Mercurial > repos > greg > plant_tribes_add_scaffold

comparison add_scaffold.py @ 7:82822d1e5119 draft

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author greg
date Tue, 22 May 2018 10:15:49 -0400
parents 7973201f23e7
children 9b2ede3e7100
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6:7973201f23e7 7:82822d1e5119
73 sql = "SELECT id FROM plant_tribes_scaffold WHERE scaffold_id = '%s';" % scaffold_id 73 sql = "SELECT id FROM plant_tribes_scaffold WHERE scaffold_id = '%s';" % scaffold_id
74 cur = self.conn.cursor() 74 cur = self.conn.cursor()
75 cur.execute(sql) 75 cur.execute(sql)
76 try: 76 try:
77 cur.fetchone()[0] 77 cur.fetchone()[0]
78 self.stop_err("The scaffold %s has already been added to the database." % scaffold_id) 78 # The scaffold has been added to the database.
79 return False 79 return False
80 except: 80 except:
81 # The scaffold has not yet been added. 81 # The scaffold has not yet been added.
82 return True 82 return True
83 83
86 self.process_annot_dir() 86 self.process_annot_dir()
87 self.process_scaffold_config_files() 87 self.process_scaffold_config_files()
88 self.process_orthogroup_fasta_files() 88 self.process_orthogroup_fasta_files()
89 self.fh.flush() 89 self.fh.flush()
90 self.fh.close() 90 self.fh.close()
91 else:
92 self.stop_err("The scaffold %s has already been added to the database." % scaffold_id)
91 93
92 def process_annot_dir(self): 94 def process_annot_dir(self):
93 """ 95 """
94 First, parse all of the *.min_evalue.summary files in the 96 First, parse all of the *.min_evalue.summary files in the
95 ~/<scaffold_id>/annot directory (e.g., ~/22Gv1.1/annot) to populate 97 ~/<scaffold_id>/annot directory (e.g., ~/22Gv1.1/annot) to populate