Merge branch 'contig_prefix' into 'dev'

Add jbrowse_links

See merge request !23

constants.py

@@ -11,6 +11,7 @@ ORG_PARAM_DESC_PICTURE_PATH = "picture_path"
 ORG_PARAM_DESC_MAIN_SPECIES = "main_species"
 ORG_PARAM_DATA = "data"
 ORG_PARAM_DATA_GENOME_PATH = "genome_path"
+ORG_PARAM_DATA_GENOME_CONTIG_PREFIX = "contig_prefix"
 ORG_PARAM_DATA_TRANSCRIPTS_PATH = "transcripts_path"
 ORG_PARAM_DATA_PROTEINS_PATH = "proteins_path"
 ORG_PARAM_DATA_GFF_PATH = "gff_path"

examples/citrus_sinensis.yml

@@ -18,6 +18,10 @@
   # Paths to the different datasets to copy and import into the galaxy container (as a shared library)
   # Must be absolute paths to the dataset
     genome_path: /path/to/repo/examples/src_data/genome/v1.0/Citrus_sinensis-scaffold00001.fasta # Mandatory!
+    # Required when they are multiple strains from the same species to map the contig name prefix to the right JBrowse dataset ID in Tripal
+    # If multiple contig name prefixes, they must be separated by ";"
+    # example: "contig_prefix1;contig_prefix2"
+    contig_prefix:
     transcripts_path: /path/to/repo/examples/src_data/annotation/v1.0/Citrus_sinensis-orange1.1g015632m.g.fasta
     proteins_path: # Mandatory!
     gff_path: /path/to/repo/examples/src_data/annotation/v1.0/Citrus_sinensis-orange1.1g015632m.g.gff3 # Mandatory!

gga_init.py

@@ -127,7 +127,7 @@ class DeploySpeciesStack(speciesData.SpeciesData):
         # Create input file vars dict
 
         input_vars = {"genus": self.genus_lowercase, "Genus": self.genus_uppercase, "species": self.species,
-                        "genus_species": self.genus_species, "genus_species_strain_sex": self.species_folder_name,
+                        "genus_species": self.genus_species, "jbrowse_dataset_id": self.species_folder_name, "jbrowse_links": self.jbrowse_links,
                         "genus_species_sex": "{0}_{1}_{2}".format(self.genus_lowercase, self.species_lowercase, self.sex),
                         "strain": self.strain, "sex": self.sex, "Genus_species": "{0} {1}".format(self.genus_uppercase, self.species_lowercase),
                         "blast": self.blast, "go": self.go, "picture_path": self.picture_path}
@@ -397,12 +397,19 @@ if __name__ == "__main__":
 
     sp_dict_list = utilities.parse_input(os.path.abspath(args.input))
 
+    #TODO: create SpeciesData objects in utilities.parse_input()
+    org_list = []
+    for sp_dict in sp_dict_list:
+        org = DeploySpeciesStack(parameters_dictionary=sp_dict)
+        org_list.append(org)
+
     # Create traefik directory and compose files if needed or specified
     if args.force_traefik or not os.path.isdir(os.path.join(os.path.abspath(main_dir), "traefik")):
         make_traefik_compose_files(config=config, main_dir=main_dir)
 
     unique_sp_dict_list = utilities.get_unique_species_dict_list(sp_dict_list=sp_dict_list)
     sp_picture_dict = utilities.get_sp_picture(sp_dict_list=sp_dict_list)
+    sp_jbrowse_links_dict = utilities.get_sp_jbrowse_links(org_list=org_list)
 
     logging.info("Deploying stacks for organisms in input file %s" % args.input)
     for sp_dict in unique_sp_dict_list:
@@ -428,6 +435,7 @@ if __name__ == "__main__":
         logging.info("Successfully generated the directory tree for %s %s", deploy_stack_for_current_organism.genus, deploy_stack_for_current_organism.species)
 
         # Make compose files
+        deploy_stack_for_current_organism.jbrowse_links = sp_jbrowse_links_dict[deploy_stack_for_current_organism.genus_species]
         deploy_stack_for_current_organism.make_compose_files()
         logging.info("Successfully generated the docker-compose files for %s %s", deploy_stack_for_current_organism.genus, deploy_stack_for_current_organism.species)
 

speciesData.py

@@ -84,6 +84,7 @@ class SpeciesData:
 
