diff --git a/ProcessFASTQ.ipynb b/ProcessFASTQ.ipynb
index 75b174b977e2ea16c3a7f533069552cf29dd8912..de406efbf7483e0ad2f842998f19ddf761250119 100644
--- a/ProcessFASTQ.ipynb
+++ b/ProcessFASTQ.ipynb
@@ -683,7 +683,7 @@
},
{
"cell_type": "code",
- "execution_count": 255,
+ "execution_count": 257,
"metadata": {
"collapsed": false
},
@@ -697,2007 +697,22 @@
"@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/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",
- "SN279:493:C84L3ACXX:4:2309:1309:2236:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:2182:2231\n",
- "SN279:493:C84L3ACXX:4:2309:1275:2239:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:1652:2216\n",
- "SN279:493:C84L3ACXX:4:2309:1652:2216:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:2260:2244\n",
- "SN279:493:C84L3ACXX:4:2309:1886:2219:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:2743:2223\n",
- "SN279:493:C84L3ACXX:4:2309:1813:2248:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:2899:2218\n",
- "SN279:493:C84L3ACXX:4:2309:2182:2231:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:1886:2219\n",
- "SN279:493:C84L3ACXX:4:2309:2387:2233:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:3284:2235\n",
- "SN279:493:C84L3ACXX:4:2309:2260:2244:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:1813:2248\n",
- "SN279:493:C84L3ACXX:4:2309:2743:2223:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:3264:2245\n",
- "SN279:493:C84L3ACXX:4:2309:2899:2218:\t0\n",
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- "SN279:493:C84L3ACXX:4:2309:3323:2241\n",
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- "SN279:493:C84L3ACXX:4:2309:2387:2233\n",
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- "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:4:2309:3266:2577\n",
- "SN279:493:C84L3ACXX:4:2309:3181:2623:\t0\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:4:2309:3269:2625\n",
- "SN279:493:C84L3ACXX:4:2309:3474:2553:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:3431:2706\n",
- "SN279:493:C84L3ACXX:4:2309:3266:2577:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:3649:2533\n",
- "SN279:493:C84L3ACXX:4:2309:3269:2625:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:3299:2530\n",
- "SN279:493:C84L3ACXX:4:2309:3431:2706:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:3260:2743\n",
- "SN279:493:C84L3ACXX:4:2309:3260:2743:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:3609:2539\n",
- "SN279:493:C84L3ACXX:4:2309:3704:2508:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:3148:2553\n",
- "SN279:493:C84L3ACXX:4:2309:3649:2533:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:3583:2681\n",
- "SN279:493:C84L3ACXX:4:2309:3609:2539:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:3708:2639\n",
- "SN279:493:C84L3ACXX:4:2309:3504:2573:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:3674:2694\n",
- "SN279:493:C84L3ACXX:4:2309:3667:2583:\t0\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:4:2309:3688:2743\n",
- "SN279:493:C84L3ACXX:4:2309:3631:2692:\t0\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:4:2309:3952:2714\n",
- "SN279:493:C84L3ACXX:4:2309:3933:2583:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:3784:2676\n",
- "SN279:493:C84L3ACXX:4:2309:3775:2621:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:3777:2721\n",
- "SN279:493:C84L3ACXX:4:2309:3784:2676:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:3787:2747\n",
- "SN279:493:C84L3ACXX:4:2309:3793:2707:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:4060:2541\n",
- "SN279:493:C84L3ACXX:4:2309:3952:2714:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:3775:2621\n",
- "SN279:493:C84L3ACXX:4:2309:3777:2721:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:4122:2607\n",
- "SN279:493:C84L3ACXX:4:2309:3864:2733:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:4096:2608\n",
- "SN279:493:C84L3ACXX:4:2309:3787:2747:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:4071:2697\n",
- "SN279:493:C84L3ACXX:4:2309:4060:2541:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:3933:2583\n",
- "SN279:493:C84L3ACXX:4:2309:4122:2607:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:4273:2503\n",
- "SN279:493:C84L3ACXX:4:2309:4096:2608:\t0\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:4:2309:4253:2615\n",
- "SN279:493:C84L3ACXX:4:2309:4291:2506:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:4444:2640\n",
- "SN279:493:C84L3ACXX:4:2309:4443:2564:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:4291:2506\n",
- "SN279:493:C84L3ACXX:4:2309:4273:2579:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:4276:2652\n",
- "SN279:493:C84L3ACXX:4:2309:4426:2593:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:4426:2593\n",
- "SN279:493:C84L3ACXX:4:2309:4253:2615:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:4294:2653\n",
- "SN279:493:C84L3ACXX:4:2309:4444:2640:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:4273:2579\n",
- "SN279:493:C84L3ACXX:4:2309:4276:2652:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:4280:2740\n",
- "SN279:493:C84L3ACXX:4:2309:4294:2653:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:4443:2564\n",
- "SN279:493:C84L3ACXX:4:2309:4404:2715:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:4548:2500\n",
- "SN279:493:C84L3ACXX:4:2309:4280:2740:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:4572:2528\n",
- "SN279:493:C84L3ACXX:4:2309:4548:2500:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:4678:2560\n",
- "SN279:493:C84L3ACXX:4:2309:4572:2528:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:4583:2583\n",
- "SN279:493:C84L3ACXX:4:2309:4678:2560:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:4614:2608\n",
- "SN279:493:C84L3ACXX:4:2309:4583:2583:\t0\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:4:2309:4818:2514\n",
- "SN279:493:C84L3ACXX:4:2309:4709:2667:\t0\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:4:2309:5245:2511\n",
- "SN279:493:C84L3ACXX:4:2309:4898:2566:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:4898:2566\n",
