###########################################################################
#                                                                         #
# 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, os
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_remanei/cremanei.genedb" % cisRoot


def loadChromosomes(db, inPath, chromOutPath):
    crGenome = Genome("cremanei", dbFile=db)
    scontigList = os.listdir(inPath)
    for scontig in scontigList:
        seq = ''
        seqArray = []
        seqLen = 0
        inFile = open("%s/%s" % (inPath, scontig), "r")
        index = 0
        header = inFile.readline()
        chromID = header.strip()[1:]
        while header != "":
            seqArray = []
            seqLen = 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
                crGenome.addSequence(("cremanei", chromID), seq, "chromosome", str(seqLen))
                crGenome.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
                crGenome.addChromosomeEntry(chromID, outFileName, "file")

            index += 1
            header = currentLine

        inFile.close()


def loadGeneEntries(db, gffFile):
    crGenome = Genome("cremanei", 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] != "CDS":
            continue

        idfield = field[8].split('"')
        gid = idfield[1]
        geneID = ("cremanei", gid)
        geneStart[geneID] = int(field[3]) - 1
        geneStop[geneID] = int(field[4]) - 1
        sense = field[6]
        geneChrom[geneID] = field[0].strip()
        if sense == "+":
            geneSense[geneID] = "F"
        else:
            geneSense[geneID] = "R"

    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)
    crGenome.addGeneEntryBatch(geneEntries)


def loadFeatureEntries(db, gffFile):
    crGenome = Genome("cremanei", 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() != "coding_exon":
            continue

        gidrev = field[8].split('"')
        gid = gidrev[1]
        geneID = ("cremanei", gid)
        gidVersion = 1
        start = int(field[3]) - 1
        stop = int(field[4]) - 1
        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)
    crGenome.addFeatureEntryBatch(featureEntries)


def createDBFile(db):
    crGenome = Genome("cremanei", version="CR20050824",  dbFile=db)
    crGenome.createGeneDB(db)


def createDBindices(db):
    crGenome = Genome("cremanei", version="CR20050824", dbFile=db)
    crGenome.createIndices()


def buildCremaneiDB(db=geneDB):
    gffPath = "%s/download/cr01_wu_merged_gff" % cisRoot # using 20050824 version
    chromoPath = "%s/download/sctg_masked_seqs/seqs" % cisRoot
    chromoOutPath = "/C_remanei/"

    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" 
    loadChromosomes(db, chromoPath, chromoOutPath)

    print "Creating Indices"
    createDBindices(db)

    print "Finished creating database %s" % db