diff --git a/ProcessFASTQ.ipynb b/ProcessFASTQ.ipynb
index ccdf43a1c332a59b97bd093e8758124455741d96..00480dfdc2bbd81f7ace527108509c519ce0af3e 100644
--- a/ProcessFASTQ.ipynb
+++ b/ProcessFASTQ.ipynb
@@ -128,6 +128,9 @@
"# This lib is needed to parse fastq easily\n",
"from Bio import SeqIO\n",
"\n",
+ "# Prettify arrays\n",
+ "from pprint import pprint\n",
+ "\n",
"# This lib is used to avoid using a bash magic cell to copy a file\n",
"from shutil import copyfile\n",
"\n",
@@ -683,7 +686,7 @@
},
{
"cell_type": "code",
- "execution_count": 259,
+ "execution_count": 262,
"metadata": {
"collapsed": false
},
@@ -698,896 +701,23 @@
"\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/testing.fastq 4-Bowtied/testing.sam\"\n",
"\n",
- "SN279:493:C84L3ACXX:4:2309:1272:2215\n",
- "SN279:493:C84L3ACXX:4:2309:1272:2215:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:1275:2239\n",
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- "SN279:493:C84L3ACXX:4:2309:4765:2225\n",
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- "SN279:493:C84L3ACXX:4:2309:2022:2624:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:1512:2655\n",
- "SN279:493:C84L3ACXX:4:2309:2010:2644:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:2010:2644\n",
- "SN279:493:C84L3ACXX:4:2309:2340:2507:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:2280:2543\n",
- "SN279:493:C84L3ACXX:4:2309:2307:2538:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:2359:2572\n",
- "SN279:493:C84L3ACXX:4:2309:2280:2543:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:2340:2507\n",
- "SN279:493:C84L3ACXX:4:2309:2273:2678:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:2394:2710\n",
- "SN279:493:C84L3ACXX:4:2309:2394:2710:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:2273:2678\n",
- "SN279:493:C84L3ACXX:4:2309:2685:2502:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:2479:2738\n",
- "SN279:493:C84L3ACXX:4:2309:2654:2517:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:2654:2517\n",
- "SN279:493:C84L3ACXX:4:2309:2525:2711:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:2506:2731\n",
- "SN279:493:C84L3ACXX:4:2309:2865:2608:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:2972:2509\n",
- "SN279:493:C84L3ACXX:4:2309:2916:2620:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:2520:2630\n",
- "SN279:493:C84L3ACXX:4:2309:2822:2632:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:2808:2572\n",
- "SN279:493:C84L3ACXX:4:2309:2774:2658:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:2917:2641\n",
- "SN279:493:C84L3ACXX:4:2309:2937:2699:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:2774:2658\n",
- "SN279:493:C84L3ACXX:4:2309:2795:2739:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:2909:2714\n",
- "SN279:493:C84L3ACXX:4:2309:3155:2521:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:3136:2534\n",
- "SN279:493:C84L3ACXX:4:2309:3170:2547:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:3033:2509\n",
- "SN279:493:C84L3ACXX:4:2309:3148:2553:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:3053:2590\n",
- "SN279:493:C84L3ACXX:4:2309:3053:2590:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:3181:2623\n",
- "SN279:493:C84L3ACXX:4:2309:3083:2611:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:3474:2553\n",
- "SN279:493:C84L3ACXX:4:2309:3119:2650:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:3190:2711\n",
- "SN279:493:C84L3ACXX:4:2309:3190:2711:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:3119:2650\n",
- "SN279:493:C84L3ACXX:4:2309:3299:2530:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:3299:2530\n",
- "SN279:493:C84L3ACXX:4:2309:3431:2706:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:3504:2573\n",
- "SN279:493:C84L3ACXX:4:2309:3708:2639:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:3704:2508\n",
- "SN279:493:C84L3ACXX:4:2309:3583:2681:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:3631:2692\n",
- "SN279:493:C84L3ACXX:4:2309:3674:2694:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:3667:2583\n",
- "SN279:493:C84L3ACXX:4:2309:3549:2742:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:3964:2541\n",
- "SN279:493:C84L3ACXX:4:2309:3688:2743:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:3831:2524\n",
