Mercurial > repos > greg > plant_tribes_gene_family_scaffold_loader
comparison gene_family_scaffold_loader.py @ 8:3841f7252b1d draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 21 Aug 2018 12:54:31 -0400 |
| parents | 9a4b0ae3d408 |
| children | 11a36e425c94 |
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| 7:976184d4d5bb | 8:3841f7252b1d |
|---|---|
| 240 # Example line: Populus trichocarpa\tSalicaceae\tMalpighiales\tRosids\tCore Eudicots | 240 # Example line: Populus trichocarpa\tSalicaceae\tMalpighiales\tRosids\tCore Eudicots |
| 241 items = line.split("\t") | 241 items = line.split("\t") |
| 242 species_name = items[0] | 242 species_name = items[0] |
| 243 i = 0 | 243 i = 0 |
| 244 for clustering_method in self.clustering_methods: | 244 for clustering_method in self.clustering_methods: |
| 245 # The format of species_genes_dict_key is <clustering_method>^^<species_name>. | |
| 245 species_genes_dict_key = "%s^^%s" % (clustering_method, species_name) | 246 species_genes_dict_key = "%s^^%s" % (clustering_method, species_name) |
| 246 # The format of species_genes_dict_key is <clustering_method>^^<species_name>. | |
| 247 species_genes_dict_key_items = species_genes_dict_key.split("^^") | |
| 248 # Get the scaffold_rec for the current scaffold_id and clustering_method. | 247 # Get the scaffold_rec for the current scaffold_id and clustering_method. |
| 249 # The list is [<scaffold_id_db>, <scaffold_id>, <clustering_method>] | 248 # The list is [<scaffold_id_db>, <scaffold_id>, <clustering_method>] |
| 250 for scaffold_rec in self.scaffold_recs: | 249 for scaffold_rec in self.scaffold_recs: |
| 251 if scaffold_id in scaffold_rec and clustering_method in scaffold_rec: | 250 if scaffold_id in scaffold_rec and clustering_method in scaffold_rec: |
| 252 scaffold_id_db = scaffold_rec[0] | 251 scaffold_id_db = scaffold_rec[0] |
| 387 if gsoai % 1000 == 0: | 386 if gsoai % 1000 == 0: |
| 388 self.log("Inserted 1000 more rows into the gene_scaffold_orthogroup_taxon_association table.") | 387 self.log("Inserted 1000 more rows into the gene_scaffold_orthogroup_taxon_association table.") |
| 389 self.log("Inserted a total of %d rows into the plant_tribes_gene table." % gi) | 388 self.log("Inserted a total of %d rows into the plant_tribes_gene table." % gi) |
| 390 self.log("Inserted a total of %d rows into the gene_scaffold_orthogroup_taxon_association table." % gsoai) | 389 self.log("Inserted a total of %d rows into the gene_scaffold_orthogroup_taxon_association table." % gsoai) |
| 391 | 390 |
| 391 | |
| 392 if __name__ == '__main__': | 392 if __name__ == '__main__': |
| 393 scaffold_loader = ScaffoldLoader() | 393 scaffold_loader = ScaffoldLoader() |
| 394 scaffold_loader.run() | 394 scaffold_loader.run() |
| 395 scaffold_loader.shutdown() | 395 scaffold_loader.shutdown() |