[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
../..//Bio/Search/Hit/GenericHit.pm:852
STACK Bio::Search::Hit::GenericHit::frac_identical
../..//Bio/Search/Hit/GenericHit.pm:1043
STACK (eval) (eval 310):1
STACK Bio::SearchIO::Writer::ResultTableWriter::__ANON__
../..//Bio/SearchIO/Writer/ResultTableWriter.pm:327
STACK Bio::SearchIO::Writer::HitTableWriter::to_string
../..//Bio/SearchIO/Writer/HitTableWriter.pm:267
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__
../..//Bio/SearchIO/Writer/ResultTableWriter.pm:329
STACK Bio::SearchIO::Writer::HitTableWriter::to_string
../..//Bio/SearchIO/Writer/HitTableWriter.pm:267
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);
above
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
Thanks,
Richard
-----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
framework).
The issue remains: What to do about backwards compatibility? Some
options:
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?
Steve
On Feb 18, 2004, at 4:57 AM, Lincoln Stein wrote:
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> 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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