Update and run all jupyter notebooks

tanghaibao · Jan 14, 2019 · 5fbcf3c · 5fbcf3c
1 parent 08a4798
commit 5fbcf3c
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Showing 10 changed files with 864 additions and 1,596 deletions.
diff --git a/goatools/rpt/rpt_lev_depth.py b/goatools/rpt/rpt_lev_depth.py
@@ -142,7 +142,7 @@ def _write_summary_cnts(self, cnts):
  self.log.write('Lev BP MF CC BP MF CC\n')
  self.log.write('--- ---- ---- ---- ---- ---- ----\n')
  for i in range(max_val+1):
- vals = ['{:>5}'.format(cnts[desc][i][ns]) for desc in cnts for ns in self.nss]
+ vals = ['{:>5}'.format(cnts[desc][i][ns]) for desc in sorted(cnts) for ns in self.nss]
  self.log.write('{:>02} {}\n'.format(i, ' '.join(vals)))
 
  @staticmethod

diff --git a/notebooks/annotation_coverage.ipynb b/notebooks/annotation_coverage.ipynb
@@ -19,10 +19,8 @@
  },
  {
  "cell_type": "code",
- "execution_count": 18,
- "metadata": {
- "collapsed": false
- },
+ "execution_count": 5,
+ "metadata": {},
  "outputs": [
  {
  "name": "stdout",
@@ -49,11 +47,18 @@
  },
  {
  "cell_type": "code",
- "execution_count": 19,
- "metadata": {
- "collapsed": false
- },
- "outputs": [],
+ "execution_count": 6,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ " 20,385 items READ: gene2go\n",
+ " 11,563 items READ: gene2go\n"
+ ]
+ }
+ ],
  "source": [
  "from goatools.associations import read_ncbi_gene2go\n",
  "\n",
@@ -70,11 +75,17 @@
  },
  {
  "cell_type": "code",
- "execution_count": 20,
- "metadata": {
- "collapsed": false
- },
- "outputs": [],
+ "execution_count": 7,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ " 31,948 items READ: gene2go\n"
+ ]
+ }
+ ],
  "source": [
  "from collections import defaultdict, namedtuple\n",
  "\n",
@@ -94,14 +105,12 @@
  },
  {
  "cell_type": "code",
- "execution_count": 21,
- "metadata": {
- "collapsed": false
- },
+ "execution_count": 8,
+ "metadata": {},
  "outputs": [],
  "source": [
- "from goatools.test_data.genes_NCBI_9606_ProteinCoding import GeneID2nt as GeneID2nt_human\n",
- "from goatools.test_data.genes_NCBI_7227_ProteinCoding import GeneID2nt as GeneID2nt_fly\n",
+ "from goatools.test_data.genes_NCBI_9606_ProteinCoding import GENEID2NT as GeneID2nt_human\n",
+ "from goatools.test_data.genes_NCBI_7227_ProteinCoding import GENEID2NT as GeneID2nt_fly\n",
  "lst = [\n",
  " (9606, GeneID2nt_human),\n",
  " (7227, GeneID2nt_fly)\n",
@@ -118,10 +127,8 @@
  },
  {
  "cell_type": "code",
- "execution_count": 22,
- "metadata": {
- "collapsed": false
- },
+ "execution_count": 9,
+ "metadata": {},
  "outputs": [],
  "source": [
  "cov_data = []\n",
@@ -156,19 +163,17 @@
  },
  {
  "cell_type": "code",
- "execution_count": 23,
- "metadata": {
- "collapsed": false
- },
+ "execution_count": 10,
+ "metadata": {},
  "outputs": [
  {
  "name": "stdout",
  "output_type": "stream",
  "text": [
  " taxid GOs GeneIDs Coverage\n",
  "------ ------ ------- ----------------------\n",
- " 9606 16,436 18,273 87% GO coverage of 20,913 protein-coding genes\n",
- " 7227 6,995 10,591 76% GO coverage of 13,919 protein-coding genes\n"
+ " 9606 17,975 18,475 88% GO coverage of 20,913 protein-coding genes\n",
+ " 7227 8,352 10,635 76% GO coverage of 13,919 protein-coding genes\n"
  ]
  }
  ],
@@ -191,29 +196,29 @@
  "cell_type": "markdown",
  "metadata": {},
  "source": [
- "Copyright (C) 2016, DV Klopfenstein, H Tang. All rights reserved."
+ "Copyright (C) 2016-2019, DV Klopfenstein, H Tang. All rights reserved."
  ]
  }
  ],
  "metadata": {
  "kernelspec": {
- "display_name": "Python 2",
+ "display_name": "Python 3",
  "language": "python",
- "name": "python2"
+ "name": "python3"
  },
  "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": "2.7.11"
+ "pygments_lexer": "ipython3",
+ "version": "3.6.1"
  }
  },
  "nbformat": 4,
- "nbformat_minor": 0
+ "nbformat_minor": 1
 }