Mercurial > repos > greg > plant_tribes_gene_family_scaffold_loader

comparison gene_family_scaffold_loader.py @ 3:48c13482e6c9 draft

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author greg
date Fri, 25 May 2018 10:21:45 -0400
parents 751b36922d59
children 3c6514d810ae
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2:751b36922d59 3:48c13482e6c9
264 VALUES (nextval('plant_tribes_taxon_id_seq'), %s, %s, %s, %s, %s, %s, %s); 264 VALUES (nextval('plant_tribes_taxon_id_seq'), %s, %s, %s, %s, %s, %s, %s);
265 """ 265 """
266 self.update(sql, tuple(args)) 266 self.update(sql, tuple(args))
267 self.flush() 267 self.flush()
268 i += 1 268 i += 1
269 self.log("Inserted %d rows into the plant_tribes_taxon table for species name: %s." % str(species_name)) 269 self.log("Inserted %d rows into the plant_tribes_taxon table for species name: %s." % (i, str(species_name)))
270 270
271 def process_orthogroup_fasta_files(self): 271 def process_orthogroup_fasta_files(self):
272 """ 272 """
273 1. Analyze all of the scaffold .fna and .faa files for each clustering 273 1. Analyze all of the scaffold .fna and .faa files for each clustering
274 method to populate the aa_dict and dna_dict sequence dictionaries. 274 method to populate the aa_dict and dna_dict sequence dictionaries.