this is for holding javascript data
Ino de Bruijn Init user given assembly plot
almost 10 years ago
Commit id: 633c95f09693ba3b74624565d5f3da48c9c1508f
deletions | additions
diff --git a/notebooks/user-contig-plot.ipynb b/notebooks/user-contig-plot.ipynb
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index 0000000..47ea072
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"source": [
"## Test notebook run from the commandline with runipy\n",
"[runipy](https://github.com/paulgb/runipy)"
]
},
{
"cell_type": "code",
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"input": [
"%%bash\n",
"mkdir -p test\n",
"cd test\n",
"IPY_FASTA_URL=\"http://ino.pm/share/figshare-error/test.fasta\"\n",
"wget $IPY_FASTA_URL\n",
"bash /media/milou/glob/github/metassemble/scripts/validate/nucmer/run-nucmer.sh \\\n",
" /media/milou/glob/projects/masmvali-partdeux/reassembly-filtered-reads/Sample_1ng_even/ref.fa \\\n",
" test.fasta \\\n",
" nucmer"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Using: /usr/bin/nucmer\n",
"Using: /usr/bin/show-coords\n"
]
},
{
"output_type": "stream",
"stream": "stderr",
"text": [
"--2014-07-09 17:21:37-- http://ino.pm/share/figshare-error/test.fasta\n",
"Sl\u00e5r upp ino.pm (ino.pm)... 46.30.212.77\n",
"Ansluter till ino.pm (ino.pm)|46.30.212.77|:80... ansluten.\n",
"HTTP-beg\u00e4ran skickad, v\u00e4ntar p\u00e5 svar... 200 OK\n",
"L\u00e4ngd: 94 [text/plain]\n",
"Sparar till: \"test.fasta.2\"\n",
"\n",
" 0K 100% 12.5M=0s\n",
"\n",
"2014-07-09 17:21:37 (12.5 MB/s) - \"test.fasta.2\" sparades [94/94]\n",
"\n",
"1: PREPARING DATA\n",
"2,3: RUNNING mummer AND CREATING CLUSTERS\n",
"# reading input file \"nucmer.ntref\" of length 169669171\n",
"# construct suffix tree for sequence of length 169669171\n",
"# (maximum reference length is 536870908)\n",
"# (maximum query length is 4294967295)\n",
"# process 1696691 characters per dot\n",
"#....................................................................................................\n",
"# CONSTRUCTIONTIME /usr/bin/mummer nucmer.ntref 144.98\n",
"# reading input file \"/media/milou/glob/github/masmvali-publication/notebooks/test/test.fasta\" of length 60\n",
"# matching query-file \"/media/milou/glob/github/masmvali-publication/notebooks/test/test.fasta\"\n",
"# against subject-file \"nucmer.ntref\"\n",
"# COMPLETETIME /usr/bin/mummer nucmer.ntref 145.17\n",
"# SPACE /usr/bin/mummer nucmer.ntref 164.51\n",
"4: FINISHING DATA\n"
]
}
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"prompt_number": 1
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"cell_type": "code",
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"input": [
"import os\n",
"fasta_url = os.environ.get('IPY_FASTA_URL', None)\n",
"if not fasta_url:\n",
" raise(Exception(\"problem no url specified!\"))"
],
"language": "python",
"metadata": {},
"outputs": [
{
"ename": "Exception",
"evalue": "problem!",
"output_type": "pyerr",
"traceback": [
"\u001b[1;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[1;31mException\u001b[0m Traceback (most recent call last)",
"\u001b[1;32m\u001b[0m in \u001b[0;36m\u001b[1;34m()\u001b[0m\n\u001b[0;32m 2\u001b[0m \u001b[0mfasta_url\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mos\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0menviron\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mget\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m'IPY_FASTA_URL'\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mNone\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 3\u001b[0m \u001b[1;32mif\u001b[0m \u001b[1;32mnot\u001b[0m \u001b[0mfasta_url\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 4\u001b[1;33m \u001b[1;32mraise\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mException\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m\"problem!\"\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[1;31mException\u001b[0m: problem!"
]
}
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{
"cell_type": "code",
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"input": [
"import urllib2\n",
"response = urllib2.urlopen(fasta_url)\n",
"html = response.read()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"ename": "AttributeError",
"evalue": "'NoneType' object has no attribute 'timeout'",
"output_type": "pyerr",
"traceback": [
"\u001b[1;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[1;31mAttributeError\u001b[0m Traceback (most recent call last)",
"\u001b[1;32m\u001b[0m in \u001b[0;36m\u001b[1;34m()\u001b[0m\n\u001b[0;32m 1\u001b[0m \u001b[1;32mimport\u001b[0m \u001b[0murllib2\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 2\u001b[1;33m \u001b[0mresponse\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0murllib2\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0murlopen\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfasta_url\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 3\u001b[0m \u001b[0mhtml\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mresponse\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mread\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;32m/usr/lib/python2.7/urllib2.pyc\u001b[0m in \u001b[0;36murlopen\u001b[1;34m(url, data, timeout)\u001b[0m\n\u001b[0;32m 124\u001b[0m \u001b[1;32mif\u001b[0m \u001b[0m_opener\u001b[0m \u001b[1;32mis\u001b[0m \u001b[0mNone\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 125\u001b[0m \u001b[0m_opener\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mbuild_opener\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 126\u001b[1;33m \u001b[1;32mreturn\u001b[0m \u001b[0m_opener\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mopen\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0murl\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mdata\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mtimeout\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 127\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 128\u001b[0m \u001b[1;32mdef\u001b[0m \u001b[0minstall_opener\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mopener\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;32m/usr/lib/python2.7/urllib2.pyc\u001b[0m in \u001b[0;36mopen\u001b[1;34m(self, fullurl, data, timeout)\u001b[0m\n\u001b[0;32m 389\u001b[0m \u001b[0mreq\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0madd_data\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 390\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 391\u001b[1;33m \u001b[0mreq\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mtimeout\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mtimeout\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 392\u001b[0m \u001b[0mprotocol\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mreq\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mget_type\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 393\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;31mAttributeError\u001b[0m: 'NoneType' object has no attribute 'timeout'"
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