usage = "usage: %prog [options] [ 1> matches.table.txt ]"

desc = """Blast has to be run with -m8."""

epilog = ""

parser = OptionParser( usage=usage,version="%prog 1.0",description=desc,epilog=epilog )

parser.add_option("-i", dest="infile", default="",

help="blast output")

parser.add_option("-j", dest="query", default="",

help="query fasta")

parser.add_option("-k", dest="target", default="",

help="target fasta")

parser.add_option("-e", dest="evalue", default=1e-05, type=float,

help="E-value cut-off [%default]" )

parser.add_option("-q", dest="qcov", default=0.3, type=float,

help="query coverage [%default]")

parser.add_option("-t", dest="tcov", default=0, type=float,

help="target coverage [%default]")

#parser.add_option("-s", dest="tsplit", default=3, type=int,

# help="split target name by '|' and print s postition [%default]")

parser.add_option("-v", dest="verbose", default=False, action="store_true" )

( o, fnames ) = parser.parse_args()

if o.verbose:

sys.stderr.write( "Options: %s\nArgs: %s\n" % ( o,fnames ) )

#check files

for fn in ( o.infile,o.query,o.target ):

if not fn:

parser.error( "Provide input file!" )

if not os.path.isfile( fn ):

parser.error( "No such file: %s" % fn )

#queries = get_

#get sizes of queries and targets

q2len = get_contig2size( o.query )

t2len = get_contig2size( o.target )

#get significant matches

matches = parse_blast( o.infile,q2len,t2len,o.evalue,0,0,o.verbose )

#parse matches

matches_collapsed = {}

print "#Query\tTarget\tIndentity\tAlignment length\tMismatches\tGaps\tQuery start\tQuery end\tTarget start\tTarget end\tE-value\tScore\tQuery aligned [%]\tTarget aligned [%]\t"

for qlocus,tlocus,identity,algLen,mismatches,gaps,qstart,qend,tstart,tend,e,score,qcov,tcov in matches:

#add qlocus to matches

if qlocus not in matches_collapsed:

matches_collapsed[qlocus]={}

if tlocus not in matches_collapsed[qlocus]:

matches_collapsed[qlocus][tlocus]=[]

#store data

matches_collapsed[qlocus][tlocus].append( (algLen,mismatches,gaps,qstart,qend,tstart,tend,e,score,qcov,tcov) )

#

matched_queries = set()

for qlocus in sorted( matches_collapsed.keys() ):

for tlocus in sorted( matches_collapsed[qlocus].keys() ):

qCov=tCov=0

for algLen,mismatches,gaps,qstart,qend,tstart,tend,e,score,qcov,tcov in matches_collapsed[qlocus][tlocus]:

qCov += qcov

tCov += tcov

if qCov<o.qcov or tCov<o.tcov:

continue

out = "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%.1f\t%.1f\n" % (qlocus,tlocus,identity,algLen,mismatches,gaps,qstart,qend,tstart,tend,e,score,qCov*100,tCov*100, )

sys.stdout.write( out )

matched_queries.add( qlocus )

#get with no valid match

sys.stderr.write( "Queries without valid matches:\n" )

i = 0

out = open( o.query + ".nomatch.fa","w" )

for r in SeqIO.parse( open(o.query),"fasta" ):

if r.id in matched_queries:

continue

i+=1

line = "%s\t%s\t%s" % (i,r.id,len(r.seq))

if r.id in matches_collapsed:

line += "\t%s" % str( matches_collapsed[r.id] )

sys.stderr.write( line+"\n" )

#save fasta