scripts/library.py

   1 import datetime
   2 from optparse import OptionParser
   3 from pprint import pprint
   4 import sqlite3
   5 import sys
   6 import time
   7
   8 class fctracker:
   9     def __init__(self):
  10         self.conn = sqlite3.connect('fctracker.db')
  11         self._get_library()
  12         self._get_species()
  13
  14     def _make_dict_from_table(self, table_name, pkey_name):
  15         table = {}
  16         c = self.conn.cursor()
  17         c.execute('select * from %s;' % (table_name))
  18         # extract just the field name
  19         description = [ f[0] for f in c.description]
  20         for row in c:
  21             row_dict = dict(zip(description, row))
  22             table[row_dict[pkey_name]] = row_dict
  23         c.close()
  24         return table
  25
  26     def _get_library(self):
  27         self.library = self._make_dict_from_table(
  28                          'fctracker_library',
  29                          'library_id')
  30
  31
  32     def _get_species(self):
  33         self.species = self._make_dict_from_table(
  34                          'fctracker_species',
  35                          'id'
  36                        )
  37
  38     def _get_flowcells(self, where=None):
  39         if where is None:
  40             where = ""
  41         self.flowcells = {}
  42         c = self.conn.cursor()
  43         c.execute('select * from fctracker_flowcell %s;' % (where))
  44         # extract just the field name
  45         description = [ f[0] for f in c.description ]
  46         for row in c:
  47             row_dict = dict(zip(description, row))
  48             for lane in [ 'lane_%d_library' % (i) for i in range(1,9) ]:
  49                 lane_library = self.library[row_dict[lane+"_id"]]
  50                 species_id = lane_library['library_species_id']
  51                 lane_library['library_species'] = self.species[species_id]
  52                 row_dict[lane] = lane_library
  53             # some useful parsing
  54             run_date = time.strptime(row_dict['run_date'],  '%Y-%m-%d %H:%M:%S')
  55             run_date = datetime.datetime(*run_date[:6])
  56             row_dict['run_date'] = run_date
  57             self.flowcells[row_dict['flowcell_id']] = row_dict
  58         return self.flowcells
  59
  60
  61 def flowcell_gone(name):
  62     if 'failed' in name:
  63         return True
  64     if 'deleted' in name:
  65         return True
  66     if 'not run' in name:
  67         return True
  68     return False
  69
  70 def report(flowcells):
  71     flowcell_list = []
  72     for key, cell in flowcells.items():
  73         flowcell_list.append( (cell['run_date'], key) )
  74     flowcell_list.sort()
  75     for run_date, flowcell_id in flowcell_list:
  76         cell = flowcells[flowcell_id]
  77         if flowcell_gone(cell['flowcell_id']):
  78             continue
  79         #pprint(cell)
  80         #print cell['flowcell_id'], cell['run_date']
  81         for l in range(1,9):
  82             lane = 'lane_%d' % (l)
  83             print cell['run_date'].strftime('%y-%b-%d'),
  84             print cell['flowcell_id'],
  85             #print "  ",
  86             print l,cell['%s_library'%(lane)]['library_name'],
  87             print '(%s)' % (cell['%s_library_id'%(lane)]),
  88             print cell['%s_library'%(lane)]['library_species']['scientific_name']
  89
  90 def make_parser():
  91     """
  92     Make parser
  93     """
  94     parser = OptionParser()
  95     parser.add_option("-w", "--where", dest="where",
  96                       help="add a where clause",
  97                       default=None)
  98     return parser
  99
 100 def main(argv=None):
 101     if argv is None:
 102         argv = []
 103     parser = make_parser()
 104
 105     opt, args = parser.parse_args(argv)
 106
 107     fc = fctracker()
 108     cells = fc._get_flowcells(opt.where)
 109
 110     report(cells)
 111     return 0
 112
 113 if __name__ == "__main__":
 114     sys.exit(main(sys.argv[1:]))