Backporting makebed.py to v0.1.x branch

diff --git a/gaworkflow/util/makebed.py b/gaworkflow/util/makebed.py
new file mode 100755 (executable)
index 0000000..738b815
--- /dev/null
+++ b/gaworkflow/util/makebed.py
@@ -0,0 +1,67 @@
+"""
+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 \
+          (chromosome_prefix is not None and \
+             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