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Update to 0-Setup.snb
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‎VCF_Comp/0-Setup.snb

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},
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"cell_type" : "markdown",
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"source" : "# Setup\n\nIn this notebook, we make sure a paired set of variants is available. We provide the annotated datafiles as well for reference."
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}, {
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"metadata" : {
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"trusted" : true,
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"input_collapsed" : false,
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"collapsed" : false,
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"id" : "F5C022C6BA6C45A296F199786753A879"
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},
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"cell_type" : "code",
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"source" : "import scala.sys.process._\nimport scala.language.postfixOps\n\ndef shellTestToBool(shellCommand:String):Boolean = {\n Some(shellCommand !)\n .map{ _ match {\n case 0 => true\n case _ => false }\n }.get\n}",
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"outputs" : [ {
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"name" : "stdout",
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"output_type" : "stream",
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"text" : "import scala.sys.process._\nimport scala.language.postfixOps\nshellTestToBool: (shellCommand: String)Boolean\n"
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}, {
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"metadata" : { },
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"data" : {
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"text/html" : ""
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},
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"output_type" : "execute_result",
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"execution_count" : 4
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} ]
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}, {
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"metadata" : {
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"trusted" : true,
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"input_collapsed" : false,
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"collapsed" : false,
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"id" : "2D0DED5DF344445382E884E80A11B4AE"
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},
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"cell_type" : "code",
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"source" : "// Update this!\nval projectDir = \"./\"\n\n// Paths\nval snpEffBaseDir = projectDir + \"snpEff/\"\nval snpEffVersionString = \"v4_2\"\nval snpEffSourceZip = s\"snpEff_${snpEffVersionString}_core.zip\"\n\n// Checks\nval runningInDocker = shellTestToBool(\"test -f /.dockerenv\")\nval wgetInstalled = shellTestToBool(\"which wget\")\nval unzipInstalled = shellTestToBool(\"which unzip\")\nval snpEffInstalled = shellTestToBool(s\"test -f ${snpEffBaseDir}${snpEffSourceZip}\")\nval snpEffBaseDirExists = shellTestToBool(s\"test -d ${snpEffBaseDir}\")",
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"outputs" : [ {
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"name" : "stdout",
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"output_type" : "stream",
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"text" : "projectDir: String = ./\nsnpEffBaseDir: String = ./snpEff/\nsnpEffVersionString: String = v4_2\nsnpEffSourceZip: String = snpEff_v4_2_core.zip\nrunningInDocker: Boolean = true\nwgetInstalled: Boolean = false\nunzipInstalled: Boolean = false\nsnpEffInstalled: Boolean = false\nsnpEffBaseDirExists: Boolean = true\n"
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}, {
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"metadata" : { },
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"data" : {
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"text/html" : ""
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},
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"output_type" : "execute_result",
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"execution_count" : 2
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} ]
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}, {
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"metadata" : {
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"id" : "96E7D50796C04924AC4E1F7F905F6F13"
@@ -40,14 +82,35 @@
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"outputs" : [ {
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"name" : "stdout",
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"output_type" : "stream",
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"text" : "total 91951\ndrwxr-xr-x 6 root root 204 May 31 12:19 .\ndrwxrwxr-x 9 daemon daemon 4096 May 31 19:43 ..\n-rw------- 1 root root 1860660 May 31 12:04 8122_N.vcf.gz\n-rw------- 1 root root 1888646 May 31 12:05 8122_T.vcf.gz\n-rw------- 1 root root 45003812 May 31 12:02 snpEff.8122_N.vcf.gz\n-rw------- 1 root root 45398741 May 31 12:02 snpEff.8122_T.vcf.gz\n\nimport sys.process._\n"
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"text" : "total 91951\ndrwxr-xr-x 6 root root 204 May 31 12:19 .\ndrwxrwxr-x 10 daemon daemon 4096 Jun 7 12:06 ..\n-rw------- 1 root root 1860660 May 31 12:04 8122_N.vcf.gz\n-rw------- 1 root root 1888646 May 31 12:05 8122_T.vcf.gz\n-rw------- 1 root root 45003812 May 31 12:02 snpEff.8122_N.vcf.gz\n-rw------- 1 root root 45398741 May 31 12:02 snpEff.8122_T.vcf.gz\n\nimport sys.process._\n"
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}, {
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"metadata" : { },
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"data" : {
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"text/plain" : ""
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},
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"output_type" : "execute_result",
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"execution_count" : 4
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} ]
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}, {
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"metadata" : {
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"trusted" : true,
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"input_collapsed" : false,
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"collapsed" : false,
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"id" : "CFBDC3020EAD41A38F79F1886F6F036C"
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},
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"cell_type" : "code",
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"source" : ":sh ls -al ./snpEff/",
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"outputs" : [ {
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"name" : "stdout",
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"output_type" : "stream",
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"text" : "total 5\ndrwxr-xr-x 3 root root 102 Jun 7 12:19 .\ndrwxrwxr-x 10 daemon daemon 4096 Jun 7 12:20 ..\n-rw-r--r-- 1 root root 122 Jun 7 11:45 README.md\n\nimport sys.process._\n"
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}, {
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"metadata" : { },
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"data" : {
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"text/plain" : ""
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},
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"output_type" : "execute_result",
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"execution_count" : 1
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"execution_count" : 3
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} ]
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}, {
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"metadata" : {
@@ -138,27 +201,6 @@
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},
