config files for all domains

src/complete90/filter_configs/archaea.json

+{
+  "FilterDomainFastas.filterScriptPath": "/exports/sascstudent/project-RefseqRelease/src/demo_test/refseqtools/filter_fasta.py", 
+  "FilterDomainFastas.domainInputDir": "/exports/sascstudent/project-RefseqRelease/data/release90/library/archaea",
+  "FilterDomainFastas.taxDbPath": "/exports/sascstudent/project-RefseqRelease/data/taxonomy/ete3_taxadb",
+  "FilterDomainFastas.outputDir": "/exports/sascstudent/project-RefseqRelease/analysis/complete90/library_filtered/archaea",
+  "FilterDomainFastas.FilterFasta.preCommand": "source activate ete3",
+  "FilterDomainFastas.dustmaskerExe": "/home/npappas/src/ncbi-blast-2.6.0+/bin/dustmasker",
+  "FilterDomainFastas.refseqJson": "/exports/sascstudent/project-RefseqRelease/analysis/demo_test/Refseq90.DNA.json",
+  "FilterDomainFastas.dustmaskOnly": true
+}

src/complete90/filter_configs/bacteria.json

+{
+  "FilterDomainFastas.filterScriptPath": "/exports/sascstudent/project-RefseqRelease/src/demo_test/refseqtools/filter_fasta.py", 
+  "FilterDomainFastas.includeAccFile": "/exports/sascstudent/project-RefseqRelease/data/accession_sets/bacteria_rep/accessions.txt",
+  "FilterDomainFastas.domainInputDir": "/exports/sascstudent/project-RefseqRelease/data/release90/library/bacteria",
+  "FilterDomainFastas.taxDbPath": "/exports/sascstudent/project-RefseqRelease/data/taxonomy/ete3_taxadb",
+  "FilterDomainFastas.outputDir": "/exports/sascstudent/project-RefseqRelease/analysis/complete90/library_filtered/bacteria",
+  "FilterDomainFastas.FilterFasta.preCommand": "source activate ete3",
+  "FilterDomainFastas.dustmaskerExe": "/home/npappas/src/ncbi-blast-2.6.0+/bin/dustmasker",
+  "FilterDomainFastas.refseqJson": "/exports/sascstudent/project-RefseqRelease/analysis/demo_test/Refseq90.DNA.json"
+}
+

src/complete90/filter_configs/fungi.json

+{
+  "FilterDomainFastas.filterScriptPath": "/exports/sascstudent/project-RefseqRelease/src/demo_test/refseqtools/filter_fasta.py", 
+  "FilterDomainFastas.domainInputDir": "/exports/sascstudent/project-RefseqRelease/data/release90/library/fungi",
+  "FilterDomainFastas.taxDbPath": "/exports/sascstudent/project-RefseqRelease/data/taxonomy/ete3_taxadb",
+  "FilterDomainFastas.outputDir": "/exports/sascstudent/project-RefseqRelease/analysis/complete90/library_filtered/fungi",
+  "FilterDomainFastas.FilterFasta.preCommand": "source activate ete3",
+  "FilterDomainFastas.dustmaskerExe": "/home/npappas/src/ncbi-blast-2.6.0+/bin/dustmasker",
+  "FilterDomainFastas.refseqJson": "/exports/sascstudent/project-RefseqRelease/analysis/demo_test/Refseq90.DNA.json",
+  "FilterDomainFastas.dustmaskOnly": true
+}

src/complete90/filter_configs/invertebrate.json

+{
+  "FilterDomainFastas.filterScriptPath": "/exports/sascstudent/project-RefseqRelease/src/demo_test/refseqtools/filter_fasta.py", 
+  "FilterDomainFastas.excludeAccFile": "/exports/sascstudent/project-RefseqRelease/data/accession_sets/redundant_accessions/redundant_accessions.txt",
+  "FilterDomainFastas.domainInputDir": "/exports/sascstudent/project-RefseqRelease/data/release90/library/invertebrate",
+  "FilterDomainFastas.taxDbPath": "/exports/sascstudent/project-RefseqRelease/data/taxonomy/ete3_taxadb/taxa.sqlite",
+  "FilterDomainFastas.outputDir": "/exports/sascstudent/project-RefseqRelease/analysis/complete90/library_filtered/invertebrate",
+  "FilterDomainFastas.FilterFasta.preCommand": "source activate ete3",
+  "FilterDomainFastas.dustmaskerExe": "/home/npappas/src/ncbi-blast-2.6.0+/bin/dustmasker",
+  "FilterDomainFastas.refseqJson": "/exports/sascstudent/project-RefseqRelease/analysis/demo_test/Refseq90.DNA.json"
+}
+

src/complete90/filter_configs/plant.json

+{
+  "FilterDomainFastas.filterScriptPath": "/exports/sascstudent/project-RefseqRelease/src/demo_test/refseqtools/filter_fasta.py", 
+  "FilterDomainFastas.excludeAccFile": "/exports/sascstudent/project-RefseqRelease/data/accession_sets/redundant_accessions/redundant_accessions.txt",
+  "FilterDomainFastas.domainInputDir": "/exports/sascstudent/project-RefseqRelease/data/release90/library/plant",
+  "FilterDomainFastas.taxDbPath": "/exports/sascstudent/project-RefseqRelease/data/taxonomy/ete3_taxadb",
+  "FilterDomainFastas.outputDir": "/exports/sascstudent/project-RefseqRelease/analysis/complete90/library_filtered/plant",
+  "FilterDomainFastas.FilterFasta.preCommand": "source activate ete3",
+  "FilterDomainFastas.dustmaskerExe": "/home/npappas/src/ncbi-blast-2.6.0+/bin/dustmasker",
+  "FilterDomainFastas.refseqJson": "/exports/sascstudent/project-RefseqRelease/analysis/demo_test/Refseq90.DNA.json"
+}
+

