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Removed mentions the ARGV and STDIN features

1/ their documentation was less than clear
2/ they seem to have been broken for quite some time
3/ tests disagree that STDIN should be used this way
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commit edf561c427ab11e85d2fd9520a68ba0fe6315c06 1 parent 91fc1d4
@fangly fangly authored
Showing with 7 additions and 13 deletions.
  1. +7 −13 Bio/SeqIO.pm
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20 Bio/SeqIO.pm
@@ -132,14 +132,9 @@ This makes the simplest ever reformatter
$seqIO = Bio::SeqIO->new(-string => $string , -format => $format);
$seqIO = Bio::SeqIO->new(-format => $format);
-The new() class method constructs a new Bio::SeqIO object. The
-returned object can be used to retrieve or print Seq objects.
-
-If neither a -file, a -fh, nor -string are specified, then the module will take
-the filename from the @ARGV array if possible. If not, it will read from STDIN,
-using the familiar E<lt>E<gt> semantics.
-
-new() accepts the following parameters:
+The new() class method constructs a new Bio::SeqIO object. The returned object
+can be used to retrieve or print Seq objects. new() accepts the following
+parameters:
=over 5
@@ -370,7 +365,7 @@ See L<Bio::SeqIO::Handler>
my $entry = 0;
sub new {
- my ($caller,@args) = @_;
+ my ($caller, @args) = @_;
my $class = ref($caller) || $caller;
# or do we want to call SUPER on an object if $caller is an
@@ -380,7 +375,6 @@ sub new {
$self->_initialize(@args);
return $self;
} else {
-
my %param = @args;
@param{ map { lc $_ } keys %param } = values %param; # lowercase keys
@@ -400,15 +394,15 @@ sub new {
my $format = $param{'-format'};
if (! $format) {
# Guess from filename extension
- $format = $class->_guess_format( $param{-file} || $ARGV[0] );
+ $format = $class->_guess_format( $param{-file} );
}
if (! $format ) {
# Guess from content
if ($param{-file}) {
- $format = Bio::Tools::GuessSeqFormat->new(-file => $param{-file}||$ARGV[0] )->guess;
+ $format = Bio::Tools::GuessSeqFormat->new(-file => $param{-file})->guess;
} elsif ($param{-fh}) {
- $format = Bio::Tools::GuessSeqFormat->new(-fh => $param{-fh}||$ARGV[0] )->guess;
+ $format = Bio::Tools::GuessSeqFormat->new(-fh => $param{-fh})->guess;
}
}
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