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example scripts of running PrecisionProDB in different mode

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Xiaolong Cao edited this page Nov 18, 2024 · 1 revision

test code in folder test_output

https://github.com/ATPs/PrecisionProDB/blob/master/test_output/test_running_summary.txt

running without sqlite, with prebuilt sqlite or build sqlite during the running.

cd /data/p/xiaolong/PrecisionProDB/test_output/Ensembl/tsv/no_sqlite && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/gnomAD.variant.txt.gz -g /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.gtf.gz -o /data/p/xiaolong/PrecisionProDB/test_output/Ensembl/tsv/no_sqlite/Ensembl.tsv.no_sqlite -a Ensembl_GTF --PEFF -t 4

cd /data/p/xiaolong/PrecisionProDB/test_output/Ensembl/tsv/sqlite_one_step && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/gnomAD.variant.txt.gz -g /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.gtf.gz -o /data/p/xiaolong/PrecisionProDB/test_output/Ensembl/tsv/sqlite_one_step/Ensembl.tsv.sqlite_one_step -a Ensembl_GTF --PEFF -t 4 -S /data/p/xiaolong/PrecisionProDB/test_output/Ensembl/Ensembl.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/Ensembl/tsv/sqlite_two_step && python /data/p/xiaolong/PrecisionProDB/src/buildSqlite.py -S /data/p/xiaolong/PrecisionProDB/test_output/Ensembl/Ensembl.sqlite -g /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.gtf.gz -a Ensembl_GTF && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/gnomAD.variant.txt.gz -o /data/p/xiaolong/PrecisionProDB/test_output/Ensembl/tsv/sqlite_two_step/Ensembl.tsv.sqlite_two_step -a Ensembl_GTF --PEFF -t 4 -S /data/p/xiaolong/PrecisionProDB/test_output/Ensembl/Ensembl.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/Ensembl/vcf/no_sqlite && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/celline.vcf.gz -g /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.gtf.gz -o /data/p/xiaolong/PrecisionProDB/test_output/Ensembl/vcf/no_sqlite/Ensembl.vcf.no_sqlite -a Ensembl_GTF --PEFF -t 4

cd /data/p/xiaolong/PrecisionProDB/test_output/Ensembl/vcf/sqlite_one_step && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/celline.vcf.gz -g /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.gtf.gz -o /data/p/xiaolong/PrecisionProDB/test_output/Ensembl/vcf/sqlite_one_step/Ensembl.vcf.sqlite_one_step -a Ensembl_GTF --PEFF -t 4 -S /data/p/xiaolong/PrecisionProDB/test_output/Ensembl/Ensembl.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/Ensembl/vcf/sqlite_two_step && python /data/p/xiaolong/PrecisionProDB/src/buildSqlite.py -S /data/p/xiaolong/PrecisionProDB/test_output/Ensembl/Ensembl.sqlite -g /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.gtf.gz -a Ensembl_GTF && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/celline.vcf.gz -o /data/p/xiaolong/PrecisionProDB/test_output/Ensembl/vcf/sqlite_two_step/Ensembl.vcf.sqlite_two_step -a Ensembl_GTF --PEFF -t 4 -S /data/p/xiaolong/PrecisionProDB/test_output/Ensembl/Ensembl.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/Ensembl/str/sqlite_one_step && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m chr1-942451-T-C,1-6253878-C-T,1-2194700-C-G,1-1719406-G-A -g /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.gtf.gz -o /data/p/xiaolong/PrecisionProDB/test_output/Ensembl/str/sqlite_one_step/Ensembl.str.sqlite_one_step -a Ensembl_GTF --PEFF -t 4 -S /data/p/xiaolong/PrecisionProDB/test_output/Ensembl/Ensembl.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/Ensembl/str/sqlite_two_step && python /data/p/xiaolong/PrecisionProDB/src/buildSqlite.py -S /data/p/xiaolong/PrecisionProDB/test_output/Ensembl/Ensembl.sqlite -g /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.gtf.gz -a Ensembl_GTF && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m chr1-942451-T-C,1-6253878-C-T,1-2194700-C-G,1-1719406-G-A -o /data/p/xiaolong/PrecisionProDB/test_output/Ensembl/str/sqlite_two_step/Ensembl.str.sqlite_two_step -a Ensembl_GTF --PEFF -t 4 -S /data/p/xiaolong/PrecisionProDB/test_output/Ensembl/Ensembl.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/GENCODE/tsv/no_sqlite && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/gnomAD.variant.txt.gz -g /data/p/xiaolong/PrecisionProDB/examples/GENCODE/GENCODE.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/GENCODE/GENCODE.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/GENCODE/GENCODE.gtf.gz -o /data/p/xiaolong/PrecisionProDB/test_output/GENCODE/tsv/no_sqlite/GENCODE.tsv.no_sqlite -a GENCODE_GTF --PEFF -t 4