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"cell_type" : "markdown",
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"source" : "## SnpEff"
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}, {
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"metadata" : {
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"trusted" : true,
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"input_collapsed" : false,
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"collapsed" : false,
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"id" : "6277EC2932474DC1AEC963BF8E02A87A"
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},
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"cell_type" : "code",
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"source" : "//val snpEffBaseDir = \"/Users/toni/Dropbox/_Janssen/CellPass/vcf-comp/snpEff/\"\nval tmpDir = \"/tmp/\"\nval snpEffBaseDir = tmpDir + \"snpEff/\"\nval snpEffVersionString = \"v4_2\"",
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"outputs" : [ {
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"name" : "stdout",
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"output_type" : "stream",
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"text" : "tmpDir: String = /tmp/\nsnpEffBaseDir: String = /tmp/snpEff/\nsnpEffVersionString: String = v4_2\n"
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}, {
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"metadata" : { },
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"data" : {
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"text/html" : ""
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},
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"output_type" : "execute_result",
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"execution_count" : 19
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} ]
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}, {
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"metadata" : {
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"trusted" : true,
@@ -167,18 +209,18 @@
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"id" : "6B65F2EC197341A8A879A4E0DD7B2B5A"
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},
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"cell_type" : "code",
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"source" : "import scala.sys.process._\nimport scala.language.postfixOps\n\n\"which wget\" #|| \"apt-get install -y wget\" !\n\n\"which unzip\" #|| \"apt-get install -y unzip\" !",
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"source" : "if (runningInDocker) {\n println(\"Running in Docker, checking wget and unzip dependencies...\")\n if (! wgetInstalled) { \n println(\"Installing wget\")\n \"apt-get install -y wget\"! \n } else println(\"wget already installed\")\n if (! unzipInstalled) { \n println(\"Installing unzip\")\n \"apt-get install -y unzip\"! \n } else println(\"unzip already installed\")\n} else {\n println(\"Not running in Docker, make sure wget and unzip are available...\")\n}",
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"outputs" : [ {
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"name" : "stdout",
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"output_type" : "stream",
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"text" : "import scala.sys.process._\nimport scala.language.postfixOps\nres54: Int = 0\n"
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"text" : "Running in Docker, checking wget and unzip dependencies...\nInstalling wget\nInstalling unzip\nres7: AnyVal = 0\n"
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}, {
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"metadata" : { },
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"data" : {
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"text/html" : "0"
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},
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"output_type" : "execute_result",
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"execution_count" : 28
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"execution_count" : 5
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} ]
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}, {
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"metadata" : {
@@ -188,36 +230,29 @@
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"id" : "EC30FE5830904E588DEAA28BE132DACA"
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},
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"cell_type" : "code",
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"source" : "s\"test -f ${snpEffBaseDir}/snpEff_${snpEffVersionString}_core.zip\" #|| \ns\"wget http://heanet.dl.sourceforge.net/project/snpeff/snpEff_${snpEffVersionString}_core.zip -P ${snpEffBaseDir}\" !\n\ns\"unzip ${snpEffBaseDir}snpEff_${snpEffVersionString}_core.zip -d ${tmpDir}\" !",
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"source" : "val snpEffDownloaded = \n if (!snpEffInstalled) {\n println(\"Downloading from Sourceforge...\")\n shellTestToBool(s\"wget http://heanet.dl.sourceforge.net/project/snpeff/${snpEffSourceZip} -P ${snpEffBaseDir}\")\n } else true\n\n// If the download is not successfull, remove the stale file\nif (!snpEffDownloaded) shellTestToBool(s\"rm ${snpEffBaseDir}${snpEffSourceZip}\")\n\nif (!snpEffInstalled && snpEffDownloaded) {\n println(\"Unzipping snpEff...\") \n shellTestToBool(s\"unzip ${snpEffBaseDir}${snpEffSourceZip} -d ${snpEffBaseDir}\")\n}\n\n\n\n\n",
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"outputs" : [ {
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"name" : "stdout",
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"output_type" : "stream",
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"text" : "res52: Int = 1\n"
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"text" : "Downloading from Sourceforge...\nUnzipping snpEff...\nsnpEffDownloaded: Boolean = true\nres55: AnyVal = true\n"
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}, {
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"metadata" : { },
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"data" : {
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"text/html" : "1"
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"text/html" : "true"
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},
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"output_type" : "execute_result",
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"execution_count" : 27
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"execution_count" : 34
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} ]
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}, {
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"metadata" : {
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"trusted" : true,
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"input_collapsed" : false,
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"collapsed" : false,
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"id" : "5F4DAE33B1E7429785F8815D24B379F4"
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"collapsed" : true,
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"id" : "32FC02C2E3F147128283B90CB9245E50"
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},
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"cell_type" : "code",
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"source" : "",
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"outputs" : [ {
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"metadata" : { },
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"data" : {
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"text/html" : ""
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},
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"output_type" : "execute_result",
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"execution_count" : 8
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} ]
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"outputs" : [ ]
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} ],
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"nbformat" : 4
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}

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