- patterns = ['s_%d_eland_result.txt',
- 's_%d_eland_result.txt.bz2',
- 's_%d_eland_result.txt.gz',
- 's_%d_eland_extended.txt',
- 's_%d_eland_extended.txt.bz2',
- 's_%d_eland_extended.txt.gz',
- 's_%d_eland_multi.txt',
- 's_%d_eland_multi.txt.bz2',
- 's_%d_eland_multi.txt.gz',]
-
- for lane_id in lane_ids:
- for p in patterns:
- pathname = check_for_eland_file(basedir, lane_id, p)
- if pathname is not None:
- break
- else:
- continue
- # yes the lane_id is also being computed in ElandLane._update
- # I didn't want to clutter up my constructor
- # but I needed to persist the sample_name/lane_id for
- # runfolder summary_report
- path, name = os.path.split(pathname)
- logging.info("Adding eland file %s" %(name,))
- split_name = name.split('_')
- lane_id = int(split_name[1])
-
- if genome_maps is not None:
- genome_map = genome_maps[lane_id]
- elif gerald is not None:
- genome_dir = gerald.lanes[lane_id].eland_genome
- genome_map = build_genome_fasta_map(genome_dir)
- else:
- genome_map = {}
+ patterns = ['s_%s_eland_result.txt',
+ 's_%s_eland_result.txt.bz2',
+ 's_%s_eland_result.txt.gz',
+ 's_%s_eland_extended.txt',
+ 's_%s_eland_extended.txt.bz2',
+ 's_%s_eland_extended.txt.gz',
+ 's_%s_eland_multi.txt',
+ 's_%s_eland_multi.txt.bz2',
+ 's_%s_eland_multi.txt.gz',]
+
+ for end in ends:
+ for lane_id in lane_ids:
+ for p in patterns:
+ pathname = check_for_eland_file(basedir, p, lane_id, end)
+ if pathname is not None:
+ break
+ else:
+ continue
+ # yes the lane_id is also being computed in ElandLane._update
+ # I didn't want to clutter up my constructor
+ # but I needed to persist the sample_name/lane_id for
+ # runfolder summary_report
+ path, name = os.path.split(pathname)
+ logging.info("Adding eland file %s" %(name,))
+ # split_name = name.split('_')
+ # lane_id = int(split_name[1])
+
+ if genome_maps is not None:
+ genome_map = genome_maps[lane_id]
+ elif gerald is not None:
+ genome_dir = gerald.lanes[lane_id].eland_genome
+ genome_map = build_genome_fasta_map(genome_dir)
+ else:
+ genome_map = {}