| 6105 |
return $out; |
return $out; |
| 6106 |
} |
} |
| 6107 |
|
|
| 6108 |
|
|
| 6109 |
|
############################################ |
| 6110 |
|
# |
| 6111 |
|
# map SEED internal references for external databases into globally "acceptable" format |
| 6112 |
|
# see: http://www.ncbi.nlm.nih.gov/collab/db_xref.html for format definition |
| 6113 |
|
# |
| 6114 |
|
sub rewrite_db_xrefs { |
| 6115 |
|
|
| 6116 |
|
my ($self, $alias) = @_; |
| 6117 |
|
|
| 6118 |
|
if ( $alias =~ /^gi/ ) { # /db_xref="GI:1234567890" |
| 6119 |
|
$alias =~ s/^gi\|/GI:/; |
| 6120 |
|
return $alias; |
| 6121 |
|
} |
| 6122 |
|
elsif ($alias =~ /^uni/) { # /db_xref=" UniProtKB/TrEMBL:Q00177" |
| 6123 |
|
$alias =~ s%uni\|%UniProtKB/TrEMBL:%; |
| 6124 |
|
return $alias |
| 6125 |
|
} |
| 6126 |
|
elsif ($alias =~ /^kegg/i){ |
| 6127 |
|
$alias =~ s/kegg\|/KEGG:/i; |
| 6128 |
|
$alias =~ s/^(.*):/$1+/; |
| 6129 |
|
return $alias |
| 6130 |
|
} |
| 6131 |
|
elsif ($alias =~ /^sp\|/) { # /db_xref="UniProtKB/Swiss-Prot:P12345" |
| 6132 |
|
$alias =~ s%sp\|%UniProtKB/Swiss-Prot:%; |
| 6133 |
|
return $alias |
| 6134 |
|
} |
| 6135 |
|
else { # unsupported external alias, return empty string |
| 6136 |
|
return ''; |
| 6137 |
|
} |
| 6138 |
|
|
| 6139 |
|
} |
| 6140 |
|
|
| 6141 |
|
|
| 6142 |
|
|
| 6143 |
=head3 by_alias |
=head3 by_alias |
| 6144 |
|
|
| 6145 |
usage: $peg = $fig->by_alias($alias) |
usage: $peg = $fig->by_alias($alias) |
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