[Bioperl-l] Bio::SeqIO modifies $_

[Francisco J. Ossandón]

Hi,
One of things that have always bugged me a little about Bioperl code is that
it extensively use "$_", when parsing blast for example:
* "while ( defined( $_ = $self->_readline ) ) {", instead of "while (
defined( my $line = $self->_readline ) ) {"
* elsif(/^Reference:\s+(.*)$/) {
* etc.

For now I have been following the current style of keeping $_ when making
fixes, but in my own scripts I always create named scalars which also avoids
confusion ("foreach my $element ()", "while (my $bar =)", etc.).

I would vote for extensive removal of $_ use, except in cases where really
needed (maybe longer code, but also more clarity), but I will not have the
free time needed to do it for several weeks.

Cheers,

Francisco J. Ossandon

-----Mensaje original-----
De: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de Carnë Draug
Enviado el: martes, 28 de enero de 2014 15:00
Para: <bioperl-l at bioperl.org>
Asunto: [Bioperl-l] Bio::SeqIO modifies $_

Hi

I was under the impression that we had changed to use the builtin bug
tracker of github but for some reason, I can't do it, so I'm reporting it
here.

Consider the following very simple example:

use Bio::SeqIO;
my @files = ("NP_001136062.gb", "NP_001137300.gb"); my @seqs = map
{Bio::SeqIO->new(-file => $_)->next_seq;} @files;

or the more canonical

foreach (@files) {
  my $seq = Bio::SeqIO->new(-file => $_)->next_seq; }

This very simple snippet modifies @files. Following this, each element of
@lines becomes the string "//\n"

Stepping through the code with the debugger (and a lot of help from the
people at #perl), one finds that this is because there's an assignment to $_
in many places of BioPerl. The first one is in Bio::SeqIO::_guess_format
[1]. Fixing it in this place is very easy but I soon found out that this
happens in multiple places. From the example above, the debugger finds that
this happens multiple times in:

Bio::Root::IO::_readline
Bio::SeqIO::genbank::_read_GenBank_References
Bio::SeqIO::genbank::next_seq
Bio::SeqIO::genbank::_read_FTHelper_GenBank

Note that simply doing "my $_" will not work in all places [2] and is not
recommended [3].

Carnë

[1]
https://github.com/bioperl/bioperl-live/blob/ee6a77761340db12c747ab8cde387e9
58e5f8a0f/Bio/SeqIO.pm#L680
[2]
https://github.com/bioperl/bioperl-live/blob/ee6a77761340db12c747ab8cde387e9
58e5f8a0f/Bio/SeqIO/genbank.pm#L838
[3]
http://search.cpan.org/dist/perl-5.18.0/pod/perldelta.pod#Lexical_$__is_now_
experimental

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