def mainFlow(folderName , mummerLink, pickupname, mapcontigsname):
print "Go Bears! ! !"
print "pickupname, mapcontigsname", pickupname, mapcontigsname
if not pickupname in ["noEmbed.fasta", "improved.fasta", "improved2.fasta"]:
print "NonRedundantResolver RemoveEmbedded"
nonRedundantResolver.removeEmbedded(folderName , mummerLink)
if not pickupname in ["improved.fasta", "improved2.fasta"]:
print "OverlapResolver FetchSuccessor"
overlapResolver.fetchSuccessor(folderName , mummerLink)
print "OverlapResolver FormSeqGraph"
overlapResolver.formSeqGraph(folderName , mummerLink)
if not pickupname in ["improved2.fasta"]:
print "GapFiller FillGap"
gapFiller.fillGap(folderName , mummerLink)
print "TwoRepeatOneBridgeSolver XPhased"
twoRepeatOneBridgeSolver.xPhased(folderName , mummerLink)
# ECReduction(folderName , mummerLink )
# compareWithReference(folderName , mummerLink)
if mapcontigsname != None:
print "HouseKeeper PerformMapping"
houseKeeper.performMapping(folderName, mummerLink, mapcontigsname)
print "<3 Do cool things that matter <3"
def mainFlow(folderName , mummerLink, pickupname, mapcontigsname):
print "Go Bears! ! !"
print "pickupname, mapcontigsname", pickupname, mapcontigsname
if not pickupname in ["noEmbed.fasta", "improved.fasta", "improved2.fasta"]:
nonRedundantResolver.removeEmbedded(folderName , mummerLink)
if not pickupname in ["improved.fasta", "improved2.fasta"]:
overlapResolver.fetchSuccessor(folderName , mummerLink)
overlapResolver.formSeqGraph(folderName , mummerLink)
if not pickupname in ["improved2.fasta"]:
gapFiller.fillGap(folderName , mummerLink)
twoRepeatOneBridgeSolver.xPhased(folderName , mummerLink)
# ECReduction(folderName , mummerLink )
# compareWithReference(folderName , mummerLink)
IORobot.fillInMissed(folderName, mummerLink, houseKeeper.globalContigName, "noEmbedtmp.fasta", "noEmbed.fasta")
IORobot.fillInMissed(folderName, mummerLink, houseKeeper.globalContigName, "improvedtmp.fasta", "improved.fasta")
IORobot.fillInMissed(folderName, mummerLink, houseKeeper.globalContigName, "improved2tmp.fasta", "improved2.fasta")
IORobot.fillInMissed(folderName, mummerLink, houseKeeper.globalContigName, "improved3tmp.fasta", "improved3.fasta")
if mapcontigsname != None:
houseKeeper.performMapping(folderName, mummerLink, mapcontigsname)
print "<3 Do cool things that matter <3"
def mainFlow(folderName, mummerLink, pickupname, mapcontigsname):
print "Go Bears! ! !"
print "pickupname, mapcontigsname", pickupname, mapcontigsname
if not pickupname in [
"noEmbed.fasta", "improved.fasta", "improved2.fasta"
]:
nonRedundantResolver.removeEmbedded(folderName, mummerLink)
if not pickupname in ["improved.fasta", "improved2.fasta"]:
overlapResolver.fetchSuccessor(folderName, mummerLink)
overlapResolver.formSeqGraph(folderName, mummerLink)
if not pickupname in ["improved2.fasta"]:
gapFiller.fillGap(folderName, mummerLink)
twoRepeatOneBridgeSolver.xPhased(folderName, mummerLink)
# ECReduction(folderName , mummerLink )
# compareWithReference(folderName , mummerLink)
IORobot.fillInMissed(folderName, mummerLink, houseKeeper.globalContigName,
"noEmbedtmp.fasta", "noEmbed.fasta")
IORobot.fillInMissed(folderName, mummerLink, houseKeeper.globalContigName,
"improvedtmp.fasta", "improved.fasta")
IORobot.fillInMissed(folderName, mummerLink, houseKeeper.globalContigName,
"improved2tmp.fasta", "improved2.fasta")
IORobot.fillInMissed(folderName, mummerLink, houseKeeper.globalContigName,
"improved3tmp.fasta", "improved3.fasta")
if mapcontigsname != None:
houseKeeper.performMapping(folderName, mummerLink, mapcontigsname)
print "<3 Do cool things that matter <3"
def mainFlow(folderName, mummerLink, pickupname, mapcontigsname):
print "Go Bears! ! !"
print "pickupname, mapcontigsname", pickupname, mapcontigsname
if not pickupname in [
"noEmbed.fasta", "improved.fasta", "improved2.fasta"
]:
print "NonRedundantResolver RemoveEmbedded"
nonRedundantResolver.removeEmbedded(folderName, mummerLink)
if not pickupname in ["improved.fasta", "improved2.fasta"]:
print "OverlapResolver FetchSuccessor"
overlapResolver.fetchSuccessor(folderName, mummerLink)
print "OverlapResolver FormSeqGraph"
overlapResolver.formSeqGraph(folderName, mummerLink)
if not pickupname in ["improved2.fasta"]:
print "GapFiller FillGap"
gapFiller.fillGap(folderName, mummerLink)
print "TwoRepeatOneBridgeSolver XPhased"
twoRepeatOneBridgeSolver.xPhased(folderName, mummerLink)
# ECReduction(folderName , mummerLink )
# compareWithReference(folderName , mummerLink)
if mapcontigsname != None:
print "HouseKeeper PerformMapping"
houseKeeper.performMapping(folderName, mummerLink, mapcontigsname)
print "<3 Do cool things that matter <3"