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More tests and POD clarification
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@fangly
fangly committed Aug 13, 2013
1 parent 6f570df commit c4a1646
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Showing 2 changed files with 42 additions and 22 deletions.
43 changes: 24 additions & 19 deletions lib/Bio/Root/IO.pm
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Expand Up @@ -521,21 +521,28 @@ sub _insert {
=head2 _readline
Title : _readline
Usage : $io->_readline(%args)
Function: Read a line of input and convert the line ending to "\n".
By default, this method uses the value of $/, Perl's input record
separator, to detect the end of each line. Note that the current
implementation does not handle pushed back input correctly unless
the pushed back input ends with the value of $/.
When the PerlIO::eol module is installed, you can use it to convert
line endings by setting $Bio::Root::IO::HAS_EOL to 1.
Args : A hash of arguments:
-raw: 1 to do not convert line endings, i.e. keep them as "\r\n"
in Windows-formatted files. This option has no effect when
using $Bio::Root::IO::HAS_EOL = 1.
Usage : local $Bio::Root::IO::HAS_EOL = 1;
my $io = Bio::Root::IO->new(-file => 'data.txt');
my $line = $io->_readline();
$io->close;
Function: Read a line of input and normalize all end of line characters.
End of line characters are typically "\n" on Linux platforms, "\r\n"
on Windows and "\r" on older Mac OS. By default, the _readline()
method uses the value of $/, Perl's input record separator, to
detect the end of each line. This means that you will not get the
expected lines if your input has Mac-formatted end of line characters.
Also, note that the current implementation does not handle pushed
back input correctly unless the pushed back input ends with the
value of $/. For each line parsed, its line ending, e.g. "\r\n" is
converted to "\n", unless you provide the -raw argument.
Altogether it is easier to let the PerlIO::eol module automatically
detect the proper end of line character and normalize it to "\n". Do
so by setting $Bio::Root::IO::HAS_EOL to 1.
Args : -raw : Avoid converting end of line characters to "\n" This option
has no effect when using $Bio::Root::IO::HAS_EOL = 1.
Returns : Line of input, or undef when there is nothing to read anymore
=cut
Expand All @@ -553,11 +560,9 @@ sub _readline {
$line = <$fh>;
}

# don't strip line endings if -raw is specified
# $line =~ s/\r\n/\n/g if( (!$param{-raw}) && (defined $line) );
# Dave Howorth's fix
if( !$HAS_EOL && !$param{-raw} && (defined $line) ) {
$line =~ s/\015\012/\012/g; # Change all CR/LF pairs to LF
# don't strip line endings if -raw or $HAS_EOL is specified
$line =~ s/\015\012/\012/g; # Change all CR/LF pairs to LF
$line =~ tr/\015/\n/ unless $ONMAC; # Change all single CRs to NEWLINE
}
return $line;
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21 changes: 18 additions & 3 deletions t/IO.t
View file
Expand Up @@ -6,7 +6,7 @@ use warnings;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 136);
test_begin(-tests => 148);
use_ok('Bio::Root::IO');
}

Expand Down Expand Up @@ -197,30 +197,36 @@ is_deeply \@content, ["insertion at line 1\n"];
{
ok my $unix_rio = Bio::Root::IO->new(-file => test_input_file('U71225.gb.unix'));
ok my $win_rio = Bio::Root::IO->new(-file => test_input_file('U71225.gb.win' ));
ok my $mac_rio = Bio::Root::IO->new(-file => test_input_file('U71225.gb.mac' ));

my $expected = "LOCUS U71225 1164 bp DNA linear VRT 27-NOV-2001\n";
is $unix_rio->_readline, $expected;
is $win_rio->_readline , $expected;
like $mac_rio->_readline, qr#^LOCUS.*//\n$#ms;
# line spans entire file because lines end with "\r" but $/ is "\n"

$expected = "DEFINITION Desmognathus quadramaculatus 12S ribosomal RNA gene, partial\n";
is $unix_rio->_readline, $expected;
is $win_rio->_readline , $expected;
is $mac_rio->_readline , undef;

$expected = " sequence; tRNA-Val gene, complete sequence; and 16S ribosomal RNA\n";
is $unix_rio->_readline, $expected;
is $win_rio->_readline , $expected;
is $mac_rio->_readline , undef;

$expected = " gene, partial sequence, mitochondrial genes for mitochondrial RNAs.\n";
is $unix_rio->_readline, $expected;
is $win_rio->_readline , $expected;
is $mac_rio->_readline , undef;

$expected = "ACCESSION U71225\n";
is $unix_rio->_readline, $expected;
is $win_rio->_readline , $expected;
is $mac_rio->_readline , undef;

is $win_rio->_readline( -raw => 1) , "VERSION U71225.1 GI:2804359\r\n";
is $win_rio->_readline( -raw => 0) , "KEYWORDS .\n";

}


Expand All @@ -229,30 +235,39 @@ is_deeply \@content, ["insertion at line 1\n"];
##############################################

SKIP: {
test_skip(-tests => 14, -requires_module => 'PerlIO::eol');
test_skip(-tests => 19, -requires_module => 'PerlIO::eol');

local $Bio::Root::IO::HAS_EOL = 1;
ok my $unix_rio = Bio::Root::IO->new(-file => test_input_file('U71225.gb.unix'));
ok my $win_rio = Bio::Root::IO->new(-file => test_input_file('U71225.gb.win' ));
ok my $mac_rio = Bio::Root::IO->new(-file => test_input_file('U71225.gb.mac' ));

my $expected = "LOCUS U71225 1164 bp DNA linear VRT 27-NOV-2001\n";
is $unix_rio->_readline, $expected;
is $win_rio->_readline , $expected;
is $mac_rio->_readline , $expected;

$expected = "DEFINITION Desmognathus quadramaculatus 12S ribosomal RNA gene, partial\n";
is $unix_rio->_readline, $expected;
is $win_rio->_readline , $expected;
is $mac_rio->_readline , $expected;

$expected = " sequence; tRNA-Val gene, complete sequence; and 16S ribosomal RNA\n";
is $unix_rio->_readline, $expected;
is $win_rio->_readline , $expected;
is $mac_rio->_readline , $expected;

$expected = " gene, partial sequence, mitochondrial genes for mitochondrial RNAs.\n";
is $unix_rio->_readline, $expected;
is $win_rio->_readline , $expected;
is $mac_rio->_readline , $expected;

$expected = "ACCESSION U71225\n";
is $unix_rio->_readline, $expected;
is $win_rio->_readline , $expected;
is $mac_rio->_readline , $expected;

# $HAS_EOL ignores -raw
is $win_rio->_readline( -raw => 1) , "VERSION U71225.1 GI:2804359\n";
is $win_rio->_readline( -raw => 0) , "KEYWORDS .\n";
}
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