Grep -v command


 
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# 8  
Old 09-13-2019
Code:
chr10    83450    83503    NB551726:5:H2HT5BGXC:1:23210:11622:11362    1    +
chr10    83673    83765    NB551726:5:H2HT5BGXC:2:21205:17604:2246    0    +
chr10    85504    85558    NB551726:5:H2HT5BGXC:2:22211:7601:16419    31    +
chr10    85636    85689    NB551726:5:H2HT5BGXC:3:13612:11620:17539    1    -
chr10    86068    86121    NB551726:5:H2HT5BGXC:4:12406:24783:2749    1    -
chr10    87062    87115    NB551726:5:H2HT5BGXC:1:11304:16254:3825    1    +
chr10    90463    90516    NB551726:5:H2HT5BGXC:1:11102:24833:4879    1    +
chr10    99875    99929    NB551726:5:H2HT5BGXC:1:12201:7805:1705    0    +
chr10    106760    106813    NB551726:5:H2HT5BGXC:3:12506:12571:10460    1    -
chr10    146518    146570    NB551726:5:H2HT5BGXC:1:22112:11102:14366    14    -
chr10    164895    164940    NB551726:5:H2HT5BGXC:1:13211:15930:15082    1    -
chr10    166771    166824    NB551726:5:H2HT5BGXC:1:12101:20188:17034    1    +
chr10    198434    198467    NB551726:5:H2HT5BGXC:1:11306:7431:3548    0    -
chr10    232590    232630    NB551726:5:H2HT5BGXC:1:12308:2911:4998    18    +
chr10    233673    233721    NB551726:5:H2HT5BGXC:1:11204:24661:6499    24    +
chr10    244426    244461    NB551726:5:H2HT5BGXC:4:22610:1450:10242    22    -
chr10    283223    283277    NB551726:5:H2HT5BGXC:1:21202:24027:11672    44    +
chr10    287019    287063    NB551726:5:H2HT5BGXC:1:22210:5587:11665    28    +
chr10    336049    336112    NB551726:5:H2HT5BGXC:4:21402:23402:10596    36    -
chr10    342089    342142    NB551726:5:H2HT5BGXC:1:13310:11131:11654    1    -
chr10    342529    342583    NB551726:5:H2HT5BGXC:1:11211:9508:1997    1    +
chr10    362697    362752    NB551726:5:H2HT5BGXC:1:11101:11174:14176    42    -
chr10    371287    371340    NB551726:5:H2HT5BGXC:4:11602:10047:13747    44    +
chr10    388618    388671    NB551726:5:H2HT5BGXC:1:11306:6809:18821    24    +
chr10    420131    420159    NB551726:5:H2HT5BGXC:2:23203:13675:14982    22    -
chr10    476607    476640    NB551726:5:H2HT5BGXC:3:22501:13073:17530    22    -
chr10    500144    500198    NB551726:5:H2HT5BGXC:2:11301:24584:1760    44    +
chr10    509180    509213    NB551726:5:H2HT5BGXC:1:11106:7603:13116    0    +
chr10    511342    511395    NB551726:5:H2HT5BGXC:1:23110:18078:12881    1    +
chr10    585380    585424    NB551726:5:H2HT5BGXC:2:12304:5393:1266    9    +
chr10    685059    685121    NB551726:5:H2HT5BGXC:1:21101:21058:3630    11    +
chr10    685205    685266    NB551726:5:H2HT5BGXC:3:11408:1925:8674    1    +
chr10    685352    685413    NB551726:5:H2HT5BGXC:3:23408:13668:1449    0    +
chr10    731130    731159    NB551726:5:H2HT5BGXC:1:13202:15125:10876    0    +
chr10    794077    794130    NB551726:5:H2HT5BGXC:1:11306:15879:10062    1    -
chr10    794971    795024    NB551726:5:H2HT5BGXC:3:21404:4215:19571    1    +
chr10    795264    795317    NB551726:5:H2HT5BGXC:2:13206:6134:9929    1    +
chr10    795524    795560    NB551726:5:H2HT5BGXC:2:21205:15853:5080    0    -
chr10    814780    814815    NB551726:5:H2HT5BGXC:4:13412:1664:12073    22    +