cd /data/p/xiaolong/PrecisionProDB/test_output/GENCODE/tsv/sqlite_one_step && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/gnomAD.variant.txt.gz -g /data/p/xiaolong/PrecisionProDB/examples/GENCODE/GENCODE.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/GENCODE/GENCODE.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/GENCODE/GENCODE.gtf.gz -o /data/p/xiaolong/PrecisionProDB/test_output/GENCODE/tsv/sqlite_one_step/GENCODE.tsv.sqlite_one_step -a GENCODE_GTF --PEFF -t 4 -S /data/p/xiaolong/PrecisionProDB/test_output/GENCODE/GENCODE.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/GENCODE/tsv/sqlite_two_step && python /data/p/xiaolong/PrecisionProDB/src/buildSqlite.py -S /data/p/xiaolong/PrecisionProDB/test_output/GENCODE/GENCODE.sqlite -g /data/p/xiaolong/PrecisionProDB/examples/GENCODE/GENCODE.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/GENCODE/GENCODE.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/GENCODE/GENCODE.gtf.gz -a GENCODE_GTF && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/gnomAD.variant.txt.gz -o /data/p/xiaolong/PrecisionProDB/test_output/GENCODE/tsv/sqlite_two_step/GENCODE.tsv.sqlite_two_step -a GENCODE_GTF --PEFF -t 4 -S /data/p/xiaolong/PrecisionProDB/test_output/GENCODE/GENCODE.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/GENCODE/vcf/no_sqlite && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/celline.vcf.gz -g /data/p/xiaolong/PrecisionProDB/examples/GENCODE/GENCODE.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/GENCODE/GENCODE.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/GENCODE/GENCODE.gtf.gz -o /data/p/xiaolong/PrecisionProDB/test_output/GENCODE/vcf/no_sqlite/GENCODE.vcf.no_sqlite -a GENCODE_GTF --PEFF -t 4

cd /data/p/xiaolong/PrecisionProDB/test_output/GENCODE/vcf/sqlite_one_step && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/celline.vcf.gz -g /data/p/xiaolong/PrecisionProDB/examples/GENCODE/GENCODE.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/GENCODE/GENCODE.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/GENCODE/GENCODE.gtf.gz -o /data/p/xiaolong/PrecisionProDB/test_output/GENCODE/vcf/sqlite_one_step/GENCODE.vcf.sqlite_one_step -a GENCODE_GTF --PEFF -t 4 -S /data/p/xiaolong/PrecisionProDB/test_output/GENCODE/GENCODE.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/GENCODE/vcf/sqlite_two_step && python /data/p/xiaolong/PrecisionProDB/src/buildSqlite.py -S /data/p/xiaolong/PrecisionProDB/test_output/GENCODE/GENCODE.sqlite -g /data/p/xiaolong/PrecisionProDB/examples/GENCODE/GENCODE.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/GENCODE/GENCODE.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/GENCODE/GENCODE.gtf.gz -a GENCODE_GTF && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/celline.vcf.gz -o /data/p/xiaolong/PrecisionProDB/test_output/GENCODE/vcf/sqlite_two_step/GENCODE.vcf.sqlite_two_step -a GENCODE_GTF --PEFF -t 4 -S /data/p/xiaolong/PrecisionProDB/test_output/GENCODE/GENCODE.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/GENCODE/str/sqlite_one_step && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m chr1-942451-T-C,1-6253878-C-T,1-2194700-C-G,1-1719406-G-A -g /data/p/xiaolong/PrecisionProDB/examples/GENCODE/GENCODE.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/GENCODE/GENCODE.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/GENCODE/GENCODE.gtf.gz -o /data/p/xiaolong/PrecisionProDB/test_output/GENCODE/str/sqlite_one_step/GENCODE.str.sqlite_one_step -a GENCODE_GTF --PEFF -t 4 -S /data/p/xiaolong/PrecisionProDB/test_output/GENCODE/GENCODE.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/GENCODE/str/sqlite_two_step && python /data/p/xiaolong/PrecisionProDB/src/buildSqlite.py -S /data/p/xiaolong/PrecisionProDB/test_output/GENCODE/GENCODE.sqlite -g /data/p/xiaolong/PrecisionProDB/examples/GENCODE/GENCODE.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/GENCODE/GENCODE.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/GENCODE/GENCODE.gtf.gz -a GENCODE_GTF && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m chr1-942451-T-C,1-6253878-C-T,1-2194700-C-G,1-1719406-G-A -o /data/p/xiaolong/PrecisionProDB/test_output/GENCODE/str/sqlite_two_step/GENCODE.str.sqlite_two_step -a GENCODE_GTF --PEFF -t 4 -S /data/p/xiaolong/PrecisionProDB/test_output/GENCODE/GENCODE.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/RefSeq/tsv/no_sqlite && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/gnomAD.variant.txt.gz -g /data/p/xiaolong/PrecisionProDB/examples/RefSeq/RefSeq.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/RefSeq/RefSeq.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/RefSeq/RefSeq.gtf.gz -o /data/p/xiaolong/PrecisionProDB/test_output/RefSeq/tsv/no_sqlite/RefSeq.tsv.no_sqlite -a RefSeq --PEFF -t 4

