TODO and experimentation

hill · Nov 11, 2024 · 6697cbb · 6697cbb
1 parent b77295f
commit 6697cbb
Show file tree

Hide file tree

Showing 10 changed files with 559,609 additions and 11 deletions.
diff --git a/README.md b/README.md
@@ -1,17 +1,12 @@
 # DNAvigate
 
+DNAvigate is Tom's experimental genome browser, primarily so he can learn about
+different file formats / methods in bioinformatics-land.
+
+Please don't expect this to be functional or useful! :)
+
 ## Existing Genome Browsers
 
 - UCSC genome brower - https://genome.ucsc.edu/
 - https://bioconductor.org/packages/release/bioc/vignettes/Gviz/inst/doc/Gviz.html
-- IGV - https://igv.org/doc/desktop/
-- 
-
-## TODO
-
-- [ ] open local files
-- [ ] connect to aws/gcp and open large files
-- [ ] Very large file streaming from GCP/AWS
-  - https://cloud.google.com/storage/docs/downloading-objects#downloading-an-object-portion
-- [ ] reference genomes
-
+- IGV - https://igv.org/doc/desktop/
diff --git a/TODO.md b/TODO.md
@@ -0,0 +1,9 @@
+- [x] open local files
+- [ ] handle 50mb files
+- [ ] handle gzip files
+- [ ] file explorer?
+- [ ] connect to aws/gcp and open large files
+- [ ] Very large file streaming from GCP/AWS
+  - https://cloud.google.com/storage/docs/downloading-objects#downloading-an-object-portion
+- [ ] reference genomes
+
diff --git a/examples/.DS_Store b/examples/.DS_Store
diff --git a/examples/HI.4019.002.index_7.ANN0831_R1.fastq b/examples/HI.4019.002.index_7.ANN0831_R1.fastq
diff --git a/examples/HI.4019.002.index_7.ANN0831_R1.fastq.gz b/examples/HI.4019.002.index_7.ANN0831_R1.fastq.gz
diff --git a/examples/P00533.fasta.txt b/examples/P00533.fasta.txt
@@ -0,0 +1,22 @@
+>sp|P00533|EGFR_HUMAN Epidermal growth factor receptor OS=Homo sapiens OX=9606 GN=EGFR PE=1 SV=2
+MRPSGTAGAALLALLAALCPASRALEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEV
+VLGNLEITYVQRNYDLSFLKTIQEVAGYVLIALNTVERIPLENLQIIRGNMYYENSYALA
+VLSNYDANKTGLKELPMRNLQEILHGAVRFSNNPALCNVESIQWRDIVSSDFLSNMSMDF
+QNHLGSCQKCDPSCPNGSCWGAGEENCQKLTKIICAQQCSGRCRGKSPSDCCHNQCAAGC
+TGPRESDCLVCRKFRDEATCKDTCPPLMLYNPTTYQMDVNPEGKYSFGATCVKKCPRNYV
+VTDHGSCVRACGADSYEMEEDGVRKCKKCEGPCRKVCNGIGIGEFKDSLSINATNIKHFK
+NCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAF
+ENLEIIRGRTKQHGQFSLAVVSLNITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKL
+FGTSGQKTKIISNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSCRNVSRGRECVDKCN
+LLEGEPREFVENSECIQCHPECLPQAMNITCTGRGPDNCIQCAHYIDGPHCVKTCPAGVM
+GENNTLVWKYADAGHVCHLCHPNCTYGCTGPGLEGCPTNGPKIPSIATGMVGALLLLLVV
+ALGIGLFMRRRHIVRKRTLRRLLQERELVEPLTPSGEAPNQALLRILKETEFKKIKVLGS
+GAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGI
+CLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAA
+RNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSY
+GVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPK
+FRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQ
+QGFFSSPSTSRTPLLSSLSATSNNSTVACIDRNGLQSCPIKEDSFLQRYSSDPTGALTED
+SIDDTFLPVPEYINQSVPKRPAGSVQNPVYHNQPLNPAPSRDPHYQDPHSTAVGNPEYLN
+TVQPTCVNSTFDSPAHWAQKGSHQISLDNPDYQQDFFPKEAKPNGIFKGSTAENAEYLRV
+APQSSEFIGA
diff --git a/experimentation/README.md b/experimentation/README.md
diff --git a/experimentation/pyproject.toml b/experimentation/pyproject.toml
@@ -0,0 +1,16 @@
+[project]
+name = "experimentation"
+version = "0.1.0"
+description = "Add your description here"
+readme = "README.md"
+requires-python = ">=3.12"
+dependencies = []
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.uv]
+dev-dependencies = [
+    "ipykernel>=6.29.5",
+]
diff --git a/experimentation/src/fasta_viz.ipynb b/experimentation/src/fasta_viz.ipynb
@@ -0,0 +1,22 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "vscode": {
+     "languageId": "plaintext"
+    }
+   },
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/experimentation/uv.lock b/experimentation/uv.lock