         # TODO: catch blocks if key is absent in input
         self.genome_path = parameters_dictionary_data[constants.ORG_PARAM_DATA_GENOME_PATH]
+        self.contig_prefix = parameters_dictionary_data[constants.ORG_PARAM_DATA_GENOME_CONTIG_PREFIX]
         self.transcripts_path = parameters_dictionary_data[constants.ORG_PARAM_DATA_TRANSCRIPTS_PATH]
         self.proteins_path = parameters_dictionary_data[constants.ORG_PARAM_DATA_PROTEINS_PATH]
         self.gff_path = parameters_dictionary_data[constants.ORG_PARAM_DATA_GFF_PATH]

templates/gspecies_compose.yml.j2

@@ -60,7 +60,8 @@ services:
             TRIPAL_ENABLE_MODULES: "tripal_analysis_blast tripal_analysis_interpro tripal_analysis_go tripal_rest_api tripal_elasticsearch"
             SITE_NAME: "{{ Genus_species }}"
             ELASTICSEARCH_HOST: elasticsearch.{{ genus_species }}
-            ENABLE_JBROWSE: /jbrowse/?data=data/{{ genus_species_strain_sex }}
+            ENABLE_JBROWSE: /jbrowse/?data=data/{{ jbrowse_dataset_id }}
+            JBROWSE_LINKS: {{ jbrowse_links }}
             ENABLE_APOLLO: 0
             ENABLE_BLAST: {{ blast }}
             ENABLE_DOWNLOAD: 1

templates/organisms.yml.j2

@@ -12,6 +12,7 @@
     {% endif %}
   {{ org_param_data }}:
     {{ org_param_data_genome_path }}: {{ org_param_data_genome_path_value }}
+    {{ org_param_data_genome_contig_prefix }}: {{ org_param_data_genome_contig_prefix_value }}
     {{ org_param_data_transcripts_path }}: {{ org_param_data_transcripts_path_value }}
     {{ org_param_data_proteins_path }}: {{ org_param_data_proteins_path_value }}
     {{ org_param_data_gff_path }}: {{ org_param_data_gff_path_value }}

utilities.py

@@ -189,6 +189,23 @@ def get_sp_picture(sp_dict_list):
                 sp_picture_dict[gspecies] = sp[constants.ORG_PARAM_DESC][constants.ORG_PARAM_DESC_PICTURE_PATH]
     return sp_picture_dict
 
+def get_sp_jbrowse_links(org_list):
+    """
+    Get the jbrowse links from all strains for each species
+    """
+
+    jbrowse_links_dict = {}
+
+    for org in org_list:
+        gspecies = org.genus_species
+        if org.contig_prefix != "":
+            if gspecies not in jbrowse_links_dict.keys():
+                jbrowse_links_dict[gspecies] = org.contig_prefix + ">" + org.species_folder_name
+            else:
+                jbrowse_links_dict[gspecies] = jbrowse_links_dict[gspecies] + ";" + org.contig_prefix + ">" + org.species_folder_name
+
+    return jbrowse_links_dict
+
 def run_tool(instance, tool_id, history_id, tool_inputs):
 
     output_dict = None
@@ -229,6 +246,7 @@ def create_org_param_dict_from_constants():
     org_param_dict["org_param_desc_main_species"] = constants.ORG_PARAM_DESC_MAIN_SPECIES
     org_param_dict["org_param_data"] = constants.ORG_PARAM_DATA
     org_param_dict["org_param_data_genome_path"] = constants.ORG_PARAM_DATA_GENOME_PATH
+    org_param_dict["org_param_data_genome_contig_prefix"] = constants.ORG_PARAM_DATA_GENOME_CONTIG_PREFIX
     org_param_dict["org_param_data_transcripts_path"] = constants.ORG_PARAM_DATA_TRANSCRIPTS_PATH
     org_param_dict["org_param_data_proteins_path"] = constants.ORG_PARAM_DATA_PROTEINS_PATH
     org_param_dict["org_param_data_gff_path"] = constants.ORG_PARAM_DATA_GFF_PATH