Tripal Cmap

This module currently provides a Tripal 3 importer for Cmap files that conforms to the Chado map module schematic. We hope to use existing modules for display (ie cmapjs by legume federation). A field utilizing cmap.js will be included in this module soon.

Installation and setup

This module is not installable with drush. Navigate to where your custom modules are installed and clone this repository. For example:

cd /var/www/html/sites/all/modules/custom/
git clone https://github.com/statonlab/tripal_cmap_loader.git
drush pm-enable tripal_cmap_loader -y

Expected CMAP data

The below table shows an example CMAP file. You can find full file in the example in the example folder. This example map is a genetic map published here.

The importer will load features in assuming that the accession is the unique name and the name is the feature name. currently we ignore the is_landmark and feature_aliases columns.

map_acc	map_name	map_stop	locus_acc	feature_name	feature_accession	feature_start	feature_stop	feature_type_acc
C_mollisima_A	A	90.4	CmSI0385	CmSI0385	CmSI0385	0	0	microsatellite
C_mollisima_A	A	90.4	CmSNP01340	CmSNP01340	CmSNP01340	1.1	1.1	SNP
C_mollisima_A	A	90.4	CmSNP01086	CmSNP01086	CmSNP01086	3.5	3.5	SNP

Using the importer

Before loading the file, create a featuremap (Tripal 3 bundle: Map) entity record.

You will need to select the following when loading a cmap file:

organism
featuremap
sequence ontology term for the mapping features.

You must choose a single organism when loading the map: this is the organism that will be used for new features created. Two types of things will be loaded into Chado: the mapping feature (a chromosome, a scaffold), and the marker feature (a SNP). The type_id for the marker is taken from the feature_type_acc column: that term must be in the sequence ontology. The mapping feature is chosen in the loader.

Cmap column to Chado mapping

Note that the cmap format is not consistent, or at least we have not found a definitive list of columns. The loader expects the following 11 columns. If your file is not 12 columns wide, it will not load. The first column must be map_acc

cmap column	chado entry
map_acc	uniquename for mapping feature IE chromosome, scaffold
map_name	name for mapping feature IE chromsome, scaffold
map_start	not used
map_stop	not used
locus_accession	uniquename for the locus feature
feature_name	name for marker feature
feature_accession	uniquename for marker feature
feature_aliases	not used
feature_start	featurepos record for start
feature_stop	featurepos record for stop
feature_type_accession	type_id for marker feature
is_landmark	not used

FPC

We have written a script to convert FPC format to cmap. See here for code).

Using this module with tripal_map

If you would look to use the Tripal Map module to visualize data loaded with this module, you need to make two small adjustments:

Replace the tripal_map_genetic_markers_mview mview.

SELECT F.uniquename as marker_locus_name, F.feature_id as marker_locus_id, F2.uniquename as genetic_marker_name,
  C1.name as map_unit_type, C2.name as marker_type, FM.name as map_name, FM.featuremap_id as map_id, FMP.value as map_type,
  F3.name as linkage_group, F3.feature_id as linkage_group_id, FPP.value as marker_pos, C.name as marker_pos_type,
  O.organism_id as organism_id, O.genus as genus, O.species as species, O.common_name as common_name
  FROM {feature} F
  INNER JOIN {feature_relationship} FR 	ON FR.subject_id = F.feature_id AND
    F.type_id = (SELECT cvterm_id  FROM {cvterm} WHERE name = 'biological_region' AND
    cv_id = (SELECT cv_id FROM {cv} WHERE name = 'sequence'))
     AND
    FR.type_id = (SELECT cvterm_id  FROM {cvterm} WHERE {cvterm}.name = 'instance_of' AND
    cv_id = (SELECT cv_id FROM {cv} WHERE name = 'OBO_REL'))

  INNER JOIN {feature} F2               	ON FR.object_id = F2.feature_id 
     AND
    FR.type_id = (SELECT cvterm_id FROM {cvterm} WHERE name = 'instance_of' AND
    cv_id = (SELECT cv_id FROM {cv} WHERE name = 'OBO_REL'))
    