cd /data/p/xiaolong/PrecisionProDB/test_output/RefSeq/tsv/sqlite_one_step && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/gnomAD.variant.txt.gz -g /data/p/xiaolong/PrecisionProDB/examples/RefSeq/RefSeq.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/RefSeq/RefSeq.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/RefSeq/RefSeq.gtf.gz -o /data/p/xiaolong/PrecisionProDB/test_output/RefSeq/tsv/sqlite_one_step/RefSeq.tsv.sqlite_one_step -a RefSeq --PEFF -t 4 -S /data/p/xiaolong/PrecisionProDB/test_output/RefSeq/RefSeq.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/RefSeq/tsv/sqlite_two_step && python /data/p/xiaolong/PrecisionProDB/src/buildSqlite.py -S /data/p/xiaolong/PrecisionProDB/test_output/RefSeq/RefSeq.sqlite -g /data/p/xiaolong/PrecisionProDB/examples/RefSeq/RefSeq.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/RefSeq/RefSeq.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/RefSeq/RefSeq.gtf.gz -a RefSeq && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/gnomAD.variant.txt.gz -o /data/p/xiaolong/PrecisionProDB/test_output/RefSeq/tsv/sqlite_two_step/RefSeq.tsv.sqlite_two_step -a RefSeq --PEFF -t 4 -S /data/p/xiaolong/PrecisionProDB/test_output/RefSeq/RefSeq.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/RefSeq/vcf/no_sqlite && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/celline.vcf.gz -g /data/p/xiaolong/PrecisionProDB/examples/RefSeq/RefSeq.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/RefSeq/RefSeq.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/RefSeq/RefSeq.gtf.gz -o /data/p/xiaolong/PrecisionProDB/test_output/RefSeq/vcf/no_sqlite/RefSeq.vcf.no_sqlite -a RefSeq --PEFF -t 4

