Extract the same lines from the two files


 
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# 1  
Old 10-01-2014
Extract the same lines from the two files

I used to use this script to extract the same lines from two files:
Code:
grep -f file1 file2 > outputfile

now I have file1
Code:
AB029895
AF208401
AF309648
AF526378
AJ444445
AJ720950
AJ851546
AY568629
AY591907
AY994087
BU116401
BU116599
BU119689
BU121308
BU125622
BU231446
BU236750
BU237045
BU268162
BU268426
BU322975
BU338092
BU364817
BU410749
BU428138
BU439949
BU456273
BX929394
BX929460
BX929509
BX929919
BX930088
BX930165
BX930175
BX930609
BX930762
BX930850
BX930983
BX931111
BX931232
BX931246
BX931297
BX931525
BX931573
BX932146
BX932298
BX932665
BX933309
BX933320
BX933382
BX933409
BX934186
BX934511
BX934532
BX934541
BX935207
BX935620
BX935710
BX936050
BX950642
CF250019
CN221750
CO506836
CR338727
CR352712
CR352964
CR353049
CR353073
CR353074
CR353204
CR353211
CR353323
CR353391
CR353519
CR353539
CR353764
CR353884
CR354168
CR354175
CR385201
CR385283
CR385555
CR385731
CR385914
CR386087
CR386696
CR386697
CR386788
CR387250
CR387429
CR387521
CR388615
CR388640
CR388652
CR388797
CR388864
CR388882
CR389294
CR389383
CR389430
CR389444
CR389538
CR389565
CR389594
CR389622
CR389659
CR389902
CR390034
CR390443
CR390543
CR391007
CR391066
CR391112
CR391289
CR391317
CR391572
CR405754
CR405789
CR405824
CR406657
CR406681
CR407341
CR407530
CR407533
CR523254
CR523285
CR523557
CR524146
CR524278
D82080
DQ092351
DQ092353
DR426245
FJ605357
GALGA_10AKII_KRT75
GALGA10_FK1
GALGA10_FK2
GALGA_11AKI_KRT42
GALGA_12AKI_KRT42
GALGA25_CL1
GALGA25_CL2
GALGA25_CL3
GALGA25_CL4
GALGA25_CL6
GALGA25_CL8
GALGA25_FL3
GALGA25_SC1
GALGA25_SC10
GALGA25_SC2
GALGA25_SC3
GALGA25_SC4
GALGA25_SC5
GALGA25_SC7
GALGA25_SC9
GALGA6_BKJ3
GALGA_UnR_CL1
GALGA_UnR_CL2
GALGA_UnR_FK10
GALGA_UnR_FK9
Histidine_rich_fast_protein_Rogers_Genes_for_Hair_and_Avian_Keratins
HQ438965
HQ878377
J02823
JF317543
JF923883
M64288
M96655
M96987
NM_001001193
NM_001001194
NM_001001460
NM_001001470
NM_001001605
NM_001001610
NM_001001775
NM_001004398
NM_001004765
NM_001005820
NM_001006264
NM_001006344
NM_001007477
NM_001007977
NM_001024830
NM_001025355
NM_001030008
NM_001030345
NM_001030363
NM_001030579
NM_001030702
NM_001030981
NM_001031314
NM_001031555
NM_001031568
NM_001044651
NM_001044657
NM_001044685
NM_001079724
NM_001080105
NM_001080890
NM_001081702
NM_001100288
NM_001113709
NM_001123031
NM_001127439
NM_001139439
NM_001142254
NM_001145228
NM_001159315
NM_001159678
NM_001165913
NM_001172781
NM_001193518
NM_001198731
NM_001199100
NM_001199438
NM_001199474
NM_001199519
NM_001199669
NM_001201386
NM_001201399
NM_001257388
NM_001277282
NM_001277393
NM_001277604
NM_001277678
NM_001277696
NM_001277711
NM_001277739
NM_001277751
NM_001277810
NM_001277927
NM_001277933
NM_001277935
NM_001277966
NM_001277973
NM_001277974
NM_001277975
NM_001277976
NM_001277978
NM_001277979
NM_001278148
NM_204107
NM_204108
NM_204117
NM_204173
NM_204176
NM_204190
NM_204214
NM_204290
NM_204336
NM_204348
NM_204448
NM_204473
NM_204498
NM_204533
NM_204540
NM_204547
NM_204602
NM_204620
NM_204634
NM_204690
NM_204707
NM_204720
NM_204764
NM_204783
NM_204814
NM_204818