chr10    837668    837722    NB551726:5:H2HT5BGXC:1:11101:25458:6217    44    +
chr10    947014    947075    NB551726:5:H2HT5BGXC:2:12102:8014:4477    17    -
chr10    973816    973878    NB551726:5:H2HT5BGXC:1:11101:10787:4355    22    +
chr10    1012283    1012336    NB551726:5:H2HT5BGXC:1:23308:13195:10976    1    +
chr10    1026458    1026492    NB551726:5:H2HT5BGXC:3:11506:7661:3547    0    -
chr10    1037982    1038035    NB551726:5:H2HT5BGXC:3:13608:13694:9588    44    -
chr10    1046219    1046262    NB551726:5:H2HT5BGXC:1:21202:3219:4865    2    -
chr10    1064331    1064378    NB551726:5:H2HT5BGXC:3:23406:24220:15886    0    -
chr10    1104334    1104387    NB551726:5:H2HT5BGXC:1:12103:16042:13671    44    +
chr10    1195895    1195988    NB551726:5:H2HT5BGXC:1:11106:13477:18629    24    +
chr10    1267381    1267426    NB551726:5:H2HT5BGXC:1:11104:13034:2182    1    -
chr10    1271055    1271108    NB551726:5:H2HT5BGXC:1:21209:2410:17494    1    +
chr10    1287684    1287737    NB551726:5:H2HT5BGXC:1:21211:11389:17162    1    +
chr10    1301770    1301823    NB551726:5:H2HT5BGXC:1:22211:19077:10160    1    +
chr10    1302816    1302869    NB551726:5:H2HT5BGXC:1:13101:17304:13773    1    +
chr10    1305284    1305341    NB551726:5:H2HT5BGXC:3:12601:23177:5879    1    +
chr10    1346480    1346533    NB551726:5:H2HT5BGXC:3:11408:4043:10920    1    -
chr10    1347666    1347719    NB551726:5:H2HT5BGXC:2:23210:23276:18735    1    +
chr10    1349156    1349209    NB551726:5:H2HT5BGXC:4:12506:4480:3779    1    -
chr10    1349869    1349922    NB551726:5:H2HT5BGXC:2:12109:10808:14290    1    -
chr10    1367503    1367553    NB551726:5:H2HT5BGXC:4:22610:5848:13809    24    +
chr10    1431352    1431392    NB551726:5:H2HT5BGXC:4:13601:10331:9778    9    +
chr10    1494893    1494940    NB551726:5:H2HT5BGXC:3:21601:4179:7024    1    +
chr10    1494948    1494990    NB551726:5:H2HT5BGXC:1:11103:26564:4480    1    -
chr10    1504933    1504976    NB551726:5:H2HT5BGXC:3:11506:21284:7335    0    -
chr10    1513840    1513893    NB551726:5:H2HT5BGXC:2:21101:1240:14937    1    -
chr10    1526949    1527003    NB551726:5:H2HT5BGXC:1:11106:4035:1555    44    +
chr10    1535924    1535977    NB551726:5:H2HT5BGXC:1:11109:6188:7918    1    -
chr10    1549714    1549765    NB551726:5:H2HT5BGXC:1:11205:14522:3538    44    +
chr10    1579039    1579093    NB551726:5:H2HT5BGXC:4:12407:2657:10053    1    +
chr10    1580121    1580165    NB551726:5:H2HT5BGXC:1:21206:18826:14008    11    +
chr10    1606485    1606538    NB551726:5:H2HT5BGXC:1:22112:9279:5865    1    +
chr10    1606828    1606881    NB551726:5:H2HT5BGXC:3:22408:20983:8297    1    +
chr10    1811297    1811350    NB551726:5:H2HT5BGXC:2:11110:2868:16729    1    -
chr10    1812327    1812380    NB551726:5:H2HT5BGXC:3:22512:22115:5787    1    +
chr10    1825561    1825590    NB551726:5:H2HT5BGXC:1:11110:2129:4021    0    -
chr10    1842110    1842171    NB551726:5:H2HT5BGXC:2:11310:26839:10836    28    +
chr10    1881715    1881753    NB551726:5:H2HT5BGXC:2:11205:3952:19358    2    +
