print >>sys.stderr, "To detect the conservation among orthologs,\

use repetitions as the query and its related orthologs as db(after \

makeblastdb). "

if len(sys.argv) != 3:

print >>sys.stderr,'Using python %s repfile dbpath/' % sys.argv[0]

sys.exit(0)

#-------------------------------------

file = sys.argv[1]

if file.find('LCSs') != -1:

label = '.LCSs'

elif file.find('HCSs') != -1:

label = '.HCSs'

#patched at 20110922. Before not give the inital value to [label].

#So it will give an error when dealing with non 'LCSs' and 'HCSs'

#files.

else:

label = ''

noOrtho = 0

path = sys.argv[2]

repDict = {}

readRep(sys.argv[1], repDict)

for locus, valueL in repDict.items():

tmppath = path + locus

#print tmppath

if not os.path.exists(tmppath):

noOrtho += 1

continue

#-------------------------------

midlen = 30

short = locus+label+'.short'

long = locus +label+'.long'

fhshort = open(short, 'w')

fhlong = open(long, 'w')

group = 0

for groupD in valueL:

group += 1

tmpDict = {}

groupDKeyL = groupD.keys()

groupDKeyL.sort()

for pos in groupDKeyL:

seq = groupD[pos]

if seq not in tmpDict:

tmpDict[seq] = [str(pos[0])]

else:

tmpDict[seq].append(str(pos[0]))

#-------------------------------------------

tmpDictKeyL = tmpDict.keys()

tmpDictKeyL.sort()

for seq in tmpDictKeyL:

lenseq = len(seq)

pos = ':'.join(tmpDict[seq])

if lenseq <= midlen:

print >>fhshort, '>%s.%s.%s\n%s' % \

(locus, str(group), pos, seq)

else:

print >>fhlong, '>%s.%s.%s\n%s' % \

(locus, str(group), pos, seq)

#--------END one group------------------------------

fhshort.close()

fhlong.close()

cmdshort = ' '.join(('psiblast -query', short, '-db', tmppath, \

'-out', short+'.out', '-num_iterations 5','-evalue 20000',\

'-matrix PAM30', '-comp_based_stats 0', '-word_size 2'))

cmdlong = ' '.join(('psiblast -query', long, '-db', tmppath, \

'-out', long+'.out', '-num_iterations 5'))

os.system(cmdshort)

os.system(cmdlong)

cmdshort = ' '.join(('psiblast -query', short, '-db', tmppath, \

'-out', short+'.table', '-num_iterations 5','-evalue 20000',\

'-matrix PAM30', '-comp_based_stats 0', '-word_size 2',

'-outfmt 7'))

cmdlong = ' '.join(('psiblast -query', long, '-db', tmppath, \

'-out', long+'.table', '-num_iterations 5', '-outfmt 7'))

#print cmd

#break

os.system(cmdshort)

os.system(cmdlong)

#------------END one locus

print noOrtho