--- /dev/null
+import glob
+import re
+import os
+
+s_comment = re.compile('^#')
+s_general_read_len = re.compile('^READ_LENGTH ')
+s_read_len = re.compile('^[1-8]+:READ_LENGTH ')
+
+s_firecrest = None
+
+def _four_digit_num_in_string(num):
+ if num < 0:
+ pass
+ elif num < 10:
+ return '000' + str(num)
+ elif num < 100:
+ return '00' + str(num)
+ elif num < 1000:
+ return '0' + str(num)
+ elif num < 10000:
+ return str(num)
+
+ msg = 'Invalid number: %s' % (num)
+ raise ValueError, msg
+
+def _two_digit_num_in_string(num):
+ if num < 0:
+ pass
+ elif num < 10:
+ return '0' + str(num)
+ elif num < 100:
+ return str(num)
+
+ msg = 'Invalid number: %s' % (num)
+ raise ValueError, msg
+
+
+# FIRECREST PATTERNS
+# _p2f(<pattern>, lane, tile, cycle)
+PATTERN_FIRECREST_INT = 's_%s_%s_%s_int.txt'
+PATTERN_FIRECREST_QCM = 's_%s_%s_%s_qcm.xml'
+PATTERN_FIRECREST_CLU1 = 's_%s_%s_%s_1_clu.txt'
+PATTERN_FIRECREST_CLU2 = 's_%s_%s_%s_2_clu.txt'
+PATTERN_FIRECREST_CLU3 = 's_%s_%s_%s_3_clu.txt'
+PATTERN_FIRECREST_CLU4 = 's_%s_%s_%s_4_clu.txt'
+
+# _p2f(<pattern>, lane, tile)
+PATTERN_FIRECREST_NSE = 's_%s_%s_nse.txt.gz'
+PATTERN_FIRECREST_POS = 's_%s_%s_pos.txt'
+PATTERN_FIRECREST_IDX = 's_%s_%s_idx.txt'
+
+
+# BUSTARD PATTERNS
+# _p2f(<pattern>, lane, tile)
+PATTERN_BUSTARD_SIG2 = 's_%s_%s_sig2.txt'
+PATTERN_BUSTARD_PRB = 's_%s_%s_prb.txt'
+
+
+
+# GERALD PATTERNS
+# _p2f(<pattern>, lane, tile)
+PATTERN_GERALD_ALL = 's_%s_%s_all.txt.tmp'
+PATTERN_GERALD_QRAW = 's_%s_%s_qraw.txt.tmp'
+PATTERN_GERALD_ALLPNGTMP = 's_%s_%s_all.tmp.png'
+PATTERN_GERALD_ALIGNTMP = 's_%s_%s_align.txt.tmp'
+PATTERN_GERALD_QVALTMP = 's_%s_%s_qval.txt.tmp'
+PATTERN_GERALD_SCORETMP = 's_%s_%s_score.txt.tmp'
+PATTERN_GERALD_PREALIGNTMP = 's_%s_%s_prealign.txt.tmp'
+PATTERN_GERALD_REALIGNTMP = 's_%s_%s_realign.txt.tmp'
+PATTERN_GERALD_RESCORETMP = 's_%s_%s_rescore.txt.tmp'
+PATTERN_GERALD_RESCOREPNG = 's_%s_%s_rescore.png'
+PATTERN_GERALD_ERRORSTMPPNG = 's_%s_%s_errors.tmp.png'
+PATTERN_GERALD_QCALTMP = 's_%s_%s_qcal.txt.tmp'
+PATTERN_GERALD_QVAL = 's_%s_%s_qval.txt'
+
+# _p2f(<pattern>, lane)
+PATTERN_GERALD_SEQPRE = 's_%s_seqpre.txt.tmp'
+PATTERN_GERALD_RESULTTMP = 's_%s_eland_result.txt.tmp'
+PATTERN_GERALD_SIGMEANS = 's_%s_Signal_Means.txt.tmp'
+PATTERN_GERALD_CALLPNG = 's_%s_call.png'
+PATTERN_GERALD_ALLPNG = 's_%s_all.png'
+PATTERN_GERALD_PERCENTALLPNG = 's_%s_percent_all.png'
+PATTERN_GERALD_PERCENTCALLPNG = 's_%s_percent_call.png'