NM_204821
NM_204830
NM_204897
NM_204899
NM_204935
NM_204957
NM_204993
NM_205000
NM_205011
NM_205013
NM_205045
NM_205065
NM_205097
NM_205112
NM_205157
NM_205190
NM_205248
NM_205249
NM_205268
NM_205274
NM_205293
NM_205304
NM_205422
NM_205434
NM_205449
NM_205459
NM_205469
NM_205478
NM_205494
NM_205525
NM_206905
NM_206982
NM_206989
NM_213577
NM_213578
U71060
U78260
U78261
U78264
U78265
X52876
X80113
XM_001231356
XM_001231471
XM_001231969
XM_001232058
XM_001232696
XM_001233690
XM_001233805
XM_001234441
XM_003641641
XM_003642480
XM_003642634
XM_003642679
XM_003642680
XM_003642792
XM_003643271
XM_004934642
XM_004934684
XM_004934709
XM_004934867
XM_004935120
XM_004935471
XM_004936175
XM_004937595
XM_004938104
XM_004938552
XM_004939276
XM_004940718
XM_004941230
XM_004941524
XM_004941549
XM_004942166
XM_004942593
XM_004942724
XM_004943755
XM_004947238
XM_004948062
XM_004948228
XM_004948550
XM_004948657
XM_413766
XM_414685
XM_414934
XM_415932
XM_416124
XM_416724
XM_416863
XM_417176
XM_417392
XM_417420
XM_417598
XM_417901
XM_418162
XM_418389
XM_419374
XM_419817
XM_420313
XM_421485
XM_423102
XM_424774
XM_425160
XM_425445
XM_425981
XM_428214
XM_428865
XM_429498
XR_211629
XR_212326
Z97238
Z97296

file2
Code:
NM_001128101
NM_205517
NM_204411
AB909129
NM_001205066
NM_205489
JC442378
NM_001004390
NM_204733
NM_205005
NM_204178
NM_204539
NM_001044638
NM_001005843
NM_205473
NM_205063
NM_204213
NM_204551
NM_204630
NM_205495
NM_205483
NM_205396
NM_001277977
NM_001194983
NM_001001203
NM_001277933
NM_001277753
NM_001277535
NM_001277489
NM_204665
NM_001030794
NM_001252280
NM_001252144
NM_001199391
NM_001195401
NM_001193616
NM_001184949
NM_001079476
NM_001163651
NM_001146131
NM_001017412
NM_001098608
NM_001097537
NM_001044693
NM_001039295
NM_001039166
NM_001031569
NM_001031076
NM_001031102
NM_001024828
NM_001024583
NM_001024582
NM_001006361
NM_213582
NM_205001
NM_204197
NM_204362
NM_204407
XM_001236757
XM_001235840
XM_004951091
XM_001235534
XM_423737
XM_429054
XM_004951070
XM_003643988
XM_004951066
XM_428483
XM_004951065
XM_004951064
XM_003643982
XM_003643981
XM_003643978
XM_004951059
XM_004951050
XM_427449
XM_426867
XM_003643967
XM_423001
XM_004951035
XM_004951028
XM_004951024
XM_003643937
XM_428130
XM_004950983
XM_004950907
XM_004950866
XM_004950856
XM_004950855
XM_004950854
XM_003643812
XM_003643799
XM_004950733
XM_004950710
XM_004950673
XM_004950659
XM_004950643
XM_004950636
XM_004950604
XM_004950595
XM_003643633
XM_003643626
XM_004950564
XM_004950562
XM_004950532
XM_003643585
XM_004950471
XM_004950446
XM_003643556
XM_003643545
XM_003643539
XM_004950390
XM_004950367
XM_004950365
XM_004950356
XM_004950338
XM_001235610
XM_003643439
XM_004950177
XM_003643381
XM_004950174
XM_004950173
XM_004950171
XM_004950170
XM_004950169
XM_004950168
XM_004950167
XM_004950166
XM_003643373
XM_003643348
XM_004950078
XM_003643300
XM_426912
XM_001236505
XM_004950056
XM_004950054
XM_428282
XM_004950051
XM_003643209
XM_003643181
XM_004949853
XM_004949820
XM_003643131
XM_004949745
XM_004949513
XM_429188
XM_004949417
XM_004949298
XM_004949269
XM_004949100
XM_004949099
XM_430486
XM_003642871
XM_004948868
XM_004948867
XM_004948866
XM_004948864
XM_004948863
