From b57812bb244267017142d0258f7c8901ddddd1dc Mon Sep 17 00:00:00 2001
From: Diane Trout <diane@caltech.edu>
Date: Wed, 9 Oct 2013 15:24:18 -0700
Subject: [PATCH] add replaces / replace_reason generation to trackhub manifest

---
 htsworkflow/templates/manifest.txt             | 4 ++--
 htsworkflow/templates/trackhub_manifest.sparql | 6 +++++-
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/htsworkflow/templates/manifest.txt b/htsworkflow/templates/manifest.txt
index adf0554..c81259c 100644
--- a/htsworkflow/templates/manifest.txt
+++ b/htsworkflow/templates/manifest.txt
@@ -1,2 +1,2 @@
-#file_name	format	output_type	experiment	replicate	enriched_in	ucsc_db{% for r in files %}
-{{ r.relative_path }}	{{ r.file_format }}	{{ r.output_type }}	{{ r.dataset_id }}	{{ r.replicate }}	{{ r.enriched_in }}	{{ r.ucsc_db }}{% endfor %}
+#file_name	format	output_type	experiment	replicate	enriched_in	ucsc_db	replaces	replace_reason{% for r in files %}
+{{ r.relative_path }}	{{ r.file_format }}	{{ r.output_type }}	{{ r.dataset_id }}	{{ r.replicate }}	{{ r.enriched_in }}	{{ r.ucsc_db }}	{{ r.replaces_accession|default_if_none:"" }}	{{ r.replace_reason|default_if_none:"" }}{% endfor %}
diff --git a/htsworkflow/templates/trackhub_manifest.sparql b/htsworkflow/templates/trackhub_manifest.sparql
index 1c83b47..cb5c4fd 100644
--- a/htsworkflow/templates/trackhub_manifest.sparql
+++ b/htsworkflow/templates/trackhub_manifest.sparql
@@ -6,7 +6,7 @@ PREFIX ncbiTaxon: <http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=>
 PREFIX geoSoft: <http://www.ncbi.nlm.nih.gov/geo/info/soft2.html#>
 PREFIX cells: <http://encodewiki.ucsc.edu/EncodeDCC/index.php/Cell_lines#>
 
-select distinct ?name ?filename ?relative_path ?file_format ?output_type ?dataset_id ?replicate ?enriched_in ?ucsc_db
+select distinct ?name ?filename ?relative_path ?file_format ?output_type ?dataset_id ?replicate ?enriched_in ?ucsc_db ?replaces_accession ?replace_reason
 WHERE {
   <{{submission}}> a submissionOntology:submission ;
                    submissionOntology:name ?name ;
@@ -17,6 +17,10 @@ WHERE {
         htswlib:library ?library ;
         a ?fileClass .
 
+  OPTIONAL { ?file encode3:replaces ?replaces_accession ;
+                   encode3:replace_reason ?replace_reason .
+  }
+
   ?fileClass geoSoft:fileTypeLabel ?file_format ;
              ucscDaf:output_type ?output_type .
   
-- 
2.30.2