+PATTERN_GERALD_PERCENTBASEPNG = 's_%s_percent_base.png'
+PATTERN_GERALD_FILTTMP = 's_%s_filt.txt.tmp'
+PATTERN_GERALD_FRAGTMP = 's_%s_frag.txt.tmp'
+PATTERN_GERALD_QREPORTTMP = 's_%s_qreport.txt.tmp'
+PATTERN_GERALD_QTABLETMP = 's_%s_qtable.txt.tmp'
+PATTERN_GERALD_QCALREPORTTMP = 's_%s_qcalreport.txt.tmp'
+PATTERN_GERALD_SEQUENCETMP = 's_%s_sequence.txt.tmp'
+PATTERN_GERALD_LANEFINISHED = 's_%s_finished.txt'
+
+
+
+def _p2f(pattern, lane, tile=None, cycle=None):
+ """
+ Converts a pattern plus info into file names
+ """
+
+ # lane, and cycle provided (INVALID)
+ if tile is None and cycle is not None:
+ msg = "Handling of cycle without tile is not currently implemented."
+ raise ValueError, msg
+
+ # lane, tile, cycle provided
+ elif cycle:
+ return pattern % (lane,
+ _four_digit_num_in_string(tile),
+ _two_digit_num_in_string(cycle))
+
+ # lane, tile provided
+ elif tile:
+ return pattern % (lane, _four_digit_num_in_string(tile))
+
+ # lane provided
+ else:
+ return pattern % (lane)
+
+
+
+class GARunStatus(object):
+
+ def __init__(self, conf_filepath):
+ """
+ Given an eland config file in the top level directory
+ of a run, predicts the files that will be generated
+ during a run and provides methods for retrieving
+ (completed, total) for each step or entire run.
+ """
+
+ self._conf_filepath = conf_filepath
+ self._base_dir, junk = os.path.split(conf_filepath)
+ self._image_dir = os.path.join(self._base_dir, 'Images')
+
+ self.lanes = []
+ self.lane_read_length = {}
+ self.tiles = None
+ self.cycles = None
+
+ self.status = {}
+ self.status['firecrest'] = {}
+ self.status['bustard'] = {}
+ self.status['gerald'] = {}
+
+ self._process_config()
+ self._count_tiles()
+ self._count_cycles()
+ self._generate_expected()
+
+
+ def _process_config(self):
+ """
+ Grabs info from self._conf_filepath
+ """
+ f = open(self._conf_filepath, 'r')
+
+ for line in f:
+
+ #Skip comment lines for now.
+ if s_comment.search(line):
+ continue
+
+ mo = s_general_read_len.search(line)
+ if mo:
+ read_length = int(line[mo.end():])
+ #Handle general READ_LENGTH
+ for i in range(1,9):
+ self.lane_read_length[i] = read_length
+
+ mo = s_read_len.search(line)
+ if mo:
+ read_length = int(line[mo.end():])
+ lanes, junk = line.split(':')
+
+ #Convert lanes from string of lanes to list of lane #s.
+ lanes = [ int(i) for i in lanes ]
+
+
+ for lane in lanes:
+
+ #Keep track of which lanes are being run.
