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()