diff --git a/ProcessFASTQ.ipynb b/ProcessFASTQ.ipynb
index c6a0225a76f30ee9d279ad3b48aebb2c6daf972d..3c9e707f9094c2c4b3fe003030e1e4ba5a82d6b5 100644
--- a/ProcessFASTQ.ipynb
+++ b/ProcessFASTQ.ipynb
@@ -41,7 +41,7 @@
},
{
"cell_type": "code",
- "execution_count": 164,
+ "execution_count": 190,
"metadata": {
"collapsed": false
},
@@ -95,11 +95,35 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 191,
"metadata": {
"collapsed": false
},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "\n",
+ "Available files :\n",
+ "\n",
+ "Undetermined_lane7_pair1\n",
+ "flowcell261_lane8_pair1_CAGATC \t\t Processsed\n",
+ "flowcell261_lane8_pair1_TGACCA \t\t Processsed\n",
+ "flowcell362_lane4_pair1_ACAGTG \t\t Processsed\n",
+ "flowcell362_lane4_pair1_ACTTGA \t\t Processsed\n",
+ "flowcell362_lane4_pair1_CAGATC \t\t Processsed\n",
+ "flowcell362_lane4_pair1_TGACCA \t\t Processsed\n",
+ "flowcell362_lane4_pair1_Undetermined\n",
+ "flowcell384_lane7_pair1_ACAGTG \t\t Processsed\n",
+ "flowcell384_lane7_pair1_ACTTGA \t\t Processsed\n",
+ "flowcell384_lane7_pair1_CAGATC \t\t Processsed\n",
+ "flowcell384_lane7_pair1_GATCAG \t\t Processsed\n",
+ "flowcell384_lane7_pair1_TGACCA \t\t Processsed\n",
+ "testing\n"
+ ]
+ }
+ ],
"source": [
"# This lib is needed to parse fastq easily\n",
"from Bio import SeqIO\n",
@@ -122,12 +146,12 @@
"# fname = \"flowcell362_lane4_pair1_ACTTGA\"\n",
"# fname = \"flowcell362_lane4_pair1_CAGATC\"\n",
"# fname = \"flowcell362_lane4_pair1_TGACCA\"\n",
- "# fname = \"flowcell362_lane4_pair1_Undetermined\"\n",
+ "fname = \"flowcell362_lane4_pair1_Undetermined\"\n",
"# fname = \"flowcell384_lane7_pair1_ACAGTG\"\n",
"# fname = \"flowcell384_lane7_pair1_ACTTGA\"\n",
"# fname = \"flowcell384_lane7_pair1_CAGATC\"\n",
"# fname = \"flowcell384_lane7_pair1_GATCAG\"\n",
- "fname = \"flowcell384_lane7_pair1_TGACCA\"\n",
+ "# fname = \"flowcell384_lane7_pair1_TGACCA\"\n",
"\n",
"# Print available files in 0-Raws/ directory\n",
"\n",
@@ -184,7 +208,7 @@
},
{
"cell_type": "code",
- "execution_count": 166,
+ "execution_count": 192,
"metadata": {
"collapsed": false
},
@@ -207,7 +231,7 @@
},
{
"cell_type": "code",
- "execution_count": 167,
+ "execution_count": 193,
"metadata": {
"collapsed": false
},
@@ -215,10 +239,10 @@
{
"data": {
"text/plain": [
- "'flowcell384_lane7_pair1_TGACCA.fastq.gz'"
+ "'flowcell362_lane4_pair1_Undetermined.fastq.gz'"
]
},
- "execution_count": 167,
+ "execution_count": 193,
"metadata": {},
"output_type": "execute_result"
}
@@ -242,7 +266,7 @@
},
{
"cell_type": "code",
- "execution_count": 168,
+ "execution_count": 194,
"metadata": {
"collapsed": false
},
@@ -252,12 +276,12 @@
"output_type": "stream",
"text": [
"\n",
- "flowcell384_lane7_pair1_TGACCA\n",
+ "flowcell362_lane4_pair1_Undetermined\n",
"\n",
- "@SN279:498:C88PKACXX:7:1109:1699:2220 1:N:0:TGACCA\n",
- "NGAGGTGCACAATCGACCGATCCTGCTGTAGGCACCATCAATAGATCGGAA\n",
+ "@SN279:493:C84L3ACXX:4:2309:1848:2226 1:N:0:TTCCGT\n",
+ "NCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTC\n",
"+\n",
- "#1=D;DDDHHFHHIIIIIIIIIIIIIIIIHIIIIFHIIIIIHHIIIIIIII\n"
+ "#4=DDDDDHHHHHIHFHJJJJJJJJIJJJHIJJJJJJJJJJJJJJJIJJJJ\n"
]
}
],
@@ -279,7 +303,7 @@
},
{
"cell_type": "code",
- "execution_count": 169,
+ "execution_count": 195,
"metadata": {
"collapsed": false
},
@@ -288,7 +312,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "Processing will take approximatively 0 hour(s) 44 minute(s) and 38 second(s)\n"
+ "Processing will take approximatively 0 hour(s) 3 minute(s) and 31 second(s)\n"
]
}
],
@@ -334,7 +358,7 @@
},
{
"cell_type": "code",
- "execution_count": 170,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
@@ -346,21 +370,11 @@
},
{
"cell_type": "code",
- "execution_count": 171,
+ "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_TGACCA.fastq.gz --quiet flowcell384_lane7_pair1_TGACCA.fastq.gz\n",
