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Commit 778bdae7 authored by Loraine Gueguen's avatar Loraine Gueguen
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fix missing method get_sp_jbrowse_links(org_list)

parent 8708daa4
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1 merge request!18Release v2.1.0
This commit is part of merge request !18. Comments created here will be created in the context of that merge request.
...@@ -151,6 +151,23 @@ def get_sp_picture(sp_dict_list): ...@@ -151,6 +151,23 @@ def get_sp_picture(sp_dict_list):
sp_picture_dict[gspecies] = sp[constants.ORG_PARAM_DESC][constants.ORG_PARAM_DESC_PICTURE_PATH] sp_picture_dict[gspecies] = sp[constants.ORG_PARAM_DESC][constants.ORG_PARAM_DESC_PICTURE_PATH]
return sp_picture_dict 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 create_org_param_dict_from_constants(): def create_org_param_dict_from_constants():
""" """
Create a dictionary of variables containing the keys needed to render the organisms.yml.j2 (NOT the values) Create a dictionary of variables containing the keys needed to render the organisms.yml.j2 (NOT the values)
......
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