newfilename = "%s/%s.txt" % (src_table_dir, name)
if not os.path.exists( newfilename ) :
fnew = open(newfilename, 'w')
fnew.write( first_line )
fnew.write( rest_lines )
fnew.close()
#update tables.txt, rebuild parsed tables
#ftables = "%s/tables.txt" % os.environ["BIOSQL_HOME"]
#ftables = open( ftables, 'a' )
#ftables.write( first_line[1:] )
#ftables.write("\n");
#ftables.close()
#pop = Popen(['bash','rebuild_parsed_tables.sh'], \
#stdin=PIPE, stdout=PIPE, stderr=PIPE)
#(out, err) = pop.communicate()
#sys.stderr.write(err)
#sys.stdout.write(out)
#check err here?
json_data = "{'status':'OK','message':'%s'}" % name
else :
json_data = "{'status':'DUPLICATE','message':'A table named: \\'%s\\' already exists.'}" % name
else :
json_data = "{'status':'ERROR','message':'Uploading went awry'}"
utils.printPayload( json_data );
#index this using the ref file (maybe not all chroms are there, or are named differently)
#also, run_biosql will need to be changed
#run script to index
for chrom in range(1, 23) + ['X', 'Y']:
bam = "%s/chr%s.bam" % (root, str(chrom))
mates = "%s/chr%s.mates" % (root, str(chrom))
indx = "%s/chr%s.mates.indx" % (root, str(chrom))
if os.path.exists(bam):
if not os.path.exists(indx):
print "popping index_all.sh"
pop = Popen(["bash",\
"index_all.sh", \
"%s/chr" % root, \
refinfo], \
stdin=PIPE, stdout=PIPE, stderr=PIPE )
(out, err) = pop.communicate()
#messages.append( "%s : %s" % (str(chrom),out) )
sys.stdout.write(out)
sys.stderr.write(err)
else:
messages.append("%s already exists" % indx)
else:
messages.append("chr%s.bam doesn't exist!" % str(chrom))
status, message = "ok", "Donor genome has finished indexing."
message = ";".join(messages)
r = '{"status":"%s","message":"%s"}' % (status, message)
utils.printPayload(r)
#also, run_biosql will need to be changed
#run script to index
for chrom in range(1,23) + ['X','Y'] :
bam = "%s/chr%s.bam" % (root, str(chrom) )
mates = "%s/chr%s.mates" % (root, str(chrom) )
indx = "%s/chr%s.mates.indx" % (root, str(chrom) )
if os.path.exists( bam ) :
if not os.path.exists( indx ) :
print "popping index_all.sh"
pop = Popen(["bash",\
"index_all.sh", \
"%s/chr" % root, \
refinfo], \
stdin=PIPE, stdout=PIPE, stderr=PIPE )
(out, err) = pop.communicate()
#messages.append( "%s : %s" % (str(chrom),out) )
sys.stdout.write( out )
sys.stderr.write( err )
else :
messages.append( "%s already exists" % indx )
else :
messages.append( "chr%s.bam doesn't exist!" % str(chrom) )
status, message = "ok", "Donor genome has finished indexing."
message = ";".join( messages )
r = '{"status":"%s","message":"%s"}' % (status,message)
utils.printPayload( r )
