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removed code that changes prefix, suffix, and zero padding #35

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removed code that changes prefix, suffix, and zero padding #35

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57 changes: 0 additions & 57 deletions lib/CXGN/Marker/Tools.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -57,74 +57,17 @@ would appear in our database. Used when someone searches for a marker
name, or when a loading script is loading new names from a
spreadsheet.

When called in list context, it returns the cleaned marker name and
any trimmed subscript. When called in scalar context, it just returns
the cleaned marker name.

my $foo = "TG123a"

my $marker = clean_marker_name($foo);
# returns "TG123"

my ($marker, $subscript) = clean_marker_name($foo);
# returns "TG123" and "a"

This function GUESSES what you want. It is very smart, and usually
correct. But we all make mistakes! Do not blindly trust this function.
It is clever and tricksy and will start giving you wrong answers the
day you let your guard down.

The cleaning routines do some or all of the following (probably not an
exhaustive list): Removes a subscript (returning it if desired, see
above); zero-pads cos markers (T25 -> T0025); removes zero-padding on
other types of markers; adds hyphens to EST markers (cLEX11k1 ->
cLEX-11-k1).

=cut

sub clean_marker_name {

my $name = shift;
my $subscript= '';

if ($name =~ /Solyc\d\dg\d{6}/) {
if (wantarray) {
return ($name, $subscript);
}
else {
return $name;
}
}

# just in case
chomp $name;
$name =~ s/\s+//g;
$name =~ s/_CAPS$//i;

# Rob's marker-massaging routines
# (1) ... to remove any subscript
if ($name =~ /^(\S+\d)_?([A-Ca-c])$/) { # require at least one digit
$name = $1;
$subscript = $2;
}
# (2) ... to format the ID's of COS markers (and others) correctly.
if ($name =~ /^T(\d+)(\W?.*)$/i) {
$name = "T" . sprintf("%04d", $1). $2;
} elsif ($name =~ /^([A-z]+)0+(\d+\S*)$/) {
# Trim extraneous leading 0's so that eg. CT0051 => CT51
$name = $1 . $2;
}
# (3) ... to format ID's of mapped EST's correctly.
if ($name =~ /^(d?c[[:alpha:]]{3})-?(\d+)-?(\w\d+)$/) {
$name = "$1-$2-$3";
}

$name =~ s/\s+//g; # remove any whitespace

# (Sunseeds uses one convention to name AFLPs, KeyGene uses another.
# we decided to stick with the KeyGene convention.)
$name =~ s/SS_([A-Z]\d+)([A-Z]\d+)_?([A-Z])_?([\d.]+)/SS_$1\/$2-$3-$4/;

if(wantarray){

return ($name, $subscript);
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