+ if lane not in self.lanes:
+ self.lanes.append(lane)
+
+ #Update with lane specific read lengths
+ self.lane_read_length[lane] = read_length
+
+ self.lanes.sort()
+
+
+ def _count_tiles(self):
+ """
+ Count the number of tiles being used
+ """
+ self.tiles = len(glob.glob(os.path.join(self._image_dir,
+ 'L001',
+ 'C1.1',
+ 's_1_*_a.tif')))
+
+ def _count_cycles(self):
+ """
+ Figures out the number of cycles that are available
+ """
+ cycle_dirs = glob.glob(os.path.join(self._image_dir, 'L001', 'C*.1'))
+ cycle_list = []
+ for cycle_dir in cycle_dirs:
+ junk, c = os.path.split(cycle_dir)
+ cycle_list.append(int(c[1:c.find('.')]))
+
+ self.cycles = max(cycle_list)
+
+
+
+
+ def _generate_expected(self):
+ """
+ generates a list of files we expect to find.
+ """
+
+ firecrest = self.status['firecrest']
+ bustard = self.status['bustard']
+ gerald = self.status['gerald']
+
+
+ for lane in self.lanes:
+ for tile in range(1,self.tiles+1):
+ for cycle in range(1, self.cycles+1):
+
+ ##########################
+ # LANE, TILE, CYCLE LAYER
+
+ # FIRECREST
+ firecrest[_p2f(PATTERN_FIRECREST_INT, lane, tile, cycle)] = False
+
+ firecrest[_p2f(PATTERN_FIRECREST_QCM, lane, tile, cycle)] = False
+
+ firecrest[_p2f(PATTERN_FIRECREST_CLU1, lane, tile, cycle)] = False
+ firecrest[_p2f(PATTERN_FIRECREST_CLU2, lane, tile, cycle)] = False
+ firecrest[_p2f(PATTERN_FIRECREST_CLU3, lane, tile, cycle)] = False
+ firecrest[_p2f(PATTERN_FIRECREST_CLU4, lane, tile, cycle)] = False
+
+ ###################
+ # LANE, TILE LAYER
+
+ # FIRECREST
+
+ firecrest[_p2f(PATTERN_FIRECREST_NSE, lane, tile)] = False
+ firecrest[_p2f(PATTERN_FIRECREST_POS, lane, tile)] = False
+ firecrest[_p2f(PATTERN_FIRECREST_IDX, lane, tile)] = False
+
+
+ # BUSTARD
+ bustard[_p2f(PATTERN_BUSTARD_SIG2, lane, tile)] = False
+ bustard[_p2f(PATTERN_BUSTARD_PRB, lane, tile)] = False
+
+
+ # GERALD
+ gerald[_p2f(PATTERN_GERALD_ALL, lane, tile)] = False
+ gerald[_p2f(PATTERN_GERALD_QRAW, lane, tile)] = False
+ gerald[_p2f(PATTERN_GERALD_ALLPNGTMP, lane, tile)] = False
+ gerald[_p2f(PATTERN_GERALD_ALIGNTMP, lane, tile)] = False
+ gerald[_p2f(PATTERN_GERALD_QVALTMP, lane, tile)] = False
+ gerald[_p2f(PATTERN_GERALD_SCORETMP, lane, tile)] = False
+ gerald[_p2f(PATTERN_GERALD_PREALIGNTMP, lane, tile)] = False
+ gerald[_p2f(PATTERN_GERALD_REALIGNTMP, lane, tile)] = False
+ gerald[_p2f(PATTERN_GERALD_RESCORETMP, lane, tile)] = False
+ gerald[_p2f(PATTERN_GERALD_RESCOREPNG, lane, tile)] = False
+ gerald[_p2f(PATTERN_GERALD_ERRORSTMPPNG, lane, tile)] = False
+ gerald[_p2f(PATTERN_GERALD_QCALTMP, lane, tile)] = False
+ gerald[_p2f(PATTERN_GERALD_QVAL, lane, tile)] = False
+
+ ###################
+ # LANE LAYER
+
+ # GERALD
+ gerald[_p2f(PATTERN_GERALD_SEQPRE, lane)] = False