  INNER JOIN {featurepos} FP            	ON F2.feature_id = FP.feature_id
  
  INNER JOIN {featuremap} FM    		ON FM.featuremap_id = FP.featuremap_id
  INNER JOIN {cvterm} C1                ON C1.cvterm_id = FM.unittype_id
  	INNER JOIN {cvterm} C2 ON C2.cvterm_id = F2.type_id
  INNER JOIN {featuremapprop} FMP       ON FMP.featuremap_id = FP.featuremap_id AND
   FMP.type_id = (SELECT cvterm_id FROM {cvterm} WHERE name = 'featuremap_type' AND
   cv_id = (SELECT cv_id FROM {cv} WHERE name = 'local'))
  INNER JOIN {featuremap_organism} FMO 	ON FMO.featuremap_id = FM.featuremap_id
  INNER JOIN {feature} F3 				ON FP.map_feature_id = F3.feature_id
  INNER JOIN {featureposprop} FPP 		ON FPP.featurepos_id = FP.featurepos_id
  INNER JOIN {cvterm} C 				ON C.cvterm_id = FPP.type_id
  INNER JOIN {organism} O 				ON FMO.organism_id = O.organism_id

Replace the tripal_map_qtl_and_mtl_mview mview

SELECT FM.name as map_name,
FM.featuremap_id as map_id,
FMP.value as map_type,
F3.name as linkage_group,
F3.feature_id as linkage_group_id,
F.uniquename as marker_locus_name,
C1.name as map_unit_type,
C2.name as marker_type,
C4.name as marker_pos_type,
FPP.value as marker_pos,
O.organism_id as organism_id, O.genus as genus, O.species as species, O.common_name as common_name,
F.feature_id as feature_id, FPP.featurepos_id as featurepos_id
FROM {feature} F
--F is the biological_region or parent marker locus
INNER JOIN {feature_relationship} FR 	ON FR.subject_id = F.feature_id AND
F.type_id = (SELECT cvterm_id  FROM {cvterm} WHERE name = 'biological_region' AND
cv_id = (SELECT cv_id FROM cv WHERE name = 'sequence'))
AND
FR.type_id = (SELECT cvterm_id  FROM {cvterm} WHERE cvterm.name = 'instance_of' AND
cv_id = (SELECT cv_id FROM cv WHERE name = 'OBO_REL'))

-- F2 is the marker feature itself
INNER JOIN {feature} F2               	ON FR.object_id = F2.feature_id
-- This mview is just for QTLs
INNER JOIN {cvterm} C ON F2.type_id = C.cvterm_id AND (C.name = 'QTL' OR C.name = 'heritable_phenotypic_marker')
INNER JOIN {featurepos} FP            	ON F2.feature_id = FP.feature_id
INNER JOIN {featuremap} FM    		ON FM.featuremap_id = FP.featuremap_id
INNER JOIN {cvterm} C1                ON C1.cvterm_id = FM.unittype_id
-- C2 is the marker type term
INNER JOIN {cvterm} C2 ON C2.cvterm_id = F2.type_id
INNER JOIN {featuremapprop} FMP       ON FMP.featuremap_id = FP.featuremap_id AND
FMP.type_id = (SELECT cvterm_id FROM cvterm WHERE name = 'featuremap_type' AND
cv_id = (SELECT cv_id FROM cv WHERE name = 'local'))
INNER JOIN {featuremap_organism} FMO 	ON FMO.featuremap_id = FM.featuremap_id
--F3 is the parent feature of the map ie the linkage group
INNER JOIN {feature} F3 				ON FP.map_feature_id = F3.feature_id
INNER JOIN {featureposprop} FPP 		ON FPP.featurepos_id = FP.featurepos_id
INNER JOIN {organism} O 				ON FMO.organism_id = O.organism_id
INNER JOIN {cvterm} C4  ON FPP.type_id = C4.cvterm_id

Ensure that the featuremap bundle ( IE Genetic Map) has a chado property with the local:featuremap_type term. I reccommend setting a default value for this property so you won't forget. Note you should only need to set this property yourself if the Tripal Entity you are using was custom created and has no type.
Go to the tripal map admin settings at /admin/tripal/extension/tripal_map. Change the start and stop property names tostart position and stop position. If you don't do this, the maps won't draw!

If your featuremap has this property set, and you've populated the altered tripal_map_genetic_markers_mview materialized view (Data Storage -> Chado -> Materialized Views, press "populate"), your field should show up on the organism and featuremap! You might need to clear the cache (drush cc all) before the field appears on the organism.

statonlab / tripal_cmap_loader