TEST EXAMPLES
To run these examples, set your PBS queue to short, walltime to 1:00:00 and ppn to 2
For the following exmaples, I assume the current location is the PRADA directory
Please use "tar xzvf U87_chr17p13.2.end1.fastq.tar.gz" to unzip the fastq file.
Please see manual how to add PRADA to system path. 

1. Run PRADA from BAM
./prada-preprocess-bi -inputdir testdata -sample U87_chr17p13.2 -tag U87 -step 1_1 -pbs frombam -outdir testdata/test1 -submit yes

2. Run PRADA from FASTQ
./prada-preprocess-bi -inputdir testdata -sample U87_chr17p13.2 -tag U87 -step 2_e1_1 -pbs fromfq -outdir testdata/test2 -submit yes

3. Run Fusion Module
./prada-fusion -bam testdata/test1/U87_chr17p13.2.withRG.GATKRecalibrated.flagged.bam -junL 50 -outdir testdata/fusion

4. Run frame prediction
./prada-frame -conf conf.txt -i testdata/frame_test.txt -docstr frame_test_result -outdir testdata/

5. Run homology prediction
./prada-homology -i testdata/homology_test.txt -o testdata/homology_test_result.txt -tmpdir testdata/tmp

6. Run GUESS-ft
./prada-guess-ft SPAG7 CAMTA2 -inputbam testdata/test1/U87_chr17p13.2.withRG.GATKRecalibrated.flagged.bam -junL 50 -outdir testdata/SPAG7_CAMTA2