Add notebooks

saketkc · Jun 20, 2019 · 3071de3 · 3071de3
1 parent 3839b6f
commit 3071de3
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Showing 14 changed files with 4,417 additions and 65 deletions.
diff --git a/notebooks/BDGP6.ipynb b/notebooks/BDGP6.ipynb
@@ -78,10 +78,16 @@
  "metadata": {},
  "outputs": [],
  "source": [
- "gtf = '/home/cmb-panasas2/skchoudh/genomes/drosophila_melanogaster_BDGP6/annotation/Drosophila_melanogaster.BDGP6.91.gtf'\n",
- "gtf_db = '/home/cmb-panasas2/skchoudh/genomes/drosophila_melanogaster_BDGP6/annotation/Drosophila_melanogaster.BDGP6.91.gtf.db'\n",
- "prefix = '/home/cmb-panasas2/skchoudh/github_projects/riboraptor/riboraptor/annotation/BDGP6/v91'\n",
- "chrsizes = '/home/cmb-panasas2/skchoudh/genomes/drosophila_melanogaster_BDGP6/fasta/Drosophila_melanogaster.BDGP6.dna.toplevel.sizes'\n",
+ "#gtf = '/home/cmb-panasas2/skchoudh/genomes/drosophila_melanogaster_BDGP6/annotation/Drosophila_melanogaster.BDGP6.91.gtf'\n",
+ "#gtf_db = '/home/cmb-panasas2/skchoudh/genomes/drosophila_melanogaster_BDGP6/annotation/Drosophila_melanogaster.BDGP6.91.gtf.db'\n",
+ "#prefix = '/home/cmb-panasas2/skchoudh/github_projects/riboraptor/riboraptor/annotation/BDGP6/v91'\n",
+ "#chrsizes = '/home/cmb-panasas2/skchoudh/genomes/drosophila_melanogaster_BDGP6/fasta/Drosophila_melanogaster.BDGP6.dna.toplevel.sizes'\n",
+ "#mkdir_p(prefix)\n",
+ "\n",
+ "gtf = '/home/cmb-panasas2/skchoudh/genomes/BDGP6/annotation/Drosophila_melanogaster.BDGP6.22.96.gtf'\n",
+ "gtf_db = '/home/cmb-panasas2/skchoudh/genomes/BDGP6/annotation/Drosophila_melanogaster.BDGP6.22.96.gtf.db'\n",
+ "prefix = '/home/cmb-panasas2/skchoudh/github_projects/riboraptor/riboraptor/annotation/BDGP6/v96'\n",
+ "chrsizes = '/home/cmb-panasas2/skchoudh/genomes/BDGP6/fasta/Drosophila_melanogaster.BDGP6.22.dna.toplevel.sizes'\n",
  "mkdir_p(prefix)"
  ]
  },
@@ -117,7 +123,7 @@
  },
  {
  "cell_type": "code",
- "execution_count": 5,
+ "execution_count": 4,
  "metadata": {},
  "outputs": [],
  "source": [
@@ -130,7 +136,7 @@
  },
  {
  "cell_type": "code",
- "execution_count": 6,
+ "execution_count": 5,
  "metadata": {},
  "outputs": [
  {
@@ -155,7 +161,7 @@
  },
  {
  "cell_type": "code",
- "execution_count": 7,
+ "execution_count": 6,
  "metadata": {},
  "outputs": [],
  "source": [
@@ -239,16 +245,16 @@
  },
  {
  "cell_type": "code",
- "execution_count": 8,
+ "execution_count": 7,
  "metadata": {},
  "outputs": [
  {
  "data": {
  "text/plain": [
- "<BedTool(/home/cmb-panasas2/skchoudh/github_projects/riboraptor/riboraptor/annotation/BDGP6/v91/cds.bed.gz)>"
+ "<BedTool(/home/cmb-panasas2/skchoudh/github_projects/riboraptor/riboraptor/annotation/BDGP6/v96/cds.bed.gz)>"
  ]
  },
- "execution_count": 8,
+ "execution_count": 7,
  "metadata": {},
  "output_type": "execute_result"
  }
@@ -331,16 +337,16 @@
  },
  {
  "cell_type": "code",
- "execution_count": 9,
+ "execution_count": 8,
  "metadata": {},
  "outputs": [
  {
  "data": {
  "text/plain": [
- "<BedTool(/home/cmb-panasas2/skchoudh/github_projects/riboraptor/riboraptor/annotation/BDGP6/v91/stop_codon.bed.gz)>"
+ "<BedTool(/home/cmb-panasas2/skchoudh/github_projects/riboraptor/riboraptor/annotation/BDGP6/v96/stop_codon.bed.gz)>"
  ]
  },
- "execution_count": 9,
+ "execution_count": 8,
  "metadata": {},
  "output_type": "execute_result"
  }
@@ -383,21 +389,21 @@
  ],
  "metadata": {
  "kernelspec": {
- "display_name": "Python [default]",
+ "display_name": "Python [conda env:riboraptor]",
  "language": "python",
- "name": "python2"
+ "name": "conda-env-riboraptor-py"
  },
  "language_info": {
  "codemirror_mode": {
  "name": "ipython",
- "version": 2
+ "version": 3
  },
  "file_extension": ".py",
  "mimetype": "text/x-python",
  "name": "python",
  "nbconvert_exporter": "python",
- "pygments_lexer": "ipython2",
- "version": "2.7.15"
+ "pygments_lexer": "ipython3",
+ "version": "3.6.7"
  }
  },
  "nbformat": 4,