src/complete90/filter_configs/protozoa.json

+{
+  "FilterDomainFastas.filterScriptPath": "/exports/sascstudent/project-RefseqRelease/src/demo_test/refseqtools/filter_fasta.py", 
+  "FilterDomainFastas.domainInputDir": "/exports/sascstudent/project-RefseqRelease/data/release90/library/protozoa",
+  "FilterDomainFastas.taxDbPath": "/exports/sascstudent/project-RefseqRelease/data/taxonomy/ete3_taxadb",
+  "FilterDomainFastas.outputDir": "/exports/sascstudent/project-RefseqRelease/analysis/complete90/library_filtered/protozoa",
+  "FilterDomainFastas.FilterFasta.preCommand": "source activate ete3",
+  "FilterDomainFastas.dustmaskerExe": "/home/npappas/src/ncbi-blast-2.6.0+/bin/dustmasker",
+  "FilterDomainFastas.refseqJson": "/exports/sascstudent/project-RefseqRelease/analysis/demo_test/Refseq90.DNA.json",
+  "FilterDomainFastas.dustmaskOnly": true
+}

src/complete90/filter_configs/vertebrate_mammalian.json

+{
+  "FilterDomainFastas.filterScriptPath": "/exports/sascstudent/project-RefseqRelease/src/demo_test/refseqtools/filter_fasta.py", 
+  "FilterDomainFastas.excludeAccFile": "/exports/sascstudent/project-RefseqRelease/data/accession_sets/redundant_accessions/redundant_accessions.txt",
+  "FilterDomainFastas.excludeAccPrefixes": ["NR", "NG"],
+  "FilterDomainFastas.includeTaxa" : ["9606", "10090", "10116"],
+  "FilterDomainFastas.domainInputDir": "/exports/sascstudent/project-RefseqRelease/data/release90/library/vertebrate_mammalian",
+  "FilterDomainFastas.taxDbPath": "/exports/sascstudent/project-RefseqRelease/data/taxonomy/ete3_taxadb/taxa.sqlite",
+  "FilterDomainFastas.outputDir": "/exports/sascstudent/project-RefseqRelease/analysis/complete90/library_filtered/vertebrate_mamalian",
+  "FilterDomainFastas.FilterFasta.preCommand": "source activate ete3",
+  "FilterDomainFastas.dustmaskerExe": "/home/npappas/src/ncbi-blast-2.6.0+/bin/dustmasker",
+  "FilterDomainFastas.refseqJson": "/exports/sascstudent/project-RefseqRelease/analysis/demo_test/Refseq90.DNA.json"
+}
+

src/complete90/filter_configs/vertebrate_other.json

+{
+  "FilterDomainFastas.filterScriptPath": "/exports/sascstudent/project-RefseqRelease/src/demo_test/refseqtools/filter_fasta.py", 
+  "FilterDomainFastas.excludeAccFile": "/exports/sascstudent/project-RefseqRelease/data/accession_sets/redundant_accessions/redundant_accessions.txt",
+  "FilterDomainFastas.domainInputDir": "/exports/sascstudent/project-RefseqRelease/data/release90/library/vertebrate_other",
+  "FilterDomainFastas.taxDbPath": "/exports/sascstudent/project-RefseqRelease/data/taxonomy/ete3_taxadb/taxa.sqlite",
+  "FilterDomainFastas.outputDir": "/exports/sascstudent/project-RefseqRelease/analysis/complete90/library_filtered/vertebrate_other",
+  "FilterDomainFastas.FilterFasta.preCommand": "source activate ete3",
+  "FilterDomainFastas.dustmaskerExe": "/home/npappas/src/ncbi-blast-2.6.0+/bin/dustmasker",
+  "FilterDomainFastas.refseqJson": "/exports/sascstudent/project-RefseqRelease/analysis/demo_test/Refseq90.DNA.json"
+}
+

src/complete90/filter_configs/viral.json

+{
+  "FilterDomainFastas.filterScriptPath": "/exports/sascstudent/project-RefseqRelease/src/demo_test/refseqtools/filter_fasta.py", 
+  "FilterDomainFastas.domainInputDir": "/exports/sascstudent/project-RefseqRelease/data/release90/library/viral",
+  "FilterDomainFastas.taxDbPath": "/exports/sascstudent/project-RefseqRelease/data/taxonomy/ete3_taxadb",
+  "FilterDomainFastas.outputDir": "/exports/sascstudent/project-RefseqRelease/analysis/complete90/library_filtered/viral",
+  "FilterDomainFastas.FilterFasta.preCommand": "source activate ete3",
+  "FilterDomainFastas.dustmaskerExe": "/home/npappas/src/ncbi-blast-2.6.0+/bin/dustmasker",
+  "FilterDomainFastas.refseqJson": "/exports/sascstudent/project-RefseqRelease/analysis/demo_test/Refseq90.DNA.json",
+  "FilterDomainFastas.dustmaskOnly": true
+}