+"""
+Utility functions to make bedfiles.
+"""
+import os
+
+def make_bed_from_eland_stream(instream, outstream, name, description, chromosome_prefix='chr'):
+ """
+ read an eland result file from instream and write a bedfile to outstream
+ """
+ # indexes into fields in eland_result.txt file
+ SEQ = 1
+ CHR = 6
+ START = 7
+ SENSE = 8
+ # map eland_result.txt sense
+ sense_map = { 'F': '+', 'R': '-'}
+ sense_color = { 'F': '0,0,255', 'R': '255,255,0' }
+ # provide default track names
+ if name is None: name = "track"
+ if description is None: description = "eland result file"
+ bed_header = 'track name="%s" description="%s" visibility=4 itemRgb="ON"'
+ bed_header += os.linesep
+ outstream.write(bed_header % (name, description))
+
+ for line in instream:
+ fields = line.split()
+ # we need more than the CHR field, and it needs to match a chromosome
+ if len(fields) <= CHR or fields[CHR][:3] != chromosome_prefix:
+ continue
+ start = fields[START]
+ stop = int(start) + len(fields[SEQ])
+ chromosome, extension = fields[CHR].split('.')
+ assert extension == "fa"
+ outstream.write('%s %s %d read 0 %s - - %s%s' % (
+ chromosome,
+ start,
+ stop,
+ sense_map[fields[SENSE]],
+ sense_color[fields[SENSE]],
+ os.linesep
+ ))
+
+def make_description(database, flowcell_id, lane):
+ """
+ compute a bedfile name and description from the fctracker database
+ """
+ from gaworkflow.util.fctracker import fctracker
+
+ fc = fctracker(database)
+ cells = fc._get_flowcells("where flowcell_id='%s'" % (flowcell_id))
+ if len(cells) != 1:
+ raise RuntimeError("couldn't find flowcell id %s" % (flowcell_id))
+ lane = int(lane)
+ if lane < 1 or lane > 8:
+ raise RuntimeError("flowcells only have lanes 1-8")
+
+ name = "%s-%s" % (flowcell_id, lane)
+
+ cell_id, cell = cells.items()[0]
+ assert cell_id == flowcell_id
+
+ cell_library_id = cell['lane_%d_library_id' %(lane,)]
+ cell_library = cell['lane_%d_library' %(lane,)]
+ description = "%s-%s" % (cell_library['library_name'], cell_library_id)
+ return name, description