cd /data/p/xiaolong/PrecisionProDB/test_output/RefSeq/vcf/sqlite_one_step && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/celline.vcf.gz -g /data/p/xiaolong/PrecisionProDB/examples/RefSeq/RefSeq.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/RefSeq/RefSeq.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/RefSeq/RefSeq.gtf.gz -o /data/p/xiaolong/PrecisionProDB/test_output/RefSeq/vcf/sqlite_one_step/RefSeq.vcf.sqlite_one_step -a RefSeq --PEFF -t 4 -S /data/p/xiaolong/PrecisionProDB/test_output/RefSeq/RefSeq.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/RefSeq/vcf/sqlite_two_step && python /data/p/xiaolong/PrecisionProDB/src/buildSqlite.py -S /data/p/xiaolong/PrecisionProDB/test_output/RefSeq/RefSeq.sqlite -g /data/p/xiaolong/PrecisionProDB/examples/RefSeq/RefSeq.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/RefSeq/RefSeq.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/RefSeq/RefSeq.gtf.gz -a RefSeq && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/celline.vcf.gz -o /data/p/xiaolong/PrecisionProDB/test_output/RefSeq/vcf/sqlite_two_step/RefSeq.vcf.sqlite_two_step -a RefSeq --PEFF -t 4 -S /data/p/xiaolong/PrecisionProDB/test_output/RefSeq/RefSeq.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/RefSeq/str/sqlite_one_step && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m chr1-942451-T-C,1-6253878-C-T,1-2194700-C-G,1-1719406-G-A -g /data/p/xiaolong/PrecisionProDB/examples/RefSeq/RefSeq.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/RefSeq/RefSeq.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/RefSeq/RefSeq.gtf.gz -o /data/p/xiaolong/PrecisionProDB/test_output/RefSeq/str/sqlite_one_step/RefSeq.str.sqlite_one_step -a RefSeq --PEFF -t 4 -S /data/p/xiaolong/PrecisionProDB/test_output/RefSeq/RefSeq.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/RefSeq/str/sqlite_two_step && python /data/p/xiaolong/PrecisionProDB/src/buildSqlite.py -S /data/p/xiaolong/PrecisionProDB/test_output/RefSeq/RefSeq.sqlite -g /data/p/xiaolong/PrecisionProDB/examples/RefSeq/RefSeq.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/RefSeq/RefSeq.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/RefSeq/RefSeq.gtf.gz -a RefSeq && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m chr1-942451-T-C,1-6253878-C-T,1-2194700-C-G,1-1719406-G-A -o /data/p/xiaolong/PrecisionProDB/test_output/RefSeq/str/sqlite_two_step/RefSeq.str.sqlite_two_step -a RefSeq --PEFF -t 4 -S /data/p/xiaolong/PrecisionProDB/test_output/RefSeq/RefSeq.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/TransDecoder/tsv/no_sqlite && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/gnomAD.variant.txt.gz -g /data/p/xiaolong/PrecisionProDB/examples/TransDecoder/TransDecoder.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/TransDecoder/TransDecoder.transcripts.fa.transdecoder.pep.gz -f /data/p/xiaolong/PrecisionProDB/examples/TransDecoder/TransDecoder.transcripts.fa.transdecoder.genome.gff3.gz -o /data/p/xiaolong/PrecisionProDB/test_output/TransDecoder/tsv/no_sqlite/TransDecoder.tsv.no_sqlite -a gtf --PEFF -t 4

cd /data/p/xiaolong/PrecisionProDB/test_output/TransDecoder/tsv/sqlite_one_step && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/gnomAD.variant.txt.gz -g /data/p/xiaolong/PrecisionProDB/examples/TransDecoder/TransDecoder.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/TransDecoder/TransDecoder.transcripts.fa.transdecoder.pep.gz -f /data/p/xiaolong/PrecisionProDB/examples/TransDecoder/TransDecoder.transcripts.fa.transdecoder.genome.gff3.gz -o /data/p/xiaolong/PrecisionProDB/test_output/TransDecoder/tsv/sqlite_one_step/TransDecoder.tsv.sqlite_one_step -a gtf --PEFF -t 4 -S /data/p/xiaolong/PrecisionProDB/test_output/TransDecoder/TransDecoder.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/TransDecoder/tsv/sqlite_two_step && python /data/p/xiaolong/PrecisionProDB/src/buildSqlite.py -S /data/p/xiaolong/PrecisionProDB/test_output/TransDecoder/TransDecoder.sqlite -g /data/p/xiaolong/PrecisionProDB/examples/TransDecoder/TransDecoder.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/TransDecoder/TransDecoder.transcripts.fa.transdecoder.pep.gz -f /data/p/xiaolong/PrecisionProDB/examples/TransDecoder/TransDecoder.transcripts.fa.transdecoder.genome.gff3.gz -a gtf && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/gnomAD.variant.txt.gz -o /data/p/xiaolong/PrecisionProDB/test_output/TransDecoder/tsv/sqlite_two_step/TransDecoder.tsv.sqlite_two_step -a gtf --PEFF -t 4 -S /data/p/xiaolong/PrecisionProDB/test_output/TransDecoder/TransDecoder.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/TransDecoder/vcf/no_sqlite && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/celline.vcf.gz -g /data/p/xiaolong/PrecisionProDB/examples/TransDecoder/TransDecoder.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/TransDecoder/TransDecoder.transcripts.fa.transdecoder.pep.gz -f /data/p/xiaolong/PrecisionProDB/examples/TransDecoder/TransDecoder.transcripts.fa.transdecoder.genome.gff3.gz -o /data/p/xiaolong/PrecisionProDB/test_output/TransDecoder/vcf/no_sqlite/TransDecoder.vcf.no_sqlite -a gtf --PEFF -t 4

