From f6bd4488f34e1ed9250cbde5d2c26aa2629d33e4 Mon Sep 17 00:00:00 2001
From: Julien Cornut <julien.cornut@hesge.ch>
Date: Thu, 25 Feb 2016 10:49:01 +0100
Subject: [PATCH] Automatic Update
---
ProcessFASTQ.ipynb | 165 +++++++++++----------------------------------
1 file changed, 39 insertions(+), 126 deletions(-)
diff --git a/ProcessFASTQ.ipynb b/ProcessFASTQ.ipynb
index 56c12a5..68a65a9 100644
--- a/ProcessFASTQ.ipynb
+++ b/ProcessFASTQ.ipynb
@@ -41,7 +41,7 @@
},
{
"cell_type": "code",
- "execution_count": 89,
+ "execution_count": 114,
"metadata": {
"collapsed": false
},
@@ -95,7 +95,7 @@
},
{
"cell_type": "code",
- "execution_count": 113,
+ "execution_count": 115,
"metadata": {
"collapsed": false
},
@@ -208,7 +208,7 @@
},
{
"cell_type": "code",
- "execution_count": 91,
+ "execution_count": 116,
"metadata": {
"collapsed": false
},
@@ -231,7 +231,7 @@
},
{
"cell_type": "code",
- "execution_count": 92,
+ "execution_count": 117,
"metadata": {
"collapsed": false
},
@@ -239,10 +239,10 @@
{
"data": {
"text/plain": [
- "'flowcell384_lane7_pair1_ACTTGA.fastq.gz'"
+ "'flowcell384_lane7_pair1_CAGATC.fastq.gz'"
]
},
- "execution_count": 92,
+ "execution_count": 117,
"metadata": {},
"output_type": "execute_result"
}
@@ -266,7 +266,7 @@
},
{
"cell_type": "code",
- "execution_count": 93,
+ "execution_count": 118,
"metadata": {
"collapsed": false
},
@@ -276,12 +276,12 @@
"output_type": "stream",
"text": [
"\n",
- "flowcell384_lane7_pair1_ACTTGA\n",
+ "flowcell384_lane7_pair1_CAGATC\n",
"\n",
- "@SN279:498:C88PKACXX:7:1109:1643:2231 1:N:0:ACTTGA\n",
- "NGAGGTGCACAATCGACCGATCCTGCTGTAGGCACCATCAATAGATCGGAA\n",
+ "@SN279:498:C88PKACXX:7:1109:1531:2224 1:N:0:CAGATC\n",
+ "NAGAGGTGCACAATCGACCGATCCTGACTGTAGGCACCATCAATAGATCGG\n",
"+\n",
- "#1:==BDDFDFFFEAFG:FG?0?BBD<?GBF3??F(??C)8=F<FF;=;;;\n"
+ "#1=DADEFHHHHHIIIIIHIIIIGIIIE?B??GB?FH;BCC3B)7888=DE\n"
]
}
],
@@ -303,7 +303,7 @@
},
{
"cell_type": "code",
- "execution_count": 94,
+ "execution_count": 119,
"metadata": {
"collapsed": false
},
@@ -312,7 +312,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "Processing will take approximatively 0 hour(s) 30 minute(s) and 25 second(s)\n"
+ "Processing will take approximatively 0 hour(s) 38 minute(s) and 1 second(s)\n"
]
}
],
@@ -358,7 +358,7 @@
},
{
"cell_type": "code",
- "execution_count": 95,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
@@ -370,21 +370,11 @@
},
{
"cell_type": "code",
- "execution_count": 96,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "This is cutadapt 1.9.1 with Python 3.5.1\n",
- "Command line parameters: -a CTGTAGGCACCATCAATAGATCGGAA -o 1-Cutadapted/flowcell384_lane7_pair1_ACTTGA.fastq.gz --quiet flowcell384_lane7_pair1_ACTTGA.fastq.gz\n",
- "Trimming 1 adapter with at most 10.0% errors in single-end mode ...\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"%%bash\n",
"source ./source\n",
@@ -402,19 +392,11 @@
},
{
"cell_type": "code",
- "execution_count": 97,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Cutadapt run time : 0:26:27.423115\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"# Store current time\n",
"after = datetime.datetime.now()\n",
@@ -427,7 +409,7 @@
},
{
"cell_type": "code",
- "execution_count": 98,
+ "execution_count": null,
"metadata": {
"collapsed": true
},
@@ -448,7 +430,7 @@
},
{
"cell_type": "code",
- "execution_count": 99,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
@@ -460,7 +442,7 @@
},
{
"cell_type": "code",
- "execution_count": 100,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
@@ -475,19 +457,11 @@
},
{
"cell_type": "code",
