From e5f80768d42a240207a6a1054a6807b842ca97f2 Mon Sep 17 00:00:00 2001
From: Julien Cornut <julien.cornut@hesge.ch>
Date: Fri, 26 Feb 2016 12:10:01 +0100
Subject: [PATCH] Automatic Update
---
ProcessFASTQ.ipynb | 1007 +++++++++++++++++++++++++++++++++++++++++++-
1 file changed, 1004 insertions(+), 3 deletions(-)
diff --git a/ProcessFASTQ.ipynb b/ProcessFASTQ.ipynb
index 7a78e1c..15b37c9 100644
--- a/ProcessFASTQ.ipynb
+++ b/ProcessFASTQ.ipynb
@@ -683,7 +683,7 @@
},
{
"cell_type": "code",
- "execution_count": 242,
+ "execution_count": 248,
"metadata": {
"collapsed": false
},
@@ -697,7 +697,1007 @@
"@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"
+ "\n",
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+ "SN279:493:C84L3ACXX:4:2309:18968:2393 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:18684:2500 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:19158:2257 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:18861:2388 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:18760:2418 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:18992:2386 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:19134:2414 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:19044:2283 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:19104:2325 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:19246:2423 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:18990:2470 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:19118:2431 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:19062:2362 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:19206:2432 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:19184:2416 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:19416:2266 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:19156:2454 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:19273:2325 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:19378:2402 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:19082:2437 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:19255:2293 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:19668:2311 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:19337:2395 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:19623:2326 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:19681:2342 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:19458:2464 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:19577:2391 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:19729:2403 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:19561:2418 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:19553:2469 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:19338:2432 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:19951:2259 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:19414:2488 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:19921:2349 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:17756:2323 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:19891:2305 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:19781:2257 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:19918:2399 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:20211:2310 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:19864:2486 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:20023:2341 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:19926:2424 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:20008:2356 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:20203:2348 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:19975:2363 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:20176:2369 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:20082:2398 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:20014:2453 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:20321:2362 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:20366:2332 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:20386:2386 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:20459:2433 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:20110:2437 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:20357:2475 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:20418:2461 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:20303:2481 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:20439:2372 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:20350:2263 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:20639:2267 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:20512:2308 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:20586:2274 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:20555:2313 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:20572:2407 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:20428:2484 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:20745:2352 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:20705:2431 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:20518:2435 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:20745:2435 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:20336:2498 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:20573:2494 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:20545:2463 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:20930:2366 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:20462:2498 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:20987:2469 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:21128:2450 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:20605:2429 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:20898:2337 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:21314:2276 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:21025:2458 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:21197:2473 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:20986:2424 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:21279:2363 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:21194:2251 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:1159:2579 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:1217:2591 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:21318:2379 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:1122:2521 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:1135:2622 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:1138:2559 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:1172:2554 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:1458:2529 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:1115:2683 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:1180:2728 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:1264:2551 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:1340:2553 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:1198:2745 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:1439:2602 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:1384:2605 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:1328:2616 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:1162:2742 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:1302:2640 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:1329:2643 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:1551:2571 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:1504:2619 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:1600:2651 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:1283:2548 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:1273:2622 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:1703:2532 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:1729:2694 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:2105:2568 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:1821:2511 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:1253:2668 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:2005:2601 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:19525:2484 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:1625:2655 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:2175:2617 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:2151:2606 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:2011:2689 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:2022:2624 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:1512:2655 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:2004:2734 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:2307:2538 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:2010:2644 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:2280:2543 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:2359:2572 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:2685:2502 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:2340:2507 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:2394:2710 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:2709:2519 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:2273:2678 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:2479:2738 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:2600:2522 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:2723:2551 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:2688:2685 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:2525:2711 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:2571:2712 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:2654:2517 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:2865:2608 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:2916:2620 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:2941:2627 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:2822:2632 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:2506:2731 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:2972:2509 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:2937:2699 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:2520:2630 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:2795:2739 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:2808:2572 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:2917:2641 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:3155:2521 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:2774:2658 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:3170:2547 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:2909:2714 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:3083:2611 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:3136:2534 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:3033:2509 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:3053:2590 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:3181:2623 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:3266:2577 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:3474:2553 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:3190:2711 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:3119:2650 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:3269:2625 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:3431:2706 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:3649:2533 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:3299:2530 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:3260:2743 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:3609:2539 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:3148:2553 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:3583:2681 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:3708:2639 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:3674:2694 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:3504:2573 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:3704:2508 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:3688:2743 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:3631:2692 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:3667:2583 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:3964:2541 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:3831:2524 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:3549:2742 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:3953:2564 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:3952:2714 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:3784:2676 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:3777:2721 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:3787:2747 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:4060:2541 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:3775:2621 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:4122:2607 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:4096:2608 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:4071:2697 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:3933:2583 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:4273:2503 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:3864:2733 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:3793:2707 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:4253:2615 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:4444:2640 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:4291:2506 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:4276:2652 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:4426:2593 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:4294:2653 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:4273:2579 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:4280:2740 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:4443:2564 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:4548:2500 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:4572:2528 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:4678:2560 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:4583:2583 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:4614:2608 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:4740:2620 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:4709:2667 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:4818:2514 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:4404:2715 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:4717:2728 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:4555:2703 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:4521:2734 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:5245:2511 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:4898:2566 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:5061:2524 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:5001:2640 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:5110:2675 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:5160:2534 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:5047:2707 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:4831:2616 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:4784:2602 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:5270:2523 : 0\n",
+ "SN279:493:C84L3ACXX:4:2309:5205:2692 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:5237:2750 : 4\n",
+ "SN279:493:C84L3ACXX:4:2309:5033:2725 : 4\n"
]
}
],
@@ -725,7 +1725,8 @@
" for record in filt_iter:\n",
" arr = matches.readline().split('\\t')\n",
" seq_id = arr[0]\n",
- " flag_field = arr[1]\n",
+ " flag = arr[1]\n",
+ " print(\"{0} : {1}\".format(seq_id,flag))\n",
" \n",
"\n",
" # Write back fastq\n",
--
GitLab