chr10    1922335    1922390    NB551726:5:H2HT5BGXC:3:11602:6835:13982    44    +
chr10    1991697    1991766    NB551726:5:H2HT5BGXC:1:13212:5870:20182    36    +
chr10    2101162    2101215    NB551726:5:H2HT5BGXC:1:21107:12547:7522    44    +
chr10    2244348    2244386    NB551726:5:H2HT5BGXC:2:11108:18028:9665    0    +
chr10    2292698    2292726    NB551726:5:H2HT5BGXC:3:13403:8382:4801    22    -
chr10    2296869    2296922    NB551726:5:H2HT5BGXC:2:13301:11582:18251    1    -
chr10    2366208    2366259    NB551726:5:H2HT5BGXC:1:12212:14624:16575    40    +
chr10    2396479    2396509    NB551726:5:H2HT5BGXC:3:22509:15130:13568    9    +
chr10    2396527    2396581    NB551726:5:H2HT5BGXC:2:22301:3292:6255    2    +
chr10    2518990    2519044    NB551726:5:H2HT5BGXC:1:11109:9354:2230    41    -
chr10    2533231    2533269    NB551726:5:H2HT5BGXC:4:11406:26398:8923    0    -
chr10    2534234    2534287    NB551726:5:H2HT5BGXC:4:22410:16649:7949    1    -
chr10    2534702    2534755    NB551726:5:H2HT5BGXC:3:13405:17174:6905    1    -
chr10    2570819    2570875    NB551726:5:H2HT5BGXC:1:11101:17058:14296    22    -
chr10    2598458    2598510    NB551726:5:H2HT5BGXC:4:23402:11741:2459    9    -
chr10    2645231    2645267    NB551726:5:H2HT5BGXC:4:23407:13046:7808    22    -
chr10    2664360    2664405    NB551726:5:H2HT5BGXC:1:12212:2600:16692    2    -
chr10    2689748    2689785    NB551726:5:H2HT5BGXC:2:13101:24861:12307    22    -
chr10    2757729    2757782    NB551726:5:H2HT5BGXC:2:13110:17135:7589    44    +
chr10    2767042    2767088    NB551726:5:H2HT5BGXC:1:22107:4789:12466    2    +
chr10    2803427    2803454    NB551726:5:H2HT5BGXC:2:11203:24404:19669    22    -
chr10    2814113    2814167    NB551726:5:H2HT5BGXC:1:12305:14313:9805    44    -
chr10    2932828    2932881    NB551726:5:H2HT5BGXC:2:11301:21719:1970    1    +
chr10    3034873    3034907    NB551726:5:H2HT5BGXC:1:23109:21910:9724    2    +
chr10    3124175    3124207    NB551726:5:H2HT5BGXC:1:22111:5657:13463    0    +
chr10    3420171    3420224    NB551726:5:H2HT5BGXC:1:12210:2214:14077    41    -
chr10    3420565    3420622    NB551726:5:H2HT5BGXC:1:11104:13745:15948    36    +
chr10    3534307    3534340    NB551726:5:H2HT5BGXC:1:13203:20883:2767    0    +
chr10    3606289    3606342    NB551726:5:H2HT5BGXC:2:11112:20795:16887    44    -
chr10    3618574    3618610    NB551726:5:H2HT5BGXC:1:13207:15169:14738    24    -
chr10    3621035    3621064    NB551726:5:H2HT5BGXC:2:11307:6461:10417    22    -
chr10    3646540    3646586    NB551726:5:H2HT5BGXC:2:22110:5058:7733    11    +
chr10    3647767    3647804    NB551726:5:H2HT5BGXC:1:11101:24494:6143    22    +
chr10    3681373    3681414    NB551726:5:H2HT5BGXC:3:21404:25227:19317    2    -
chr10    3683054    3683110    NB551726:5:H2HT5BGXC:1:11107:12183:9835    19    +
chr10    3687341    3687385    NB551726:5:H2HT5BGXC:3:22603:1787:10818    9    -
chr10    3723453    3723491    NB551726:5:H2HT5BGXC:2:22106:13995:13538    0    +
chr10    3731481    3731507    NB551726:5:H2HT5BGXC:4:13407:26161:10111    22    +
chr10    3773260    3773316    NB551726:5:H2HT5BGXC:1:11101:8820:18166    22    +


