data = {}
for k, v in row.items():
data[k] = v
- lane = str(data['lane'])
- lanes.setdefault(lane, []).append(data)
+ library = str(data['library'])
+ lanes.setdefault(library, []).append(data)
result = []
- for lane, files in lanes.items():
+ for library, files in lanes.items():
if len(files) > 2:
errmsg = "Don't know what to do with more than 2 raw files"
raise ValueError(errmsg)
elif len(files) == 1:
is_paired = False
elif len(files) == 0:
- raise RuntimeError("Empty lane list discovered")
+ raise RuntimeError("Empty library list discovered")
files = self._format_filename(files, is_paired)
files = self._format_flowcell_type(files, is_paired)
files = self._format_read_length(files, is_paired)
PREFIX geoSoft: <http://www.ncbi.nlm.nih.gov/geo/info/soft2.html#>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
-select distinct ?lane ?filename, ?md5sum, ?file_type ?file_type_label ?flowcell_id ?read_length ?flowcell_type ?image_software ?image_version ?basecall_software ?basecall_version ?sequencer_model
+select distinct ?library ?filename, ?md5sum, ?file_type ?file_type_label ?flowcell_id ?read_length ?flowcell_type ?image_software ?image_version ?basecall_software ?basecall_version ?sequencer_model
WHERE {
<{{submission}}> ucscDaf:has_file ?file ;
submissionOntology:library ?library ;