diff usearch_map_reads_to_otu/scripts/uc.py @ 0:c10d09023766 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/usearch_map_reads_to_otu/scripts/uc.py	Thu May 29 00:51:18 2014 -0400
@@ -0,0 +1,149 @@
+import re
+import sys
+import progress
+
+# Tab-separated fields:
+# 1=Type, 2=ClusterNr, 3=SeqLength or ClusterSize, 4=PctId, 5=Strand, 6=QueryStart, 7=SeedStart, 8=Alignment, 9=Label
+# Record types (field 1): L=LibSeed, S=NewSeed, H=Hit, R=Reject, D=LibCluster, C=NewCluster, N=NotMatched
+# For C and D types, PctId is average id with seed.
+# QueryStart and SeedStart are zero-based relative to start of sequence.
+# If minus strand, SeedStart is relative to reverse-complemented seed.
+
+MaxError = -1
+
+Type = '?'
+ClusterNr = -1
+Size = -1
+PctId = -1.0
+LocalScore = -1.0
+Evalue = -1.0
+Strand = '.'
+QueryStart = -1
+SeedStart = -1
+Alignment = ""
+QueryLabel = ""
+TargetLabel = ""
+FileName = "?"
+Line = ""
+
+def Die(s):
+	print >> sys.stderr, "*** ERROR ***", s, sys.argv
+	sys.exit(1)
+
+def ProgressFile(File, FileSize):
+#	if not sys.stderr.isatty():
+#	return
+	Pos = File.tell()
+	Pct = (100.0*Pos)/FileSize
+	Str = "%s %5.1f%%\r" % (FileName, Pct)
+	sys.stderr.write(Str)
+
+def Progress(i, N):
+#	if not sys.stderr.isatty():
+	return
+	Pct = (100.0*i)/N
+	Str = "%5.1f%%\r" % Pct
+	sys.stderr.write(Str)
+
+def PrintLine():
+	print Line
+
+def ParseRec(Line):
+	global Type
+	global ClusterNr
+	global Size
+	global PctId
+	global Strand
+	global QueryStart
+	global SeedStart
+	global Alignment
+	global QueryLabel
+	global TargetLabel
+	global LocalScore
+	global Evalue
+	
+	Fields = Line.split("\t")
+	N = len(Fields)
+	if N != 9 and N != 10:
+		Die("Expected 9 or 10 fields in .uc record, got: " + Line)
+	Type = Fields[0]
+	
+	try:
+		ClusterNr = int(Fields[1])
+	except:
+		ClusterNr = -1
+		
+	try:	
+		Size = int(Fields[2])
+	except:
+		Size = -1
+
+	Fields2 = Fields[3].split('/')
+	LocalScore = -1.0
+	Evalue = -1.0
+	if len(Fields2) == 3:
+		try:
+			PctId = float(Fields2[0])
+			LocalScore = float(Fields2[1])
+			Evalue = float(Fields2[2])
+		except:
+			PctId = -1.0
+	else:
+		try:
+			PctId = float(Fields[3])
+		except:
+			PctId = -1.0
+
+	Strand = Fields[4]
+	
+	try:
+		QueryStart = int(Fields[5])
+	except:
+		QueryStart = -1
+
+	try:
+		SeedStart = int(Fields[6])
+	except:
+		SeedStart = -1
+
+	Alignment = Fields[7]
+	QueryLabel = Fields[8]
+	
+	if len(Fields) > 9:
+		TargetLabel = Fields[9]
+
+def GetRec(File, OnRecord):
+	global Line
+	while 1:
+		Line = File.readline()
+		if len(Line) == 0:
+			return 0
+		if Line[0] == '#':
+			continue
+		Line = Line.strip()
+		if len(Line) == 0:
+			return 1
+		ParseRec(Line)
+		Ok = OnRecord()
+		if Ok != None and Ok == 0:
+			return 0
+		return 1
+
+def ReadRecs(argFileName, OnRecord, ShowProgress = True):
+	return ReadFile(argFileName, OnRecord, ShowProgress)
+
+def GetRecs(argFileName, OnRecord, ShowProgress = True):
+	return ReadFile(argFileName, OnRecord, ShowProgress)
+
+def ReadFile(argFileName, OnRecord, ShowProgress = True):
+	global FileName
+	FileName = argFileName
+	File = open(FileName)
+
+	if ShowProgress:
+		progress.InitFile(File, FileName)
+	while GetRec(File, OnRecord):
+		if ShowProgress:
+			progress.File()
+	if ShowProgress:
+		progress.FileDone()