Last edited by Peasant; 09-13-2019 at 10:09 AM..
# 9  
Old 09-13-2019
Hi,

Using the data that you provided in the previous post and the "grep" already supplied I get;

Code:
[e434069@fbakirpomd4 data]$ grep -v " [01] *[+-]" test_01.txt
chr10 85504 85558 NB551726:5:H2HT5BGXC:2:22211:7601:16419 31 +
chr10 146518 146570 NB551726:5:H2HT5BGXC:1:22112:11102:14366 14 -
chr10 232590 232630 NB551726:5:H2HT5BGXC:1:12308:2911:4998 18 +
chr10 233673 233721 NB551726:5:H2HT5BGXC:1:11204:24661:6499 24 +
chr10 244426 244461 NB551726:5:H2HT5BGXC:4:22610:1450:10242 22 -
chr10 283223 283277 NB551726:5:H2HT5BGXC:1:21202:24027:11672 44 +
chr10 287019 287063 NB551726:5:H2HT5BGXC:1:22210:5587:11665 28 +
chr10 336049 336112 NB551726:5:H2HT5BGXC:4:21402:23402:10596 36 -
chr10 362697 362752 NB551726:5:H2HT5BGXC:1:11101:11174:14176 42 -
chr10 371287 371340 NB551726:5:H2HT5BGXC:4:11602:10047:13747 44 +
chr10 388618 388671 NB551726:5:H2HT5BGXC:1:11306:6809:18821 24 +
chr10 420131 420159 NB551726:5:H2HT5BGXC:2:23203:13675:14982 22 -
chr10 476607 476640 NB551726:5:H2HT5BGXC:3:22501:13073:17530 22 -
chr10 500144 500198 NB551726:5:H2HT5BGXC:2:11301:24584:1760 44 +
chr10 585380 585424 NB551726:5:H2HT5BGXC:2:12304:5393:1266 9 +
chr10 685059 685121 NB551726:5:H2HT5BGXC:1:21101:21058:3630 11 +
chr10 814780 814815 NB551726:5:H2HT5BGXC:4:13412:1664:12073 22 +
chr10 837668 837722 NB551726:5:H2HT5BGXC:1:11101:25458:6217 44 +
chr10 947014 947075 NB551726:5:H2HT5BGXC:2:12102:8014:4477 17 -
chr10 973816 973878 NB551726:5:H2HT5BGXC:1:11101:10787:4355 22 +
chr10 1037982 1038035 NB551726:5:H2HT5BGXC:3:13608:13694:9588 44 -
chr10 1046219 1046262 NB551726:5:H2HT5BGXC:1:21202:3219:4865 2 -
chr10 1104334 1104387 NB551726:5:H2HT5BGXC:1:12103:16042:13671 44 +
chr10 1195895 1195988 NB551726:5:H2HT5BGXC:1:11106:13477:18629 24 +
chr10 1367503 1367553 NB551726:5:H2HT5BGXC:4:22610:5848:13809 24 +
chr10 1431352 1431392 NB551726:5:H2HT5BGXC:4:13601:10331:9778 9 +
chr10 1526949 1527003 NB551726:5:H2HT5BGXC:1:11106:4035:1555 44 +
chr10 1549714 1549765 NB551726:5:H2HT5BGXC:1:11205:14522:3538 44 +
chr10 1580121 1580165 NB551726:5:H2HT5BGXC:1:21206:18826:14008 11 +
chr10 1842110 1842171 NB551726:5:H2HT5BGXC:2:11310:26839:10836 28 +
chr10 1881715 1881753 NB551726:5:H2HT5BGXC:2:11205:3952:19358 2 +
chr10 1922335 1922390 NB551726:5:H2HT5BGXC:3:11602:6835:13982 44 +
chr10 1991697 1991766 NB551726:5:H2HT5BGXC:1:13212:5870:20182 36 +
chr10 2101162 2101215 NB551726:5:H2HT5BGXC:1:21107:12547:7522 44 +
chr10 2292698 2292726 NB551726:5:H2HT5BGXC:3:13403:8382:4801 22 -
chr10 2366208 2366259 NB551726:5:H2HT5BGXC:1:12212:14624:16575 40 +
chr10 2396479 2396509 NB551726:5:H2HT5BGXC:3:22509:15130:13568 9 +
chr10 2396527 2396581 NB551726:5:H2HT5BGXC:2:22301:3292:6255 2 +
chr10 2518990 2519044 NB551726:5:H2HT5BGXC:1:11109:9354:2230 41 -
chr10 2570819 2570875 NB551726:5:H2HT5BGXC:1:11101:17058:14296 22 -
chr10 2598458 2598510 NB551726:5:H2HT5BGXC:4:23402:11741:2459 9 -
chr10 2645231 2645267 NB551726:5:H2HT5BGXC:4:23407:13046:7808 22 -
chr10 2664360 2664405 NB551726:5:H2HT5BGXC:1:12212:2600:16692 2 -
chr10 2689748 2689785 NB551726:5:H2HT5BGXC:2:13101:24861:12307 22 -
chr10 2757729 2757782 NB551726:5:H2HT5BGXC:2:13110:17135:7589 44 +
chr10 2767042 2767088 NB551726:5:H2HT5BGXC:1:22107:4789:12466 2 +
chr10 2803427 2803454 NB551726:5:H2HT5BGXC:2:11203:24404:19669 22 -
chr10 2814113 2814167 NB551726:5:H2HT5BGXC:1:12305:14313:9805 44 -
chr10 3034873 3034907 NB551726:5:H2HT5BGXC:1:23109:21910:9724 2 +
chr10 3420171 3420224 NB551726:5:H2HT5BGXC:1:12210:2214:14077 41 -
chr10 3420565 3420622 NB551726:5:H2HT5BGXC:1:11104:13745:15948 36 +
chr10 3606289 3606342 NB551726:5:H2HT5BGXC:2:11112:20795:16887 44 -
chr10 3618574 3618610 NB551726:5:H2HT5BGXC:1:13207:15169:14738 24 -
chr10 3621035 3621064 NB551726:5:H2HT5BGXC:2:11307:6461:10417 22 -
chr10 3646540 3646586 NB551726:5:H2HT5BGXC:2:22110:5058:7733 11 +
chr10 3647767 3647804 NB551726:5:H2HT5BGXC:1:11101:24494:6143 22 +
chr10 3681373 3681414 NB551726:5:H2HT5BGXC:3:21404:25227:19317 2 -
chr10 3683054 3683110 NB551726:5:H2HT5BGXC:1:11107:12183:9835 19 +
chr10 3687341 3687385 NB551726:5:H2HT5BGXC:3:22603:1787:10818 9 -
chr10 3731481 3731507 NB551726:5:H2HT5BGXC:4:13407:26161:10111 22 +
chr10 3773260 3773316 NB551726:5:H2HT5BGXC:1:11101:8820:18166 22 +

