├── .gitignore ├── LICENSE.txt ├── MANIFEST.in ├── README.txt ├── doc ├── .gitignore ├── Makefile └── rest │ ├── conf.py │ ├── contents.rst │ ├── guidelist.rst │ ├── guides │ ├── devguide.rst │ ├── libnclist.rst │ └── testing.rst │ ├── recipes │ └── alignment_recipes.rst │ ├── reference │ ├── annotation.rst │ ├── blast.rst │ ├── classutil.rst │ ├── cnestedlist.rst │ ├── coordinator.rst │ ├── downloader.rst │ ├── mapping.rst │ ├── metabase.rst │ ├── seqdb.rst │ ├── sequence.rst │ ├── sequtil.rst │ ├── sqlgraph.rst │ └── worldbase.rst │ ├── sequences.rst │ ├── static │ ├── contents.png │ ├── data-browser.png │ ├── pygr-doc.css │ ├── pygr-epydoc.css │ └── pygr-logo.gif │ ├── team.rst │ ├── templates │ ├── index.html │ ├── indexsidebar.html │ ├── layout.html │ └── media.html │ ├── tutorials │ ├── alignment.rst │ ├── annotating-yeast.rst │ ├── annotation.rst │ ├── annotation2.rst │ ├── compgenomics.rst │ ├── db.rst │ ├── db_basic.rst │ ├── develop.rst │ ├── gene.rst │ ├── graphquery.rst │ ├── sequence.rst │ ├── slice_pickle_obj.py │ ├── ucsc_ensembl.rst │ ├── worldbase.rst │ ├── worldbase2.rst │ └── xmlrpc.rst │ └── whatsnew.rst ├── misc ├── debian │ ├── changelog │ ├── compat │ ├── control │ ├── copyright │ ├── pycompat │ ├── rules │ └── watch ├── fink │ ├── pygr-doc.info │ └── pygr-py.info ├── portage │ ├── pygr-9999.ebuild │ └── pygr-VER.ebuild └── pygrrc.example ├── pygr ├── .gitignore ├── Data.py ├── Makefile ├── __init__.py ├── annotation.py ├── apps │ ├── __init__.py │ ├── catalog_downloads.py │ ├── leelabdb.py │ ├── maf2VSgraph.py │ ├── maf2nclist.c │ ├── maf2nclist.h │ ├── maf2nclist.py │ ├── seqref.py │ ├── splicegraph.py │ └── ucsc_ensembl_annot.py ├── blast.py ├── cdict.pxd ├── cdict.pyx ├── cgraph.c ├── cgraph.h ├── classutil.py ├── cnestedlist.pxd ├── cnestedlist.pyx ├── coordinator.py ├── dbfile.py ├── default.h ├── downloader.py ├── graphquery.py ├── intervaldb.c ├── intervaldb.h ├── logger.py ├── mapping.py ├── metabase.py ├── nlmsa_utils.py ├── parse_blast.py ├── schema.py ├── seqdb.py ├── seqfmt.pyx ├── sequence.py ├── sequtil.py ├── sqlgraph.py ├── translationDB.py └── xnestedlist.py ├── setup.cfg ├── setup.py └── tests ├── .gitignore ├── COMMENTS ├── README.txt ├── annotation_dm2_megatest.py ├── annotation_hg18_megatest.py ├── annotation_test.py ├── apps_ucscensembl_test.py ├── blast_test.py ├── data ├── alignments.fa ├── bad_tblastn.txt ├── blastp_output.txt ├── blastx_output.txt ├── dnaseq.fasta ├── exontuples.txt ├── funnyseq.fasta ├── gapping.fa ├── hbb1_mouse.fa ├── hbb1_mouse_rc.fa ├── multiblast_long_correct.txt ├── multiblast_long_output.txt ├── multiblast_output.txt ├── partial-yeast.fasta ├── prefixUnionDict-1.txt ├── prefixUnionDict-2.txt ├── prefixUnionDict-3.txt ├── sp_all_hbb ├── sp_hbb1 ├── tblastn_output.txt ├── test.gz └── test.zip ├── doctests_test.py ├── downloadNLMSA_megatest.py ├── graph_test.py ├── metabase_test.py ├── nlmsa_dm2_megatest.py ├── nlmsa_hg18_megatest.py ├── nlmsa_test.py ├── 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