hotdogee / exonerate-gff3

exonerate fork with added gff3 support

exonerate-gff3

This is an exonerate fork with added gff3 support.
Original website with user guides: http://www.ebi.ac.uk/~guy/exonerate/

New Option: --gff3 [FALSE]

Using the "--gff3 yes" option with the "--showtargetgff yes" option will output GFF3. Without the "--gff3 yes" option, everything works just as before so previous scripts relying on the old output format won’t break.

Example Command:
exonerate -q protein.fa -t genome.fa --model protein2genome --querytype protein --targettype dna --showvulgar no --softmaskquery yes --softmasktarget yes --minintron 20 --maxintron 3000 --showalignment no --showtargetgff yes --showcigar no --geneseed 250 --score 250 --verbose 0 --gff3 yes

Example Output:

Scaffold1	exonerate:protein2genome:local	match	188318	189587	649	-	.	ID=match00012;Name=EDAN000750-PA;Target=EDAN000750-PA 1 129 +;Gap=M135 D884 M251
Scaffold1	exonerate:protein2genome:local	match_part	189452	189587	.	-	.	Parent=match00012
Scaffold1	exonerate:protein2genome:local	match_part	188318	188568	.	-	.	Parent=match00012
Scaffold1	exonerate:protein2genome:local	match	183667	183897	392	-	.	ID=match00013;Name=EDAN000750-PA;Target=EDAN000750-PA 127 203;Gap=M231
Scaffold1	exonerate:protein2genome:local	match_part	183667	183897	.	-	.	Parent=match00013
Scaffold1	exonerate:protein2genome:local	match	45007	45165	265	-	.	ID=match00014;Name=EDAN000738-PA;Target=EDAN000738-PA 10 62;Gap=M159
Scaffold1	exonerate:protein2genome:local	match_part	45007	45165	.	-	.	Parent=match00014
Scaffold1	exonerate:protein2genome:local	match	218654	221996	1577	+	.	ID=match00015;Name=EDAN000753-PA;Target=EDAN000753-PA 1 337 +;Gap=M30 D61 M100 D61 M127 D373 M181 D56 M225 D1183 M189 D604 M153
Scaffold1	exonerate:protein2genome:local	match_part	218654	218685	.	+	.	Parent=match00015
Scaffold1	exonerate:protein2genome:local	match_part	218745	218846	.	+	.	Parent=match00015
Scaffold1	exonerate:protein2genome:local	match_part	218906	219034	.	+	.	Parent=match00015
Scaffold1	exonerate:protein2genome:local	match_part	219406	219586	.	+	.	Parent=match00015
Scaffold1	exonerate:protein2genome:local	match_part	219643	219867	.	+	.	Parent=match00015
Scaffold1	exonerate:protein2genome:local	match_part	221051	221239	.	+	.	Parent=match00015
Scaffold1	exonerate:protein2genome:local	match_part	221844	221996	.	+	.	Parent=match00015

exonerate-gff3's Issues

Error compiling

Hi!

Just tried to compile this, but I get an error. This is on Ubuntu.

make[2]: Entering directory '/temp/exonerate-gff3/src/general'
gcc  -g -O2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS  -lpthread -o socket.test socket.test.o socket.o  -lglib-2.0
/usr/bin/ld: socket.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5'
/lib/x86_64-linux-gnu/libpthread.so.0: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
Makefile:244: recipe for target 'socket.test' failed
make[2]: *** [socket.test] Error 1