this is for holding javascript data
Ino de Bruijn Start counting kmers for chimerism detection
almost 10 years ago
Commit id: c89407e09226d4aee5d04528cd21f50517e48fef
deletions | additions
diff --git a/notebooks/kmer-counting.ipynb b/notebooks/kmer-counting.ipynb
new file mode 100644
index 0000000..d290f19
--- /dev/null
+++ b/notebooks/kmer-counting.ipynb
...
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"input": [
"from Bio import SeqIO\n",
"\n",
"with open(\"/media/milou/glob/projects/masmvali-partdeux/reassembly-filtered-reads/Sample_1ng_even/Mircea_07102013_selected_refs.fasta\") as ffile:\n",
" record_dict = SeqIO.to_dict(SeqIO.parse(ffile, 'fasta'))"
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"input": [
"!echo \"`cd /media/milou/glob/github/masm-vali/masmvali/ && git log -1`\""
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"commit 5e4c182ff5f75d603319cffc11533b810840d2ed\r\n",
"Author: Ino de Bruijn \r\n",
"Date: Tue Jul 8 18:07:20 2014 +0200\r\n",
"\r\n",
" Add contig-metagenome-cover property for backward compatibility\r\n"
]
}
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{
"cell_type": "code",
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"input": [
"import sys\n",
"import os\n",
"import re\n",
"sys.path.append('/media/milou/glob/github/masm-vali/masmvali/')\n",
"import assembly\n",
"reload(assembly)\n",
"import nucmer\n",
"reload(nucmer)\n",
"import refgenome\n",
"reload(refgenome)\n",
"import validation\n",
"reload(validation)\n",
"import metassemble\n",
"reload(metassemble)\n",
"import jellyfish\n",
"reload(jellyfish)\n",
"\n",
"import utils\n",
"reload(utils)\n",
"\n",
"import warnings\n",
"import numpy as np\n",
"import matplotlib as mpl\n",
"import matplotlib.pyplot as plt"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 27
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{
"cell_type": "code",
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"input": [
"jellyfish.Jellyfish(\"/media/milou/glob/projects/masmvali-partdeux/reassembly-filtered-reads/Sample_1ng_even/ref-jellyfish/Bacteroides_thetaiotaomicron_VPI-5482-19.jf\").count_kmer(\"GTCCCATGGAATCAATAGC\")"
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"prompt_number": 26,
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"0"
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"jfr = jellyfish.JellyfishRef(\"/media/milou/glob/projects/masmvali-partdeux/reassembly-filtered-reads/Sample_1ng_even/Mircea_07102013_selected_refs.fasta\", \n",
" \"/media/milou/glob/projects/masmvali-partdeux/reassembly-filtered-reads/Sample_1ng_even/ref-jellyfish/\")"
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"language": "python",
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"prompt_number": 28
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{
"cell_type": "code",
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"input": [
"jfr.get_refs_with_kmer_count_of_seq(record_dict[\"Acidobacterium_capsulatum_ATCC_51196\"].seq, 19)"
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"\u001b[1;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[1;31mKeyboardInterrupt\u001b[0m Traceback (most recent call last)",
"\u001b[1;32m\u001b[0m in \u001b[0;36m\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0mjfr\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mget_refs_with_kmer_count_of_seq\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mrecord_dict\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m\"Acidobacterium_capsulatum_ATCC_51196\"\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mseq\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;36m19\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[1;32m/media/milou/glob/github/masm-vali/masmvali/jellyfish.py\u001b[0m in \u001b[0;36mget_refs_with_kmer_count_of_seq\u001b[1;34m(self, seq, kmer_size)\u001b[0m\n\u001b[0;32m 51\u001b[0m \u001b[1;32mif\u001b[0m \u001b[1;32mnot\u001b[0m \u001b[0mos\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mexists\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 52\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_run_kmer\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mkmer_size\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m---> 53\u001b[1;33m \u001b[0mrefs\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mr\u001b[0m\u001b[1;33m]\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mJellyfish\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfn\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mcount_kmer\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mseq\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 54\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 55\u001b[0m \u001b[1;32mreturn\u001b[0m \u001b[0mrefs\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;32m/media/milou/glob/github/masm-vali/masmvali/jellyfish.py\u001b[0m in \u001b[0;36mcount_kmer\u001b[1;34m(self, seq)\u001b[0m\n\u001b[0;32m 12\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 13\u001b[0m \u001b[1;32mdef\u001b[0m \u001b[0mcount_kmer\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mseq\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m---> 14\u001b[1;33m \u001b[0mawk_count\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0msh\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mawk\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0msh\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mjellyfish\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m\"query\"\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mjf\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;34m\"-s\"\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;34m\"/dev/fd/0\"\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0m_in\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;34m\">seq\\n%s\"\u001b[0m \u001b[1;33m%\u001b[0m \u001b[0mseq\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;34m\"{rv+=$2} END {print rv}\"\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 15\u001b[0m \u001b[1;32mreturn\u001b[0m \u001b[0mint\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mawk_count\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mstdout\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 16\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n",
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"\u001b[1;32m/home/idb/virtual-environments/py27-env/local/lib/python2.7/site-packages/sh.pyc\u001b[0m in \u001b[0;36mwait\u001b[1;34m(self)\u001b[0m\n\u001b[0;32m 332\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 333\u001b[0m \u001b[1;32mdef\u001b[0m \u001b[0mwait\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 334\u001b[1;33m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_handle_exit_code\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mprocess\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mwait\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 335\u001b[0m \u001b[1;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 336\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n",
"\u001b[1;32m/home/idb/virtual-environments/py27-env/local/lib/python2.7/site-packages/sh.pyc\u001b[0m in \u001b[0;36mwait\u001b[1;34m(self)\u001b[0m\n\u001b[0;32m 1150\u001b[0m \u001b[1;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mexit_code\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 1151\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mlog\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mdebug\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m\"exit code not set, waiting on pid\"\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m-> 1152\u001b[1;33m \u001b[0mpid\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mexit_code\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mos\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mwaitpid\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mpid\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;36m0\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 1153\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mexit_code\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_handle_exit_code\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mexit_code\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 1154\u001b[0m \u001b[1;32melse\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
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