- "execution_count": 101,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Zcat run time : 0:00:26.676984\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"# Store current time\n",
"after = datetime.datetime.now()\n",
@@ -513,7 +487,7 @@
},
{
"cell_type": "code",
- "execution_count": 102,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
@@ -525,7 +499,7 @@
},
{
"cell_type": "code",
- "execution_count": 103,
+ "execution_count": null,
"metadata": {
"collapsed": true
},
@@ -550,19 +524,11 @@
},
{
"cell_type": "code",
- "execution_count": 104,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Filtering run time : 0:23:41.536965\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"# Store current time\n",
"after = datetime.datetime.now()\n",
@@ -598,28 +564,12 @@
},
{
"cell_type": "code",
- "execution_count": 105,
+ "execution_count": null,
"metadata": {
"collapsed": false,
"scrolled": false
},
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "Time loading forward index: 00:00:00\n",
- "Time loading mirror index: 00:00:00\n",
- "End-to-end 2/3-mismatch full-index search: 00:02:59\n",
- "# reads processed: 31626224\n",
- "# reads with at least one reported alignment: 22981667 (72.67%)\n",
- "# reads that failed to align: 8644557 (27.33%)\n",
- "Reported 22981667 alignments to 1 output stream(s)\n",
- "Time searching: 00:02:59\n",
- "Overall time: 00:02:59\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"%%bash\n",
"source ./source\n",
@@ -668,7 +618,7 @@
},
{
"cell_type": "code",
- "execution_count": 106,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
@@ -681,24 +631,11 @@
},
{
"cell_type": "code",
- "execution_count": 107,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "@SQ\tSN:tW(UCA)Q\tLN:74\n",
- "\n",
- "@SQ\tSN:tY(GUA)Q\tLN:84\n",
- "\n",
- "@PG\tID:Bowtie\tVN:1.1.2\tCL:\"bowtie --wrapper basic-0 -S -v 3 -p 8 --time --best ref/2-Indexes/Yeast-Noncoding/Yeast-Noncoding 3-Filtered/flowcell384_lane7_pair1_ACTTGA.fastq 4-Bowtied/flowcell384_lane7_pair1_ACTTGA.sam\"\n",
- "\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"with open(\"3-Filtered/\" +fname+\".fastq\",\"r\") as filtered, \\\n",
" open(\"4-Bowtied/\" +fname+\".sam\",\"r\") as matches, \\\n",
@@ -726,19 +663,11 @@
},
{
"cell_type": "code",
- "execution_count": 108,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Filtering non-codant tRNA run time : 0:16:54.929962\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"# Store current time\n",
"after = datetime.datetime.now()\n",
@@ -760,27 +689,11 @@
},
{
"cell_type": "code",
- "execution_count": 109,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "Time loading forward index: 00:00:00\n",
- "Time loading mirror index: 00:00:00\n",
- "End-to-end 2/3-mismatch full-index search: 00:00:47\n",
- "# reads processed: 8644557\n",
- "# reads with at least one reported alignment: 7053261 (81.59%)\n",
- "# reads that failed to align: 1591296 (18.41%)\n",
- "Reported 7053261 alignments to 1 output stream(s)\n",
- "Time searching: 00:00:47\n",
- "Overall time: 00:00:47\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"%%bash\n",
"source ./source\n",
@@ -805,7 +718,7 @@
},
{
"cell_type": "code",
- "execution_count": 110,
+ "execution_count": null,
"metadata": {
"collapsed": true
},
@@ -836,7 +749,7 @@
},
{
"cell_type": "code",
- "execution_count": 111,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
@@ -880,7 +793,7 @@
},
{
"cell_type": "code",
- "execution_count": 112,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
--
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