Which looks to be correct.

Regards

Gull04
These 2 Users Gave Thanks to gull04 For This Post:
# 10  
Old 09-14-2019
Perhaps also:
Code:
awk '$5!~/^[01]$/' file

or
Code:
awk '$5>1' file

This User Gave Thanks to Scrutinizer For This Post:
# 11  
Old 09-15-2019
Perhaps tab characters were converted to spaces? Often copy/paste of text does it.

The awk sample in the previous post works with tabs or spaces.
# 12  
Old 09-16-2019
Hey Amit,

grep doesn't really work on delimited row data, rather it works as individual character in the file.

in your case awk is always a better approach. You may try the below: (assuming you are using tab delimiter from your example)
Code:
awk -F "\t" '($5) > 1' filename | sort -u | cut -d '\t' -f 1,2,3,4,5,6 > outputfile

Thanks!

Last edited by RavinderSingh13; 09-16-2019 at 10:08 AM..
This User Gave Thanks to hawk_eye For This Post:
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Hi, im taking an entry Unix class, and as part of my lab assignment I have to copy all files in the /home/david/lab3 directory that have the file extension .save to your lab3/temp directory. I'm having trouble getting the grep to do anything worth while I've been trying to do: cp... (6 Replies)
Discussion started by: Critical jeff
6 Replies

7. Shell Programming and Scripting

can anyone help with shell script command about searching word with grep command?

i want to search in the current directory all the files that contain one word for example "hello" i want to achieve it with the grep command but not with the grep * (2 Replies)
Discussion started by: aintour
2 Replies

8. UNIX for Advanced & Expert Users

how to exclude the GREP command from GREP

I am doing "ps -f" to see my process. but I get lines that one of it represents the ps command itself. I want to grep it out using -v flag, but than I get another process that belongs to the GREP itself : I would like to exclude # ps -f UID PID PPID C STIME TTY TIME CMD... (2 Replies)
Discussion started by: yamsin789
2 Replies

9. UNIX for Dummies Questions & Answers

grep command

hi all i have directory /usr under this directory i have subdirectories tmp1,tmp2,tmp3 like this /usr/tmp1 /usr/tmp2 /usr/tmp3 and so on i want to search string in files (i don't know the name of the files)and i want to serch it in all the directories under the /usr how shell i do... (3 Replies)
Discussion started by: naamas03
3 Replies

10. Shell Programming and Scripting

grep command

What is the meaning of this grep -v $object grant_BU.sql>temp (1 Reply)
Discussion started by: debasis.mishra
1 Replies
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