├── .gitattributes ├── .github └── workflows │ └── LocusPocus.yml ├── .gitignore ├── .travis.yml ├── 0Record ├── AEGeAn.def ├── CHANGELOG.md ├── INSTALL.md ├── LICENSE ├── LocusPocus ├── .gitattributes ├── .gitignore ├── LocusPocus │ ├── __init__.py │ ├── _version.py │ ├── am10.py │ ├── cdhit.py │ ├── crg.py │ ├── download.py │ ├── exons.py │ ├── fasta.py │ ├── generic.py │ ├── genomedb.py │ ├── hymbase.py │ ├── iloci.py │ ├── mrnas.py │ ├── pdom.py │ ├── proteins.py │ ├── refseq.py │ ├── registry.py │ ├── stats.py │ └── tair.py ├── MANIFEST.in ├── genome_configs │ ├── Aaeg.yml │ ├── Acen.yml │ ├── Acep.yml │ ├── Ador.yml │ ├── Aech.yml │ ├── Aflo.yml │ ├── Agam.yml │ ├── Am10.yml │ ├── Am32.yml │ ├── Am45.yml │ ├── Amel.yml │ ├── Apro.yml │ ├── Atha.yml │ ├── Att6.yml │ ├── Bdis.yml │ ├── Bimp.yml │ ├── Bole.yml │ ├── Btau.yml │ ├── Bter.yml │ ├── Cari.yml │ ├── Cele.yml │ ├── Cf75.yml │ ├── Cfhb.yml │ ├── Cflo.yml │ ├── Clan.yml │ ├── Crei.yml │ ├── Csub.yml │ ├── Cvar.yml │ ├── Dmel.yml │ ├── Dnov.yml │ ├── Dqcr.yml │ ├── Dqua.yml │ ├── Drer.yml │ ├── Emex.yml │ ├── Gmax.yml │ ├── Grai.yml │ ├── Hlab.yml │ ├── Hs85.yml │ ├── Hsal.yml │ ├── Hsap.yml │ ├── Hshb.yml │ ├── Lalb.yml │ ├── Lcan.yml │ ├── Lhum.yml │ ├── Macu.yml │ ├── Mcom.yml │ ├── Mmus.yml │ ├── Mpus.yml │ ├── Mqua.yml │ ├── Mrot.yml │ ├── Mtru.yml │ ├── Mvit.yml │ ├── Nvit.yml │ ├── Ob54.yml │ ├── Obir.yml │ ├── Ocin.yml │ ├── Oluc.yml │ ├── Osat.yml │ ├── Otau.yml │ ├── Pbar.yml │ ├── Pcan.yml │ ├── Pccr.yml │ ├── Pdom.yml │ ├── Pdtl.yml │ ├── Pfal.yml │ ├── Scer.yml │ ├── Sihb.yml │ ├── Sinv.yml │ ├── Tcac.yml │ ├── Tcas.yml │ ├── Turt.yml │ ├── Vcar.yml │ ├── Xtro.yml │ ├── Znev.yml │ ├── bumblebees.txt │ ├── bwasp.txt │ ├── chlorophyta.txt │ ├── honeybees.txt │ └── hymenoptera.txt ├── install.sh ├── scripts │ ├── fidibus │ ├── fidibus-compact.py │ ├── fidibus-filens.py │ ├── fidibus-format-gff3.py │ ├── fidibus-glean-to-gff3.py │ ├── fidibus-ilocus-summary.py │ ├── fidibus-milocus-summary.py │ ├── fidibus-monitor-refseq.py │ ├── fidibus-namedup.py │ ├── fidibus-pilocus-summary.py │ ├── fidibus-stats.py │ └── fidibus-uniq.py ├── setup.cfg ├── setup.py ├── testdata │ ├── conf │ │ ├── Bimp.yml │ │ ├── Bvul.yml │ │ ├── Osat.yml │ │ ├── Pccr.yml │ │ ├── Pdtl.yml │ │ ├── bumblebees.txt │ │ ├── honeybees.txt │ │ └── mythical.txt │ ├── demo-workdir │ │ ├── Ador │ │ │ └── GCF_000469605.1_Apis_dorsata_1.3_genomic.gff.gz │ │ ├── Aech │ │ │ └── GCF_000204515.1_Aech_3.9_genomic.gff.gz │ │ ├── Am10 │ │ │ ├── Amel_2.0_scaffolds.fa.gz │ │ │ ├── amel_OGSv1.0.gff.gz │ │ │ └── amel_OGSv1.0_pep.fa.gz │ │ ├── Am32 │ │ │ ├── Amel_4.5_scaffolds.fa.gz │ │ │ └── amel_OGSv3.2_pep.fa.gz │ │ ├── Atha │ │ │ ├── .gitignore │ │ │ ├── Atha.gdna.fa │ │ │ ├── Atha.gff3 │ │ │ ├── Atha.ilocus.mrnas.gff3 │ │ │ ├── Atha.mrnas.txt │ │ │ └── Atha.with-introns.gff3 │ │ ├── Att6 │ │ │ ├── TAIR6-gdna.fa.gz │ │ │ └── TAIR6-genes.gff3.gz │ │ ├── Bdis │ │ │ ├── .gitignore │ │ │ ├── Bdis.gdna.fa │ │ │ └── Bdis.gff3 │ │ ├── Cfhb │ │ │ ├── Cflo_3.3_scaffolds.fa.gz │ │ │ └── cflo_OGSv3.3.gff3.gz │ │ ├── Dmfb │ │ │ ├── Dmfb.orig.fa.gz │ │ │ ├── dmel-5.48-ncbi.gff3.gz │ │ │ └── protein.fa.gz │ │ ├── Dnov │ │ │ ├── .gitignore │ │ │ ├── Dnov.gff3 │ │ │ └── Dnov.ilocus.mrnas.gff3 │ │ ├── Hlab │ │ │ ├── Habropoda_laboriosa.v1.0.fa.gz │ │ │ ├── Habropoda_laboriosa_v1.2.gff.gz │ │ │ └── Habropoda_laboriosa_v1.2.pep.fa.gz │ │ ├── Hsal │ │ │ ├── GCF_000147195.1_HarSal_1.0_genomic.fna.gz │ │ │ └── GCF_000147195.1_HarSal_1.0_protein.faa.gz │ │ ├── Mmus │ │ │ └── GCF_000001635.24_GRCm38.p4_genomic.fna.gz │ │ ├── Pbar │ │ │ └── GCF_000187915.1_Pbar_UMD_V03_genomic.gff.gz │ │ ├── Pccr │ │ │ ├── PCAN.v01.fa.gz │ │ │ ├── PCAN.v01.gff3.gz │ │ │ └── PCAN.v01.pep.fa.gz │ │ ├── Pdtl │ │ │ ├── pdom-annot.gff3 │ │ │ ├── pdom-gdna.fa.gz │ │ │ └── pdom-proteins.fa │ │ ├── Scer │ │ │ ├── .gitignore │ │ │ ├── Scer.all.prot.fa │ │ │ └── Scer.protids.txt │ │ ├── Sihb │ │ │ ├── Sinv_1.0_scaffolds.fa.gz │ │ │ ├── sinv_OGSv2.2.3.gff3.gz │ │ │ └── sinv_OGSv2.2.3_pep.fa.gz │ │ ├── Tcas │ │ │ └── GCF_000002335.2_Tcas_3.0_genomic.fna.gz │ │ └── Vcar │ │ │ ├── GCF_000143455.1_v1.0_genomic.fna.gz │ │ │ ├── GCF_000143455.1_v1.0_genomic.gff.gz │ │ │ ├── GCF_000143455.1_v1.0_protein.faa.gz │ │ │ ├── Vcar.all.cds.fa │ │ │ ├── Vcar.all.mrnas.fa │ │ │ ├── Vcar.all.mrnas.gff3 │ │ │ ├── Vcar.all.pre-mrnas.fa │ │ │ ├── Vcar.cds.fa │ │ │ ├── Vcar.cds.tsv │ │ │ ├── Vcar.exons.fa │ │ │ ├── Vcar.exons.tsv │ │ │ ├── Vcar.filens.tsv │ │ │ ├── Vcar.ilens.tsv │ │ │ ├── Vcar.iloci.fa │ │ │ ├── Vcar.iloci.gff3 │ │ │ ├── Vcar.iloci.tsv │ │ │ ├── Vcar.ilocus.mrnas.gff3 │ │ │ ├── Vcar.ilocus.mrnas.temp │ │ │ ├── Vcar.ilocus.mrnas.txt │ │ │ ├── Vcar.introns.fa │ │ │ ├── Vcar.introns.tsv │ │ │ ├── Vcar.miloci.fa │ │ │ ├── Vcar.miloci.gff3 │ │ │ ├── Vcar.miloci.tsv │ │ │ ├── Vcar.mrnas.fa │ │ │ ├── Vcar.mrnas.gff3 │ │ │ ├── Vcar.mrnas.temp │ │ │ ├── Vcar.mrnas.tsv │ │ │ ├── Vcar.mrnas.txt │ │ │ ├── Vcar.pre-mrnas.fa │ │ │ ├── Vcar.pre-mrnas.tsv │ │ │ ├── Vcar.prot.fa │ │ │ ├── Vcar.protein2ilocus.tsv │ │ │ ├── Vcar.protids.txt │ │ │ ├── Vcar.simple-iloci.txt │ │ │ ├── Vcar.with-introns.gff3 │ │ │ └── ilens.temp │ ├── fasta │ │ ├── am10-gdna-out.fa │ │ ├── am10-prot-out.fa │ │ ├── am32-gdna-out.fa │ │ ├── am32-prot-out.fa │ │ ├── atha-all-mrnas.fa │ │ ├── atha-all-pre-mrnas.fa │ │ ├── atha-cds.fa │ │ ├── atha-exons.fa │ │ ├── atha-introns.fa │ │ ├── atha-mrnas.fa │ │ ├── atha-pre-mrnas.fa │ │ ├── bdis-iloci.fa │ │ ├── bdis-miloci.fa │ │ ├── dmel-fb-gdna-ut-out.fa │ │ ├── dmel-fb-prot-ut-out.fa │ │ ├── generic.gdna.fa.gz │ │ ├── generic.prot.fa │ │ ├── hlab-first-20-prot-out.fa │ │ ├── hlab-first-20-prot.fa.gz │ │ ├── hlab-first-6-out.fa │ │ ├── hlab-first-6.fa.gz │ │ ├── hsal-13-prot-out.fa │ │ ├── hsal-first-7-out.fa │ │ ├── hymbase-format-Sihb-prot.fa │ │ ├── hymbase-format-sihb.fa │ │ ├── mmus-gdna.fa │ │ ├── scer-few-prots.fa │ │ ├── tair6-gdna-out.fa │ │ └── tcas-first-33-out.fa │ ├── gff3 │ │ ├── am10-format.gff3 │ │ ├── am10-loci.gff3 │ │ ├── atha-all-mrnas.gff3 │ │ ├── atha-mrnas.gff3 │ │ ├── bdis-iloci.gff3 │ │ ├── bdis-ilocus-mrnas.gff3 │ │ ├── bdis-miloci.gff3 │ │ ├── bdis-reps.gff3 │ │ ├── beebase-format-hlab.gff3 │ │ ├── dmel-net-loci.gff3 │ │ ├── dmel-net.gff3 │ │ ├── dnov-all-mrnas.gff3 │ │ ├── dnov-mrnas.gff3 │ │ ├── dqua-275-loci.gff3 │ │ ├── dqua-275.gff3 │ │ ├── generic.gff3 │ │ ├── hlab-238-loci.gff3 │ │ ├── hlab-238.gff3 │ │ ├── hymbase-format-cfhb.gff3 │ │ ├── hymbase-format-sihb.gff3 │ │ ├── ncbi-format-ador.gff3 │ │ ├── ncbi-format-aech.gff3 │ │ ├── ncbi-format-dmel.gff3 │ │ ├── ncbi-format-pbar.gff3 │ │ ├── pdom-266-loci.gff3 │ │ ├── pdom-266.gff3 │ │ ├── tair6-format.gff3 │ │ ├── tair6-loci.gff3 │ │ ├── xtro-3genes-loci.gff3 │ │ └── xtro-3genes.gff3 │ └── misc │ │ ├── bdis-filens.tsv │ │ ├── bdis-ilens.tsv │ │ ├── bdis-ilocus-mrnas.tsv │ │ ├── bdis-mrnas.txt │ │ ├── bdis-simple-iloci.txt │ │ ├── bdis-simple.txt │ │ └── hymhub-head.clstr ├── uninstall.sh └── versioneer.py ├── Makefile ├── README.md ├── VERSION ├── data ├── fasta │ ├── mrj.cds.fa │ ├── mrj.gdna.fa │ └── mrj.mrna.fa ├── gff3 │ ├── AT1G05320-codons.gff3 │ ├── AT1G05320-sansexons.gff3 │ ├── AT1G05320-sansutrs.gff3 │ ├── AT1G05320-withprot.gff3 │ ├── AT1G05320.gff3 │ ├── FBgn0035002-codons.gff3 │ ├── FBgn0035002-sansexons.gff3 │ ├── FBgn0035002-sansutrs.gff3 │ ├── FBgn0035002.gff3 │ ├── acep-syndrome.gff3 │ ├── ador-except-in.gff3 │ ├── ador-except-out.gff3 │ ├── aech-dachsous-out.gff3 │ ├── aech-dachsous.gff3 │ ├── amel-aug-athal-param.gff3 │ ├── amel-aug-dmel-param.gff3 │ ├── amel-aug-nvit-param.gff3 │ ├── amel-dock-pmrna.gff3 │ ├── amel-dock.gff3 │ ├── amel-gene-multitrans-canon.gff3 │ ├── amel-gene-multitrans.gff3 │ ├── amel-lsm-out-cds.gff3 │ ├── amel-lsm.gff3 │ ├── amel-ncbi-g7.gff3 │ ├── amel-ncbi-g716.gff3 │ ├── amel-ogs-g7.gff3 │ ├── amel-ogs-g716.gff3 │ ├── amel-plap-out-cds.gff3 │ ├── amel-plap-out.gff3 │ ├── amel-plap.gff3 │ ├── amel-pseudo-pmrna.gff3 │ ├── amel-pseudo.gff3 │ ├── amel-shal-pmrna.gff3 │ ├── amel-shal.gff3 │ ├── bogus-three-genes.gff3 │ ├── dmel-pseudofeat-sort-test-in.gff3 │ ├── gaeval-example1-fixed.gff3 │ ├── gaeval-example1-in.gff3 │ ├── gaeval-example5-fixed.gff3 │ ├── gaeval-example5-in.gff3 │ ├── gaeval-simple.gff3 │ ├── gaeval-stream-unit-test-1-out.gff3 │ ├── gaeval-stream-unit-test-1.gff3 │ ├── gaeval-stream-unit-test-2-out.gff3 │ ├── gaeval-stream-unit-test-2.gff3 │ ├── gene-stream-data.gff3 │ ├── grape-cds.gff3 │ ├── grape-codons.gff3 │ ├── grape-pred-mrnas.gff3 │ ├── grape-pred.gff3 │ ├── grape-refr-mrnas.gff3 │ ├── grape-refr.gff3 │ ├── grape-test.gff3 │ ├── grape-utrs.gff3 │ ├── ilocus.in.genes.gff3 │ ├── ilocus.in.gff3 │ ├── ilocus.out.noskipends.gff3 │ ├── ilocus.out.skipends.gff3 │ ├── infer-parent-1-in.gff3 │ ├── mrj.gff3 │ ├── mrot-cst-out-cds.gff3 │ ├── mrot-cst.gff3 │ ├── nvit-exospindle-out.gff3 │ ├── nvit-exospindle.gff3 │ ├── pbar-partial.gff3 │ ├── pd0159-pred.gff3 │ ├── pd0159-refr.gff3 │ ├── single-exon-cds.gff3 │ ├── single-exon-codons.gff3 │ ├── single-exon-test.gff3 │ ├── single-exon-utrs.gff3 │ ├── tair-altsplice.gff3 │ ├── zitest-01.gff3 │ ├── zitest-02.gff3 │ └── zitest-03.gff3 ├── misc │ ├── amel-ogs-ilens.txt │ ├── amel-ogs-vs-ncbi-parseval-delta.txt │ ├── amel-ogs-vs-ncbi-parseval-html │ │ ├── Group7.16 │ │ │ ├── 110654-116915.html │ │ │ ├── 117229-119778.html │ │ │ ├── 120837-124114.html │ │ │ ├── 35004-53221.html │ │ │ ├── 54607-73036.html │ │ │ ├── 613-12837.html │ │ │ ├── 75713-79494.html │ │ │ ├── 88301-109742.html │ │ │ └── index.html │ │ ├── LICENSE │ │ ├── aegean-logo-v1.0-128.png │ │ ├── bg.gif │ │ ├── cdsmatches.html │ │ ├── index.html │ │ ├── nonmatches.html │ │ ├── parseval-logo-h100px.png │ │ ├── parseval.css │ │ ├── pe.filter │ │ ├── pe.style │ │ └── vendor │ │ │ ├── jquery.dataTables.js │ │ │ ├── jquery.js │ │ │ ├── mootools-core-1.3.2-full-nocompat-yc.js │ │ │ └── mootools-more-1.3.2.1.js │ ├── amel-ogs-vs-ncbi-parseval.txt │ ├── libpango.supp │ ├── libpixman.supp │ ├── zitest-01-ilens.tsv │ ├── zitest-02-ilens.tsv │ └── zitest-03-ilens.tsv ├── scripts │ ├── align-convert.py │ ├── build-docs.pl │ ├── check-gff3.py │ ├── github-actions-prereqs.sh │ ├── glb2lcl.pl │ ├── lcl2glb.pl │ ├── lpdriver.py │ ├── miloci.py │ ├── post-commit │ ├── pre-commit │ ├── seq-reg.py │ ├── uloci.py │ └── version.py └── share │ ├── LICENSE │ ├── aegean-logo-v1.0-128.png │ ├── bg.gif │ ├── parseval-logo-h100px.png │ ├── parseval.css │ ├── pe.filter │ ├── pe.style │ └── vendor │ ├── jquery.dataTables.js │ ├── jquery.js │ ├── mootools-core-1.3.2-full-nocompat-yc.js │ └── mootools-more-1.3.2.1.js ├── docs ├── Makefile ├── aegean-logo-v1_0-128.png ├── api.rst ├── bogus.png ├── canon.rst ├── citing.rst ├── conf.py ├── contrib.rst ├── gaeval.rst ├── gff3.rst ├── index.rst ├── install.rst ├── license.rst ├── loci.rst ├── locuspocus.rst └── parseval.rst ├── inc └── core │ ├── AgnAttributeFilterStream.h │ ├── AgnCliquePair.h │ ├── AgnCompareReportHTML.h │ ├── AgnCompareReportText.h │ ├── AgnComparison.h │ ├── AgnFilterStream.h │ ├── AgnGaevalVisitor.h │ ├── AgnGeneStream.h │ ├── AgnIdFilterStream.h │ ├── AgnInferCDSVisitor.h │ ├── AgnInferExonsVisitor.h │ ├── AgnInferParentStream.h │ ├── AgnLocus.h │ ├── AgnLocusFilterStream.h │ ├── AgnLocusMapVisitor.h │ ├── AgnLocusRefineStream.h │ ├── AgnLocusStream.h │ ├── AgnMrnaRepVisitor.h │ ├── AgnPseudogeneFixVisitor.h │ ├── AgnRemoveChildrenVisitor.h │ ├── AgnTranscriptClique.h │ ├── AgnTypecheck.h │ ├── AgnUnitTest.h │ ├── AgnUtils.h │ └── aegean.h ├── src ├── ParsEval │ ├── parseval.c │ ├── pe_options.c │ ├── pe_options.h │ ├── pe_utils.c │ └── pe_utils.h ├── canon-gff3.c ├── core │ ├── AgnAttributeFilterStream.c │ ├── AgnCliquePair.c │ ├── AgnCompareReportHTML.c │ ├── AgnCompareReportText.c │ ├── AgnComparison.c │ ├── AgnFilterStream.c │ ├── AgnGaevalVisitor.c │ ├── AgnGeneStream.c │ ├── AgnIdFilterStream.c │ ├── AgnInferCDSVisitor.c │ ├── AgnInferExonsVisitor.c │ ├── AgnInferParentStream.c │ ├── AgnLocus.c │ ├── AgnLocusFilterStream.c │ ├── AgnLocusMapVisitor.c │ ├── AgnLocusRefineStream.c │ ├── AgnLocusStream.c │ ├── AgnMrnaRepVisitor.c │ ├── AgnPseudogeneFixVisitor.c │ ├── AgnRemoveChildrenVisitor.c │ ├── AgnTranscriptClique.c │ ├── AgnTypecheck.c │ ├── AgnUnitTest.c │ └── AgnUtils.c ├── gaeval.c ├── locuspocus.c ├── pmrna.c ├── tidygff3.c └── xtractore.c └── test ├── AT1G05320.sh ├── AmelOGSvsNCBI.sh ├── FBgn0035002.sh ├── align-convert.sh ├── canon-gff3-ft.sh ├── gaeval-ft.sh ├── iLocusParsing.sh ├── misc-ft.sh ├── unittests.c └── xtractore-ft.sh /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BrendelGroup/AEGeAn/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/workflows/LocusPocus.yml: -------------------------------------------------------------------------------- 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