+ gerald[_p2f(PATTERN_GERALD_RESULTTMP, lane)] = False
+ gerald[_p2f(PATTERN_GERALD_SIGMEANS, lane)] = False
+ gerald[_p2f(PATTERN_GERALD_CALLPNG, lane)] = False
+ gerald[_p2f(PATTERN_GERALD_ALLPNG, lane)] = False
+ gerald[_p2f(PATTERN_GERALD_PERCENTALLPNG, lane)] = False
+ gerald[_p2f(PATTERN_GERALD_PERCENTCALLPNG, lane)] = False
+ gerald[_p2f(PATTERN_GERALD_PERCENTBASEPNG, lane)] = False
+ gerald[_p2f(PATTERN_GERALD_FILTTMP, lane)] = False
+ gerald[_p2f(PATTERN_GERALD_FRAGTMP, lane)] = False
+ gerald[_p2f(PATTERN_GERALD_QREPORTTMP, lane)] = False
+ gerald[_p2f(PATTERN_GERALD_QTABLETMP, lane)] = False
+ gerald[_p2f(PATTERN_GERALD_QCALREPORTTMP, lane)] = False
+ gerald[_p2f(PATTERN_GERALD_SEQUENCETMP, lane)] = False
+ gerald[_p2f(PATTERN_GERALD_LANEFINISHED, lane)] = False
+
+
+
+ #################
+ # LOOPS FINISHED
+
+ # FIRECREST
+ firecrest['offsets_finished.txt'] = False
+ firecrest['finished.txt'] = False
+
+ # BUSTARD
+ bustard['finished.txt'] = False
+
+ # GERALD
+ gerald['tiles.txt'] = False
+ gerald['FullAll.htm'] = False
+ gerald['All.htm.tmp'] = False
+ gerald['Signal_Means.txt.tmp'] = False
+ gerald['plotIntensity_for_IVC'] = False
+ gerald['IVC.htm.tmp'] = False
+ gerald['FullError.htm'] = False
+ gerald['FullPerfect.htm'] = False
+ gerald['Error.htm.tmp'] = False
+ gerald['Perfect.htm.tmp'] = False
+ gerald['Summary.htm.tmp'] = False
+ gerald['Tile.htm.tmp'] = False
+ gerald['finished.txt'] = False
+
+
+
+
+ def statusFirecrest(self):
+ """
+ returns (<completed>, <total>)
+ """
+ firecrest = self.status['firecrest']
+ total = len(firecrest)
+ completed = firecrest.values().count(True)
+
+ return (completed, total)
+
+
+ def statusBustard(self):
+ """
+ returns (<completed>, <total>)
+ """
+ bustard = self.status['bustard']
+ total = len(bustard)
+ completed = bustard.values().count(True)
+
+ return (completed, total)
+
+
+ def statusGerald(self):
+ """
+ returns (<completed>, <total>)
+ """
+ gerald = self.status['gerald']
+ total = len(gerald)
+ completed = gerald.values().count(True)
+
+ return (completed, total)
+
+
+ def statusTotal(self):
+ """
+ returns (<completed>, <total>)
+ """
+ #f = firecrest c = completed
+ #b = bustard t = total
+ #g = gerald
+ fc, ft = self.statusFirecrest()
+ bc, bt = self.statusBustard()
+ gc, gt = self.statusGerald()
+
+ return (fc+bc+gc, ft+bt+gt)
+
+
+ def updateFirecrest(self, filename):
+ """
+ Marks firecrest filename as being completed.
+ """
+ self.status['firecrest'][filename] = True
+
+
+ def updateBustard(self, filename):
+ """
+ Marks bustard filename as being completed.
+ """
+ self.status['bustard'][filename] = True
+
+
+ def updateGerald(self, filename):
+ """
+ Marks gerald filename as being completed.
+ """
+ self.status['gerald'][filename] = True
projects / htsworkflow.git / commitdiff