@ISA
=
qw(Bio::ConnectDots::ConnectorSet)
;
sub
parse_entry {
my
(
$self
) =
@_
;
my
$input_fh
=
$self
->input_fh;
while
(<
$input_fh
>) {
chomp
;
if
(/^
"Probe Set ID"
/) {
next
;
}
my
@field_array
=
split
/
","
/;
my
$probeSetID
=
$field_array
[0];
$probeSetID
=~ s/\"//;
if
(
$probeSetID
ne
'---'
) {
$self
->put_dot(
'ProbeSet_ID'
,
$probeSetID
);
}
my
$chip
=
$field_array
[1];
if
(
$chip
ne
'---'
) {
$self
->put_dot(
'Chip'
,
$chip
);
}
my
$organism
=
$field_array
[2];
if
(
$organism
ne
'---'
) {
$self
->put_dot(
'Organism'
,
$organism
);
}
my
$sequenceType
=
$field_array
[4];
if
(
$sequenceType
ne
'---'
) {
$self
->put_dot(
'Sequence_Type'
,
$sequenceType
);
}
my
$sequenceSource
=
$field_array
[5];
if
(
$sequenceSource
ne
'---'
) {
$self
->put_dot(
'Sequence_Source'
,
$sequenceSource
);
}
my
$SDF
=
$field_array
[6];
if
(
$SDF
ne
'---'
) {
$SDF
=~ s/\.\d+//;
$self
->put_dot(
'SequenceDerivedFrom'
,
$SDF
);
}
my
$geneSymbol
=
$field_array
[12];
if
(
$geneSymbol
ne
'---'
) {
$self
->put_dot(
'GeneSymbol'
,
$geneSymbol
);
}
my
$location
=
$field_array
[13];
if
(
$location
ne
'---'
) {
$self
->put_dot(
'Location'
,
$location
);
}
my
$unigene
=
$field_array
[14];
$unigene
=~ s/\s*\/\/\s*\S*\s*\S*\s*\S*//;
if
(
$unigene
ne
'---'
){
$self
->put_dot(
'UniGene'
,
$unigene
);
}
my
$locuslink
=
$field_array
[15];
if
(
$locuslink
ne
'---'
) {
$self
->put_dot(
'LocusLink'
,
$locuslink
);}
my
$swissProt
=
$field_array
[16];
if
(
$swissProt
ne
'---'
) {
if
(
$swissProt
=~ /\/\/\//) {
my
@sp
=
split
(/\/\/\//,
$swissProt
);
foreach
my
$tmp
(
@sp
) {
$tmp
=~ s/\s*//;
$self
->put_dot(
'SwissProt'
,
$tmp
);
}
}
else
{
$self
->put_dot(
'SwissProt'
,
$swissProt
);
}
}
my
$ECnumber
=
$field_array
[17];
if
(
$ECnumber
ne
'---'
) {
$self
->put_dot(
'ECnumber'
,
$ECnumber
);}
my
$omim
=
$field_array
[18];
if
(
$omim
ne
'---'
) {
$self
->put_dot(
'OMIM'
,
$omim
);}
my
$ensemblID
=
$field_array
[19];
if
(
$ensemblID
ne
'---'
){
if
(
$ensemblID
=~ /\/\/\//) {
my
@ensemblid
=
split
(/\/\/\//,
$ensemblID
);
foreach
my
$tmp
(
@ensemblid
) {
$tmp
=~ s/\s*//;
$self
->put_dot(
'Ensembl'
,
$tmp
);
}
}
else
{
$self
->put_dot(
'Ensembl'
,
$ensemblID
);
}
}
return
$self
->have_dots;
}
return
undef
;
}
1;