cd /data/p/xiaolong/PrecisionProDB/test_output/TransDecoder/vcf/sqlite_one_step && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/celline.vcf.gz -g /data/p/xiaolong/PrecisionProDB/examples/TransDecoder/TransDecoder.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/TransDecoder/TransDecoder.transcripts.fa.transdecoder.pep.gz -f /data/p/xiaolong/PrecisionProDB/examples/TransDecoder/TransDecoder.transcripts.fa.transdecoder.genome.gff3.gz -o /data/p/xiaolong/PrecisionProDB/test_output/TransDecoder/vcf/sqlite_one_step/TransDecoder.vcf.sqlite_one_step -a gtf --PEFF -t 4 -S /data/p/xiaolong/PrecisionProDB/test_output/TransDecoder/TransDecoder.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/TransDecoder/vcf/sqlite_two_step && python /data/p/xiaolong/PrecisionProDB/src/buildSqlite.py -S /data/p/xiaolong/PrecisionProDB/test_output/TransDecoder/TransDecoder.sqlite -g /data/p/xiaolong/PrecisionProDB/examples/TransDecoder/TransDecoder.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/TransDecoder/TransDecoder.transcripts.fa.transdecoder.pep.gz -f /data/p/xiaolong/PrecisionProDB/examples/TransDecoder/TransDecoder.transcripts.fa.transdecoder.genome.gff3.gz -a gtf && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/celline.vcf.gz -o /data/p/xiaolong/PrecisionProDB/test_output/TransDecoder/vcf/sqlite_two_step/TransDecoder.vcf.sqlite_two_step -a gtf --PEFF -t 4 -S /data/p/xiaolong/PrecisionProDB/test_output/TransDecoder/TransDecoder.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/TransDecoder/str/sqlite_one_step && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m chr1-942451-T-C,1-6253878-C-T,1-2194700-C-G,1-1719406-G-A -g /data/p/xiaolong/PrecisionProDB/examples/TransDecoder/TransDecoder.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/TransDecoder/TransDecoder.transcripts.fa.transdecoder.pep.gz -f /data/p/xiaolong/PrecisionProDB/examples/TransDecoder/TransDecoder.transcripts.fa.transdecoder.genome.gff3.gz -o /data/p/xiaolong/PrecisionProDB/test_output/TransDecoder/str/sqlite_one_step/TransDecoder.str.sqlite_one_step -a gtf --PEFF -t 4 -S /data/p/xiaolong/PrecisionProDB/test_output/TransDecoder/TransDecoder.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/TransDecoder/str/sqlite_two_step && python /data/p/xiaolong/PrecisionProDB/src/buildSqlite.py -S /data/p/xiaolong/PrecisionProDB/test_output/TransDecoder/TransDecoder.sqlite -g /data/p/xiaolong/PrecisionProDB/examples/TransDecoder/TransDecoder.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/TransDecoder/TransDecoder.transcripts.fa.transdecoder.pep.gz -f /data/p/xiaolong/PrecisionProDB/examples/TransDecoder/TransDecoder.transcripts.fa.transdecoder.genome.gff3.gz -a gtf && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m chr1-942451-T-C,1-6253878-C-T,1-2194700-C-G,1-1719406-G-A -o /data/p/xiaolong/PrecisionProDB/test_output/TransDecoder/str/sqlite_two_step/TransDecoder.str.sqlite_two_step -a gtf --PEFF -t 4 -S /data/p/xiaolong/PrecisionProDB/test_output/TransDecoder/TransDecoder.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/UniProt/tsv/no_sqlite && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/gnomAD.variant.txt.gz -g /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.gtf.gz -o /data/p/xiaolong/PrecisionProDB/test_output/UniProt/tsv/no_sqlite/UniProt.tsv.no_sqlite -a Ensembl_GTF --PEFF -U /data/p/xiaolong/PrecisionProDB/examples/UniProt/UniProt.protein.fa.gz -t 4 -D Uniprot