- "SN279:493:C84L3ACXX:4:2309:3831:2524:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:3549:2742\n",
- "SN279:493:C84L3ACXX:4:2309:3964:2541:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:3953:2564\n",
- "SN279:493:C84L3ACXX:4:2309:3953:2564:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:3775:2621\n",
- "SN279:493:C84L3ACXX:4:2309:3777:2721:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:3933:2583\n",
- "SN279:493:C84L3ACXX:4:2309:4122:2607:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:3864:2733\n",
- "SN279:493:C84L3ACXX:4:2309:4071:2697:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:3793:2707\n",
- "SN279:493:C84L3ACXX:4:2309:4273:2503:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:4291:2506\n",
- "SN279:493:C84L3ACXX:4:2309:4273:2579:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:4426:2593\n",
- "SN279:493:C84L3ACXX:4:2309:4253:2615:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:4273:2579\n",
- "SN279:493:C84L3ACXX:4:2309:4276:2652:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:4443:2564\n",
- "SN279:493:C84L3ACXX:4:2309:4404:2715:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:4740:2620\n",
- "SN279:493:C84L3ACXX:4:2309:4614:2608:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:4709:2667\n",
- "SN279:493:C84L3ACXX:4:2309:4740:2620:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:4404:2715\n",
- "SN279:493:C84L3ACXX:4:2309:4555:2703:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:4717:2728\n",
- "SN279:493:C84L3ACXX:4:2309:4717:2728:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:4555:2703\n",
- "SN279:493:C84L3ACXX:4:2309:4521:2734:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:4521:2734\n",
- "SN279:493:C84L3ACXX:4:2309:4818:2514:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:4898:2566\n",
- "SN279:493:C84L3ACXX:4:2309:4784:2602:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:4831:2616\n",
- "SN279:493:C84L3ACXX:4:2309:5110:2675:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:4784:2602\n",
- "SN279:493:C84L3ACXX:4:2309:5205:2692:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:5205:2692\n",
- "SN279:493:C84L3ACXX:4:2309:5033:2725:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:5237:2750\n",
- "SN279:493:C84L3ACXX:4:2309:5237:2750:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:5033:2725\n",
- "SN279:493:C84L3ACXX:4:2309:5270:2523:\t4\n"
+ "ID: SN279:493:C84L3ACXX:4:2309:1272:2215\n",
+ "Name: SN279:493:C84L3ACXX:4:2309:1272:2215\n",
+ "Description: SN279:493:C84L3ACXX:4:2309:1272:2215 1:N:0:CAGATC\n",
+ "Number of features: 0\n",
+ "Per letter annotation for: phred_quality\n",
+ "Seq('NGAGGACCGAACCGACTTACGTT', SingleLetterAlphabet())\n"
+ ]
+ },
+ {
+ "ename": "NameError",
+ "evalue": "name 'pprint' is not defined",
+ "output_type": "error",
+ "traceback": [
+ "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
+ "\u001b[1;31mNameError\u001b[0m Traceback (most recent call last)",
+ "\u001b[1;32m<ipython-input-262-737603416198>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[0;32m 22\u001b[0m \u001b[0mprint\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mrecord\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 23\u001b[0m \u001b[0marr\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mmatches\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mreadline\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0msplit\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m'\\t'\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m---> 24\u001b[1;33m \u001b[0mpprint\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0marr\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 25\u001b[0m \u001b[1;32mbreak\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 26\u001b[0m \u001b[0mseq_id\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0marr\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[1;31mNameError\u001b[0m: name 'pprint' is not defined"
]
}
],
@@ -1615,7 +745,10 @@
" seqiter = []\n",
" \n",
" for record in filt_iter:\n",
+ " print(record)\n",
" arr = matches.readline().split('\\t')\n",
+ " pprint(arr)\n",
+ " break\n",
" seq_id = arr[0]\n",
" flag = arr[1]\n",
" if(flag=='4'):\n",