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#!/usr/bin/python3
import sys, getopt, subprocess, multiprocessing
def run( cmd, spots, q ) :
p = subprocess.Popen( cmd, stdout = subprocess.PIPE )
n = 0
l = 0
lines = None
if spots != None :
lines = spots * 4
bases = None
while True :
line = p.stdout.readline().decode( 'ascii' ).strip()
if line != '' :
if l == 1 :
bases = line
elif l == 3 :
q.put( ( bases, line ) )
n += 1
if lines != None :
if n > lines :
p.kill()
break
l += 1
if l > 3 :
l = 0
else :
break
q.put( None )
def fastq_dump_full( fastq_dump, acc, spots, q ) :
print( "starting fastq-dump" )
run( [ fastq_dump, '--split-3', '-Z', acc ], spots, q )
print( "fastq-dump done" )
def sam_dump_full( sam_dump, acc, spots, q ) :
print( "starting sam-dump" )
run( [ sam_dump, '-u', '--fastq', acc ], spots, q )
print( "sam-dump done" )
def handle_q( d, q ) :
res = 0
t = q.get()
if t != None :
res = 1
( bases, quality ) = t
try :
d[ bases ].append( quality )
except :
d[ bases ] = [ quality ]
return res
def compare_lists( l1, l2 ) :
cmn = 0
rev = 0
nom = 0
for item in l1 :
if item in l2 :
cmn += 1
elif item[::-1] in l2 :
rev += 1
else :
nom += 1
return ( cmn, rev, nom )
def reverse_compl( bases ) :
res = ""
for c in bases[::-1] :
if c == 'A' :
res += 'T'
elif c == 'C' :
res += 'G'
elif c == 'G' :
res += 'C'
elif c == 'T' :
res += 'A'
else :
res += c
return res
class join_stats() :
def __init__( self ) :
self.n_matches = 0
self.nr_matches = 0
self.n_reversed = 0
self.nr_reversed = 0
self.n_no_match = 0
self.nr_no_match = 0
self.n_not_found = 0
def add_match_res( self, m, r, n ) :
self.n_matches += m
self.n_reversed += r
self.n_no_match += n
def add_rmatch_res( self, m, r, n ) :
self.nr_matches += m
self.nr_reversed += r
self.nr_no_match += n
def __str__( self ) :
res = "matches : %d\n" % self.n_matches
res += "r-matches : %d\n" % self.nr_matches
res += "reversed : %d\n" % self.n_reversed
res += "r-reversed : %d\n" % self.nr_reversed
res += "no_match : %d\n" % self.n_no_match
res += "r-no_match : %d\n" % self.nr_no_match
res += "not_found : %d" % self.n_not_found
return res
def non_matches( self ) :
res = self.nr_matches
res += self.n_reversed
res += self.nr_reversed
res += self.n_no_match
res += self.nr_no_match
res += self.n_not_found
return res
def extract_matches( d1, d2 ) :
res = 0
l = []
for bases in d1 :
if bases in d2 :
l.append( bases )
for bases in l :
l1 = d1[ bases ]
l2 = d2[ bases ]
if len( l1 ) == 1 and len( l2 ) == 1 :
if l1[ 0 ] == l2[ 0 ] :
res += 1
del d1[ bases ]
del d2[ bases ]
return res
def join_2( q1, q2, q3 ) :
#the key is the bases
#the value is a ist of qualities
d1 = {}
d2 = {}
n1 = 0
n2 = 0
r1 = 1
r2 = 1
loop = 0
js = join_stats()
while ( r1 + r2 ) > 0 :
loop += 1
if loop % 10000 == 0 :
js.n_matches += extract_matches( d1, d2 )
#sys.stdout.write( '.' )
#sys.stdout.flush()
if r1 > 0 :
r1 = handle_q( d1, q1 )
n1 += r1
if r2 > 0:
r2 = handle_q( d2, q2 )
n2 += r2
print( "from fastq-dump : %d" % n1 )
print( "from sam-dump : %d" % n2 )
for bases in d1 :
ql_1 = d1[ bases ]
ql_2 = d2.get( bases, None )
if ql_2 != None :
( m, r, n ) = compare_lists( ql_1, ql_2 )
if n > 0 :
ql_2 = d2.get( reverse_compl( bases ), None )
if ql_2 != None :
( m1, r1, n1 ) = compare_lists( ql_1, ql_2 )
js.add_rmatch_res( m1, r1, n1 )
else :
js.add_match_res( m, r, n )
else :
ql_2 = d2.get( reverse_compl( bases ), None )
if ql_2 != None :
( m2, r2, n2 ) = compare_lists( ql_1, ql_2 )
js.add_rmatch_res( m2, r2, n2 )
else :
js.n_not_found += 1
print( js )
q3.put( js.non_matches() )
if __name__ == '__main__':
print( "running: ", __file__ )
if sys.version_info[ 0 ] < 3 :
print( "does not work with python version < 3!" )
sys.exit( 3 )
acc = 'SRR3332402'
spots = None
fastq_dump = 'fastq-dump'
sam_dump = 'sam-dump'
short_opts = "ha:s:f:m:"
long_opts = [ "acc=", "spots=", "fastq_dump=", "sam_dump=" ]
try :
opts, args = getopt.getopt( sys.argv[ 1: ], short_opts, long_opts )
except getopt.GetoptError :
print ( sys.argv[ 0 ], ' -a <accession> -s <spots> -f <fastq-dump-binary> -m <sam-dump-binary>' )
sys.exit( 2 )
for opt, arg in opts :
if opt == '-h' :
print ( sys.argv[ 0 ], ' -a <accession> -s <spots> -f <fastq-dump-binary> -m <sam-dump-binary>' )
sys.exit()
elif opt in ( "-a", "--acc" ) :
acc = arg
elif opt in ( "-s", "--spots" ) :
spots = int( arg )
elif opt in ( "-f", "--fastq_dump" ) :
fastq_dump = arg
elif opt in ( "-m", "--sam_dump" ) :
sam_dump = arg
print( "accession = ", acc )
if spots != None :
print( "spots = ", spots )
q1 = multiprocessing.Queue()
q2 = multiprocessing.Queue()
q3 = multiprocessing.Queue()
p1 = multiprocessing.Process( target = fastq_dump_full, args = ( fastq_dump, acc, spots, q1 ), )
p2 = multiprocessing.Process( target = sam_dump_full, args = ( sam_dump, acc, spots, q2 ), )
p3 = multiprocessing.Process( target = join_2, args = ( q1, q2, q3 ), )
p1.start()
p2.start()
p3.start()
p1.join()
p2.join()
p3.join()
nm = q3.get()
print( "non-matches : ", nm )
if nm > 0 :
sys.exit( 3 )
print( "success: ", __file__, "\n" )
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