cd /data/p/xiaolong/PrecisionProDB/test_output/UniProt/tsv/sqlite_one_step && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/gnomAD.variant.txt.gz -g /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.gtf.gz -o /data/p/xiaolong/PrecisionProDB/test_output/UniProt/tsv/sqlite_one_step/UniProt.tsv.sqlite_one_step -a Ensembl_GTF --PEFF -U /data/p/xiaolong/PrecisionProDB/examples/UniProt/UniProt.protein.fa.gz -t 4 -D Uniprot -S /data/p/xiaolong/PrecisionProDB/test_output/UniProt/UniProt.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/UniProt/tsv/sqlite_two_step && python /data/p/xiaolong/PrecisionProDB/src/buildSqlite.py -S /data/p/xiaolong/PrecisionProDB/test_output/UniProt/UniProt.sqlite -g /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.gtf.gz -a Ensembl_GTF && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/gnomAD.variant.txt.gz -o /data/p/xiaolong/PrecisionProDB/test_output/UniProt/tsv/sqlite_two_step/UniProt.tsv.sqlite_two_step -a Ensembl_GTF --PEFF -U /data/p/xiaolong/PrecisionProDB/examples/UniProt/UniProt.protein.fa.gz -t 4 -D Uniprot -S /data/p/xiaolong/PrecisionProDB/test_output/UniProt/UniProt.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/UniProt/vcf/no_sqlite && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/celline.vcf.gz -g /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.gtf.gz -o /data/p/xiaolong/PrecisionProDB/test_output/UniProt/vcf/no_sqlite/UniProt.vcf.no_sqlite -a Ensembl_GTF --PEFF -U /data/p/xiaolong/PrecisionProDB/examples/UniProt/UniProt.protein.fa.gz -t 4 -D Uniprot

cd /data/p/xiaolong/PrecisionProDB/test_output/UniProt/vcf/sqlite_one_step && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/celline.vcf.gz -g /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.gtf.gz -o /data/p/xiaolong/PrecisionProDB/test_output/UniProt/vcf/sqlite_one_step/UniProt.vcf.sqlite_one_step -a Ensembl_GTF --PEFF -U /data/p/xiaolong/PrecisionProDB/examples/UniProt/UniProt.protein.fa.gz -t 4 -D Uniprot -S /data/p/xiaolong/PrecisionProDB/test_output/UniProt/UniProt.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/UniProt/vcf/sqlite_two_step && python /data/p/xiaolong/PrecisionProDB/src/buildSqlite.py -S /data/p/xiaolong/PrecisionProDB/test_output/UniProt/UniProt.sqlite -g /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.gtf.gz -a Ensembl_GTF && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m /data/p/xiaolong/PrecisionProDB/examples/celline.vcf.gz -o /data/p/xiaolong/PrecisionProDB/test_output/UniProt/vcf/sqlite_two_step/UniProt.vcf.sqlite_two_step -a Ensembl_GTF --PEFF -U /data/p/xiaolong/PrecisionProDB/examples/UniProt/UniProt.protein.fa.gz -t 4 -D Uniprot -S /data/p/xiaolong/PrecisionProDB/test_output/UniProt/UniProt.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/UniProt/str/sqlite_one_step && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m chr1-942451-T-C,1-6253878-C-T,1-2194700-C-G,1-1719406-G-A -g /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.gtf.gz -o /data/p/xiaolong/PrecisionProDB/test_output/UniProt/str/sqlite_one_step/UniProt.str.sqlite_one_step -a Ensembl_GTF --PEFF -t 4 -S /data/p/xiaolong/PrecisionProDB/test_output/UniProt/UniProt.sqlite

cd /data/p/xiaolong/PrecisionProDB/test_output/UniProt/str/sqlite_two_step && python /data/p/xiaolong/PrecisionProDB/src/buildSqlite.py -S /data/p/xiaolong/PrecisionProDB/test_output/UniProt/UniProt.sqlite -g /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.genome.fa.gz -p /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.protein.fa.gz -f /data/p/xiaolong/PrecisionProDB/examples/Ensembl/Ensembl.gtf.gz -a Ensembl_GTF && python /data/p/xiaolong/PrecisionProDB/src/PrecisionProDB.py -m chr1-942451-T-C,1-6253878-C-T,1-2194700-C-G,1-1719406-G-A -o /data/p/xiaolong/PrecisionProDB/test_output/UniProt/str/sqlite_two_step/UniProt.str.sqlite_two_step -a Ensembl_GTF --PEFF -t 4 -S /data/p/xiaolong/PrecisionProDB/test_output/UniProt/UniProt.sqlite

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