def test(): fname = "test/Firre.fasta" handle = open(fname,'r') fastaIter = sequencelib.FastaIterator(handle) mySeq = fastaIter.next() tiles = scanSequence(mySeq['sequence'],mySeq['name']) print len(tiles) # Remove duplicate tile sequences tiles = findUnique(tiles) # for tile in tiles: # print "%s\t%0.2f\t%d" % (tile,tile.GC,len(tile)) print len(tiles)
def main():
#######################
# Variables
#######################
universalPrimers = {
'M13 forward sequencing primer (-20)': 'GTAAAACGACGGCCAGT',
'M13 forward sequencing primer (-40)': 'GTTTTCCCAGTCACGAC',
'M13 forward sequencing primer (-47)': 'CGCCAGGGTTTTCCCAGTCACGAC',
'M13 reverse sequencing primer (-24)': 'AACAGCTATGACCATG',
'M13 reverse sequencing primer (-48)': 'AGCGGATAACAATTTCACACAGGA',
'T3 promoter': 'ATTAACCCTCACTAAAGGGA',
'T7 universal primer': 'TAATACGACTCACTATAGGG',
'T7 Terminator': 'GCTAGTTATTGCTCAGCGG',
'SP6 promoter': 'CATACGATTTAGGTGACACTATAG',
'SP6 universal primer': 'ATTTAGGTGACACTATAG',
'VF2': 'tgccacctgacgtctaagaa',
'VR': 'attaccgcctttgagtgagc'
}
MPRATags = {
'prefix': 'ACTGGCCGCTTCACTG',
'suffix': 'GGTACCTCTAGA@AGATCGGAAGAGCGTCG'
}
maxTileSize = 150
tileStep = 1
tagLength = 10
numTagsPerTile = 5
prefix = MPRATags['prefix']
suffix = MPRATags['suffix']
sites = "KpnI,XbaI,SfiI"
#Argument handling
try:
opts,args = getopt.getopt(sys.argv[1:],"ho:vp:s:l:w:te:n:r:",["help","output=","verbose","prefix=","suffix=","max-tile-length=","tile-step=","tag","tag-length=","num-tags-per-tile=","restriction-sites="])
except getopt.GetoptError as err:
print(err)
usage()
sys.exit(2)
output = None
verbose = False
for o,a in opts:
if o == "-v":
verbose = True
elif o in ("-h","--help"):
usage()
sys.exit()
elif o in ("-o","--output"):
output = a
elif o in ("-p","--prefix"):
if onlyNucleic(a):
prefix = a
else:
raise(TileError,"Prefix is not a valid nucleic acid sequence.")
elif o in ("-s","--suffix"):
if onlyNucleic(a):
suffix = a
else:
raise(TileError,"Suffix is not a valid nucleic acid sequence.")
elif o in ("-l","--max-tile-length"):
maxTileSize = int(a)
elif o in ("-w","--tile-step"):
tileStep = int(a)
elif o in ("-t","--tag"):
addTag = True
elif o in ("-e","--tag-length"):
tagLength = int(a)
elif o in ("-n","--num-tags-per-tile"):
numTagsPerTile = int(a)
elif o in ("-r","--restriction-sites"):
sites = a.strip()
if sites == "":
sites = None
else:
assert False, "Unhandled option"
# Grab fname as remainder argument
try:
fname = str(args[0])
handle = open(fname,'r')
except:
usage()
sys.exit(2)
#print fname
#Estimate prefix and suffix length
prefixLength = estimateAffixLength(prefix,tagLength)
suffixLength = estimateAffixLength(suffix,tagLength)
#Find window size
tileSize = maxTileSize-prefixLength-suffixLength
#Fetch all tile sequences
fastaIter = sequencelib.FastaIterator(handle)
tiles = []
for mySeq in fastaIter:
#Warn about masked regions
if sites != None:
warnRestrictionSites(mySeq['sequence'],mySeq['name'],sites)
#Get tiles from sequence
tmpTiles = scanSequence(mySeq['sequence'],mySeq['name'],tileStep=tileStep,tileSize=tileSize)
tiles += tmpTiles
# Remove duplicate tile sequences
tiles = findUnique(tiles)
# Check tiles for restriction sites
if sites != None:
cleanTiles = set()
for tile in tiles:
if hasRestrictionSites(tile.sequence, sites):
continue
else:
cleanTiles.add(tile)
tiles = list(cleanTiles)
#determine number of tags needed
numTagsReq = len(tiles) * numTagsPerTile
tags = buildTags(numTagsReq,tagLength,sites=sites)
assert len(tags) == len(tiles) * numTagsPerTile
#Create numTagsPerTile tiles for each sequence
tmpTiles = set()
#Add prefix, suffix, and tag
for i in xrange(len(tiles)):
for j in xrange(numTagsPerTile):
tmpTile = copy.copy(tiles[i])
tmpTile.name = "%s:%d" % (tmpTile.name,j)
tmpTile.prefix = prefix
tmpTile.suffix = suffix
tmpTile.tag = tags.pop()
tmpTiles.add(tmpTile)
tiles = list(tmpTiles)
tiles.sort()
#Just for QC
#for i in xrange(10):
outputTable(tiles)
print >>sys.stderr, "There are a total of %d unique tiles" % len(tiles)