- "Trimming 1 adapter with at most 10.0% errors in single-end mode ...\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"%%bash\n",
"source ./source\n",
@@ -378,19 +392,11 @@
},
{
"cell_type": "code",
- "execution_count": 172,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Cutadapt run time : 0:38:47.798753\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"# Store current time\n",
"after = datetime.datetime.now()\n",
@@ -403,7 +409,7 @@
},
{
"cell_type": "code",
- "execution_count": 173,
+ "execution_count": null,
"metadata": {
"collapsed": true
},
@@ -424,7 +430,7 @@
},
{
"cell_type": "code",
- "execution_count": 174,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
@@ -436,7 +442,7 @@
},
{
"cell_type": "code",
- "execution_count": 175,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
@@ -451,19 +457,11 @@
},
{
"cell_type": "code",
- "execution_count": 176,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Zcat run time : 0:00:40.103272\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"# Store current time\n",
"after = datetime.datetime.now()\n",
@@ -489,7 +487,7 @@
},
{
"cell_type": "code",
- "execution_count": 177,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
@@ -501,7 +499,7 @@
},
{
"cell_type": "code",
- "execution_count": 178,
+ "execution_count": null,
"metadata": {
"collapsed": true
},
@@ -526,19 +524,11 @@
},
{
"cell_type": "code",
- "execution_count": 179,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Filtering run time : 0:35:14.961783\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"# Store current time\n",
"after = datetime.datetime.now()\n",
@@ -574,28 +564,12 @@
},
{
"cell_type": "code",
- "execution_count": 180,
+ "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: 00:04:29\n",
- "# reads processed: 46620824\n",
- "# reads with at least one reported alignment: 33736079 (72.36%)\n",
- "# reads that failed to align: 12884745 (27.64%)\n",
- "Reported 33736079 alignments to 1 output stream(s)\n",
- "Time searching: 00:04:29\n",
- "Overall time: 00:04:29\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"%%bash\n",
"source ./source\n",
@@ -644,7 +618,7 @@
},
{
"cell_type": "code",
- "execution_count": 181,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
@@ -657,24 +631,11 @@
},
{
"cell_type": "code",
- "execution_count": 182,
+ "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_TGACCA.fastq 4-Bowtied/flowcell384_lane7_pair1_TGACCA.sam\"\n",
- "\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"with open(\"3-Filtered/\" +fname+\".fastq\",\"r\") as filtered, \\\n",
" open(\"4-Bowtied/\" +fname+\".sam\",\"r\") as matches, \\\n",
@@ -702,19 +663,11 @@
},
{
"cell_type": "code",
- "execution_count": 183,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Filtering non-codant tRNA run time : 0:25:12.216325\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"# Store current time\n",
"after = datetime.datetime.now()\n",
@@ -736,27 +689,11 @@
},
{
"cell_type": "code",
- "execution_count": 184,
+ "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: 00:01:06\n",
- "# reads processed: 12884745\n",
- "# reads with at least one reported alignment: 10864699 (84.32%)\n",
- "# reads that failed to align: 2020046 (15.68%)\n",
- "Reported 10864699 alignments to 1 output stream(s)\n",
- "Time searching: 00:01:06\n",
- "Overall time: 00:01:06\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"%%bash\n",
"source ./source\n",
@@ -781,7 +718,7 @@
},
{
"cell_type": "code",
- "execution_count": 185,
+ "execution_count": null,
"metadata": {
"collapsed": true
},
@@ -812,7 +749,7 @@
},
{
"cell_type": "code",
- "execution_count": 186,
+ "execution_count": null,
"metadata": {
"collapsed": false
},
@@ -856,7 +793,7 @@
},
{
"cell_type": "code",
- "execution_count": 187,
+ "execution_count": null,
"metadata": {
"collapsed": false
},