###########################################################################
#                                                                         #
# C O P Y R I G H T   N O T I C E                                         #
#  Copyright (c) 2003-10 by:                                              #
#    * California Institute of Technology                                 #
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#
# data for Caenorhaditis remanei
import string
from cistematic.genomes import Genome
from os import environ

if environ.get("CISTEMATIC_ROOT"):
    cisRoot = environ.get("CISTEMATIC_ROOT") 
else:
    cisRoot = "/proj/genome"

geneDB = "%s/C_brenneri/cbrenneri.genedb" % cisRoot


def loadChromosome(db, chromPath, chromOutPath):
    seqArray = []
    seqLen = 0
    cbGenome = Genome("cbrenneri", dbFile=db)
    inFile = open(chromPath, "r")
    header = inFile.readline()
    while header != "":
        seqArray = []
        seqLen = 0
        chromHeader = header.strip()[1:].split()
        chromID = chromHeader[0]
        currentLine = inFile.readline()

        while currentLine != "" and currentLine[0] != ">":
            lineSeq = currentLine.strip()
            seqLen += len(lineSeq)
            seqArray.append(lineSeq)
            currentLine = inFile.readline()

        seq = string.join(seqArray, "")
        if seqLen < 100000:
            print "Added contig %s to database" % chromID
            cbGenome.addSequence(("cbrenneri", chromID), seq, "chromosome", str(seqLen))
            cbGenome.addChromosomeEntry(chromID, chromID, "db")
        else:
            outFileName = "%s%s.bin" % (chromOutPath, chromID)
            outFile = open( "%s%s" % (cisRoot, outFileName), "w")
            outFile.write(seq)
            outFile.close()
            print "Added contig file %s to database" % outFileName
            cbGenome.addChromosomeEntry(chromID, outFileName, "file")

        header = currentLine

    inFile.close()


def loadGeneEntries(db, gffFile):
    cbGenome = Genome("cbrenneri", dbFile=db)
    geneFile = open(gffFile, "r")
    geneStart = {}
    geneStop = {}
    geneChrom = {}
    geneSense = {}
    geneEntries = []
    for line in geneFile:
        if line[0] == "#":
            continue

        if line[0] == "\n":
            continue

        field = line[:-1].split("\t")
        if field[2] != "stop_codon" and field[2] != "start_codon":
            continue

        idfield = field[8].split('"')
        gid = idfield[1]
        geneID = ("cbrenneri", gid)
        sense = field[6]
        geneChrom[geneID] = field[0].strip()
        if sense == "+":
            geneSense[geneID] = "F"
        else:
            geneSense[geneID] = "R"

        if field[2] == "start_codon":
            if sense == "+":
                geneStart[geneID] = int(field[3])
            else:
                geneStart[geneID] = int(field[4])
        else:
            if sense == "+":
                geneStop[geneID] = int(field[3])
            else:
                geneStop[geneID] = int(field[4])

    for geneID in geneStart:
        if geneID not in geneStop:
            print "geneID %s not in geneStop - skipping" % str(geneID)
            continue

        geneEntries.append((geneID, geneChrom[geneID], geneStart[geneID], geneStop[geneID], geneSense[geneID], "CDS", 1))

    print "Adding %d gene entries" % len(geneEntries)
    cbGenome.addGeneEntryBatch(geneEntries)


def loadFeatureEntries(db, gffFile):
    cbGenome = Genome("cbrenneri", dbFile=db)
    featureFile = open(gffFile, "r")
    featureEntries = []
    for line in featureFile:
        if line[0] == "#":
            continue

        if line[0] == "\n":
            continue

        field = line.split("\t")
        if field[2].strip() != "CDS":
            continue

        gidrev = field[8].split('"')
        gid = gidrev[1]
        geneID = ("cbrenneri", gid)
        gidVersion = 1

        start = int(field[3])
        stop = int(field[4])

        sense = field[6]
        chrom = field[0].strip()
        if sense == "+":
            sense = "F"
        else:
            sense = "R"

        featureEntries.append((geneID, gidVersion, chrom, start, stop, sense, "CDS"))

    print "Adding %d feature entries" % len(featureEntries)
    cbGenome.addFeatureEntryBatch(featureEntries)


def createDBFile(db):
    cbGenome = Genome("cbrenneri", version="PB2801_001",  dbFile=db)
    cbGenome.createGeneDB(db)


def createDBindices(db):
    cbGenome = Genome("cbrenneri", version="PB2801_001", dbFile=db)
    cbGenome.createIndices()


def buildCbrenneriDB(db=geneDB):
    gffPath = "%s/download/PB2801_2007feb09.gff" % cisRoot # using EMS special version
    chromoPath = "%s/download/PB2801_supercontigs.fa" % cisRoot
    chromoOutPath = "/C_brenneri/"

    print "Creating database %s" % db
    createDBFile(db)

    print "Adding gene entries"
    loadGeneEntries(db, gffPath)

    print "Adding feature entries"
    loadFeatureEntries(db, gffPath)

    print "Loading genomic sequence" 
    loadChromosome(db, chromoPath, chromoOutPath)

    print "Creating Indices"
    createDBindices(db)

    print "Finished creating database %s" % db