Mercurial > repos > greg > plant_tribes_gene_family_scaffold_loader
changeset 8:3841f7252b1d draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 21 Aug 2018 12:54:31 -0400 |
| parents | 976184d4d5bb |
| children | 1a5fecd8e5c1 |
| files | .shed.yml gene_family_scaffold_loader.py |
| diffstat | 2 files changed, 6 insertions(+), 5 deletions(-) [+] |
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--- a/.shed.yml Fri Jun 08 13:07:42 2018 -0400 +++ b/.shed.yml Tue Aug 21 12:54:31 2018 -0400 @@ -1,11 +1,12 @@ name: plant_tribes_gene_family_scaffold_loader owner: greg description: | - Contains a tool that analyzes a Planttribes scaffold and inserts information about it into the Galaxy PlantTribes database. + Contains a tool that analyzes a PlantTribes scaffold and inserts information about it into the Galaxy PlantTribes database. homepage_url: https://github.com/dePamphilis/PlantTribes long_description: | - Contains a tool that analyzes a Planttribes scaffold, installed into Galaxy via the PlantTribes scaffolds data manager - tool, and inserts information about it into the Galaxy PlantTribes database. + Contains a tool that analyzes a PlantTribes scaffold, installed into Galaxy via the PlantTribes Scaffolds Downloader + data manager tool, and inserts information about it into the Galaxy PlantTribes database for querying and additional + analysis. remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/phylogenetics/plant_tribes/gene_family_scaffold_loader type: unrestricted categories:
--- a/gene_family_scaffold_loader.py Fri Jun 08 13:07:42 2018 -0400 +++ b/gene_family_scaffold_loader.py Tue Aug 21 12:54:31 2018 -0400 @@ -242,9 +242,8 @@ species_name = items[0] i = 0 for clustering_method in self.clustering_methods: + # The format of species_genes_dict_key is <clustering_method>^^<species_name>. species_genes_dict_key = "%s^^%s" % (clustering_method, species_name) - # The format of species_genes_dict_key is <clustering_method>^^<species_name>. - species_genes_dict_key_items = species_genes_dict_key.split("^^") # Get the scaffold_rec for the current scaffold_id and clustering_method. # The list is [<scaffold_id_db>, <scaffold_id>, <clustering_method>] for scaffold_rec in self.scaffold_recs: @@ -389,6 +388,7 @@ self.log("Inserted a total of %d rows into the plant_tribes_gene table." % gi) self.log("Inserted a total of %d rows into the gene_scaffold_orthogroup_taxon_association table." % gsoai) + if __name__ == '__main__': scaffold_loader = ScaffoldLoader() scaffold_loader.run()