'm not sure why this is...
>> (getting late).
>> BTW, platforms tested: Perl 5.6.1 and 5.8.0 on Linux (RH9) and Perl
>> 5.8.1-RC3 on MacOS X (10.3.2).
>> Steve
>> On Feb 17, 2004, at 3:14 PM, Richard Rouse wrote:
>>> I recent installed bioperl-1.4 and am having problems with the
>>> blast report
>>> parsers in /examples/searchio/
>>> When I run:
>>> perl hitwriter.pl blastreport
>>> I get:
>>> Using SearchIO->new()
>>> 0 Blast report(s) processed.
>>> Output sent to file: >hitwriter.out
>>> I get the same result with rawwriter.pl, hspwriter.pl and
>>> custom_writer.pl
>>> although the htmlwriter.pl and the blast_example.pl work fine.
>>> Has anyone else encountered this problem and figured out how to
>>> fix it?
>>> Thanks,
>>> Richard
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> - --
> Lincoln D. Stein
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
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