- "SN279:493:C84L3ACXX:4:2309:4784:2602:\t4\n",
- "SN279:493:C84L3ACXX:4:2309:5061:2524\n",
- "SN279:493:C84L3ACXX:4:2309:4831:2616:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:5001:2640\n",
- "SN279:493:C84L3ACXX:4:2309:5245:2511:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:5110:2675\n",
- "SN279:493:C84L3ACXX:4:2309:5061:2524:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:5160:2534\n",
- "SN279:493:C84L3ACXX:4:2309:5160:2534:\t0\n",
- "SN279:493:C84L3ACXX:4:2309:5047:2707\n",
- "SN279:493:C84L3ACXX:4:2309:5001:2640:\t0\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:4:2309:5270:2523\n",
- "SN279:493:C84L3ACXX:4:2309:5047:2707:\t0\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"
+ "\n"
+ ]
+ },
+ {
+ "ename": "AttributeError",
+ "evalue": "'str' object has no attribute 'seq'",
+ "output_type": "error",
+ "traceback": [
+ "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
+ "\u001b[1;31mAttributeError\u001b[0m Traceback (most recent call last)",
+ "\u001b[1;32m<ipython-input-257-a450f159b46b>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[0;32m 30\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 31\u001b[0m \u001b[1;31m# Write back fastq\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m---> 32\u001b[1;33m \u001b[0mSeqIO\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mwrite\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mseqiter\u001b[0m\u001b[1;33m,\u001b[0m\u001b[0msubstracted\u001b[0m\u001b[1;33m,\u001b[0m\u001b[1;34m\"fastq\"\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
+ "\u001b[1;32m/root/anaconda3/lib/python3.5/site-packages/Bio/SeqIO/__init__.py\u001b[0m in \u001b[0;36mwrite\u001b[1;34m(sequences, handle, format)\u001b[0m\n\u001b[0;32m 481\u001b[0m \u001b[1;32mif\u001b[0m \u001b[0mformat\u001b[0m \u001b[1;32min\u001b[0m \u001b[0m_FormatToWriter\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 482\u001b[0m \u001b[0mwriter_class\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0m_FormatToWriter\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mformat\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 483\u001b[1;33m \u001b[0mcount\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mwriter_class\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfp\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mwrite_file\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0msequences\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 484\u001b[0m \u001b[1;32melif\u001b[0m \u001b[0mformat\u001b[0m \u001b[1;32min\u001b[0m \u001b[0mAlignIO\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_FormatToWriter\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 485\u001b[0m \u001b[1;31m# Try and turn all the records into a single alignment,\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
+ "\u001b[1;32m/root/anaconda3/lib/python3.5/site-packages/Bio/SeqIO/Interfaces.py\u001b[0m in \u001b[0;36mwrite_file\u001b[1;34m(self, records)\u001b[0m\n\u001b[0;32m 209\u001b[0m \"\"\"\n\u001b[0;32m 210\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mwrite_header\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 211\u001b[1;33m \u001b[0mcount\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mwrite_records\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mrecords\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 212\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mwrite_footer\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 213\u001b[0m \u001b[1;32mreturn\u001b[0m \u001b[0mcount\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
+ "\u001b[1;32m/root/anaconda3/lib/python3.5/site-packages/Bio/SeqIO/Interfaces.py\u001b[0m in \u001b[0;36mwrite_records\u001b[1;34m(self, records)\u001b[0m\n\u001b[0;32m 194\u001b[0m \u001b[0mcount\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;36m0\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 195\u001b[0m \u001b[1;32mfor\u001b[0m \u001b[0mrecord\u001b[0m \u001b[1;32min\u001b[0m \u001b[0mrecords\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m--> 196\u001b[1;33m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mwrite_record\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[0m\u001b[0;32m 197\u001b[0m \u001b[0mcount\u001b[0m \u001b[1;33m+=\u001b[0m \u001b[1;36m1\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 198\u001b[0m \u001b[1;31m# Mark as true, even if there where no records\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
+ "\u001b[1;32m/root/anaconda3/lib/python3.5/site-packages/Bio/SeqIO/QualityIO.py\u001b[0m in \u001b[0;36mwrite_record\u001b[1;34m(self, record)\u001b[0m\n\u001b[0;32m 1429\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_record_written\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;32mTrue\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 1430\u001b[0m \u001b[1;31m# TODO - Is an empty sequence allowed in FASTQ format?\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m-> 1431\u001b[1;33m \u001b[1;32mif\u001b[0m \u001b[0mrecord\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mseq\u001b[0m \u001b[1;32mis\u001b[0m \u001b[1;32mNone\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 1432\u001b[0m \u001b[1;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m\"No sequence for record %s\"\u001b[0m \u001b[1;33m%\u001b[0m \u001b[0mrecord\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mid\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 1433\u001b[0m \u001b[0mseq_str\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mstr\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mrecord\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[1;31mAttributeError\u001b[0m: 'str' object has no attribute 'seq'"
]
}
],
@@ -2731,11 +746,11 @@
" if(flag=='4'):\n",
" seqiter.append(record)\n",
" \n",
- " print(\"{0}\\n{1}:\\t{2}\".format(seq_id,record.id,flag,))\n",
+ " #print(\"{0}\\n{1}:\\t{2}\".format(seq_id,record.id,flag,))\n",
" \n",
"\n",
" # Write back fastq\n",
- " SeqIO.write(sub_iter,substracted,\"fastq\")"
+ " SeqIO.write(seqiter,substracted,\"fastq\")"
]
},
{