Add extra gnt:location term when transforming ProbeSet metadata.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>

1 files changed, 30 insertions, 0 deletions

diff --git a/examples/probeset.scm b/examples/probeset.scm
index 9e41781..e01fe84 100755
--- a/examples/probeset.scm
+++ b/examples/probeset.scm
@@ -20,6 +20,8 @@
    (gnt:hasTargetId a owl:ObjectProperty)
    (gnt:hasTargetId rdfs:domain gnc:Probeset)
    (gnt:symbol rdfs:domain gnc:Probeset)
+   (gnt:location rdfs:domain gnc:ProbeSet)
+   (gnt:location a owl:ObjectProperty)
    (gnt:strandPosition rdfs:domain gnc:ProbeSet)
    (gnt:strandPosition a owl:ObjectProperty)
    (gnt:targetsRegion a owl:ObjectProperty)
@@ -81,6 +83,34 @@
                   Probe_set_target_region))))
     (set gnt:chr (field ProbeSet Chr))
     (set gnt:mb (annotate-field (field ("IFNULL(ProbeSet.Mb, '')" Mb)) '^^xsd:double))
+    (set gnt:location
+         (let* ((mb (field ProbeSet Mb))
+                (chr (field ProbeSet Chr))
+                (strand-probe (field ProbeSet Strand_Probe))
+                (location (list chr mb)))
+           (match location
+             (("Un" mb)
+              (format #f "Not available"))
+             ((chr "")
+              (format #f "Chr ~a @ Unknown position ~a~:[~;~a~]"
+                      chr mb
+                      (and (string? strand-probe) (or (string=? "+" strand-probe)
+                                                      (string=? "-" strand-probe)))
+                      (cond ((string=? "+" strand-probe)
+                             " on the plus strand")
+                            ((string=? "-" strand-probe)
+                             " on the minus strand")
+                            (else ""))))
+             (_
+              (format #f "Chr ~a @ ~a~:[~;~a~]"
+                      chr mb
+                      (and (string? strand-probe) (or (string=? "+" strand-probe)
+                                                      (string=? "-" strand-probe)))
+                      (cond ((string=? "+" strand-probe)
+                             " on the plus strand")
+                            ((string=? "-" strand-probe)
+                             " on the minus strand")
+                            (else "")))))))
     (set gnt:strandProbe
          (field ProbeSet Strand_Probe))
     (set gnt:hasSpecificity