- for i in range(1,7):
- lane = eland_container.results[0][i]
- self.failUnlessEqual(lane.reads, 6)
- self.failUnlessEqual(lane.sample_name, "s")
- self.failUnlessEqual(lane.lane_id, i)
- self.failUnlessEqual(len(lane.mapped_reads), 17)
- self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
- self.failUnlessEqual(lane.match_codes['U0'], 3)
- self.failUnlessEqual(lane.match_codes['R0'], 2)
- self.failUnlessEqual(lane.match_codes['U1'], 1)
- self.failUnlessEqual(lane.match_codes['R1'], 9)
- self.failUnlessEqual(lane.match_codes['U2'], 0)
- self.failUnlessEqual(lane.match_codes['R2'], 12)
- self.failUnlessEqual(lane.match_codes['NM'], 1)
- self.failUnlessEqual(lane.match_codes['QC'], 0)
-
- # test scarf
- lane = eland_container.results[0][7]
- self.failUnlessEqual(lane.reads, 5)
- self.failUnlessEqual(lane.sample_name, 's')
- self.failUnlessEqual(lane.lane_id, 7)
- self.failUnlessEqual(lane.sequence_type, eland.SequenceLane.SCARF_TYPE)
-
- # test fastq
- lane = eland_container.results[0][8]
- self.failUnlessEqual(lane.reads, 3)
- self.failUnlessEqual(lane.sample_name, 's')
- self.failUnlessEqual(lane.lane_id, 8)
- self.failUnlessEqual(lane.sequence_type, eland.SequenceLane.FASTQ_TYPE)
+ for key in eland_container:
+ lane = eland_container[key]
+ if key.lane in [1,2,3,4,5,6]:
+ self.failUnlessEqual(lane.reads, 6)
+ self.failUnlessEqual(lane.sample_name, "s")
+ self.failUnlessEqual(lane.lane_id, key.lane)
+ self.failUnlessEqual(len(lane.mapped_reads), 17)
+ self.failUnlessEqual(lane.mapped_reads['hg18/chr5.fa'], 4)
+ self.failUnlessEqual(lane.match_codes['U0'], 3)
+ self.failUnlessEqual(lane.match_codes['R0'], 2)
+ self.failUnlessEqual(lane.match_codes['U1'], 1)
+ self.failUnlessEqual(lane.match_codes['R1'], 9)
+ self.failUnlessEqual(lane.match_codes['U2'], 0)
+ self.failUnlessEqual(lane.match_codes['R2'], 12)
+ self.failUnlessEqual(lane.match_codes['NM'], 1)
+ self.failUnlessEqual(lane.match_codes['QC'], 0)
+ elif key.lane == 7:
+ self.failUnlessEqual(lane.reads, 5)
+ self.failUnlessEqual(lane.sample_name, 's')
+ self.failUnlessEqual(lane.lane_id, 7)
+ self.failUnlessEqual(lane.sequence_type,
+ eland.SequenceLane.SCARF_TYPE)
+ elif key.lane == 8:
+ self.failUnlessEqual(lane.reads, 3)
+ self.failUnlessEqual(lane.sample_name, 's')
+ self.failUnlessEqual(lane.lane_id, 8)
+ self.failUnlessEqual(lane.sequence_type,
+ eland.SequenceLane.FASTQ_TYPE)