XM_001233947
XM_004948862
XM_004948861
XM_004948860
XM_004948859
XM_004948858
XM_004948857
XM_004948856
XM_004948855
XM_004948854
XM_004948853
XM_004948852
XM_004948851
XM_004948850
XM_004948849
XM_004948848
XM_004948847
XM_004948846
XM_004948845
XM_004948763
XM_004948474
XM_004948439
XM_003642736
XM_004935047
XM_004935046
XM_004934934
XM_004934805
XM_004948223
XM_004947710
XM_004947665
XM_417442
XM_004947013
XM_004946737
XM_415739
XM_004946441
XM_004934415
XM_001233877
XM_415281
XM_003642214
XM_004945624
XM_001231561
XM_004945437
XM_425243
XM_414566
XM_004944910
XM_004944828
XM_004944827
XM_004944826
XM_004944825
XM_004944824
XM_414481
XM_004944806
XM_414443
XM_004944219
XM_004944218
XM_425119
XM_004944217
XM_004944186
XM_003641908
XM_001231930
XM_001233272
XM_004937011
XM_422447
XM_422095
XM_004942629
XM_004942625
XM_004942592
XM_004942510
XM_004942509
XM_004942496
XM_004942395
XM_004942394
XM_421837
XM_004942392
XM_001234860
XM_004942322
XM_004942074
XM_004942073
XM_004942021
XM_004942020
XM_004936487
XM_004936216
XM_420730
XM_004940955
XM_004940709
XM_001233044
XM_004940620
XM_004935811
XM_004940416
XM_004940415
XM_004940414
XM_419864
XM_004940413
XM_004940412
XM_001235446
XM_004940111
XM_004939913
XM_429803
XM_004939392
XM_004939391
XM_418742
XM_004939063
XM_004939013
XM_417265
XM_004938825
XM_003640528
XM_001234360
XM_004938515
XM_004937758
XM_004937720
XM_416064
XM_001233677
XM_416845
XM_004937431
XM_004937430
XM_004937429
XM_003640318
HG313856
XM_001231851
XM_427634
HE605042
NM_001245927
NM_001031543
NM_001277927
S82826
KC818438
NM_001097533
NM_205141
JX827244
NM_001031514
EF635923
JQ927548
JQ927547
JF936864
JF936842
JQ268269
DQ272256
AY753296
U37277
U26148
S83102
S60800
M33059
M34330
FN178490
NM_001006201
NM_001197036
FJ655775
GU474517
EU082129
EF551041
EF193863
DQ848155
HQ015472
HM584710
AB530390
AB530388
AB530386
AB530380
AB530379
AB530349
AY534895
AY582132
S78729
U26946
U18261
U04613
L19258
M87294
M25774
M11674
M36167
M92037
AY332743
AY225966
AF463494
AF465207
AF330010
AF058287
AF033495
GU230782
GU230775
GU053726
GQ203625
GQ203624
DQ129667
AY849320
AY849319
AY699713
AY583536
AY491057
AF488728
AY029523
AF081672
M73995
J00860
FJ891063
AY375530
AJ582607
EF626644
EF554722
EF554721
CR385737
BX933738
AM492777
D38404
EU334507
AM773255
DQ855410
AM076725
EF062570
EF457884
EF117324
DQ279788
AB231849
DQ858341
DQ858327
DQ858314
DQ858301
DQ867000
DQ677635
AM177496
AB233025
AB233021
AB232993
AB090806
AB204802
AB204801
AJ879989
AJ879982
AJ879974
AJ879972
AJ879970
AJ879958
AJ879957
CR733408
CR733336
CR733325
CR732872
AF498322
AB214887
DQ003337
V00412
AJ851499
AJ719737
AJ634337
AJ634334
AJ243435
AJ293700
AJ401469
AJ634336
AB096098
AJ719386
AJ720728
AJ720687
AJ720674
AJ720558
AJ720304
AJ719669
Y08386
CR524401
CR524356
CR524222
CR524210
CR524107
CR524077
CR524064
CR524056
CR524027
CR523875
CR523862
CR523844
CR523826
CR523735
CR523688
CR523615
CR523605
CR523597
CR523591
CR523488
CR523465
CR523361
CR523272
CR523137
CR523007
CR522904
CR522895
CR522885
CR407537
CR407462
CR407452
CR407435
CR407425
CR407373
CR407312
CR407255
CR407253
CR407241
CR407224
CR407221
CR407219
CR407152
CR407105
CR406735
CR406732
CR406637
CR406616
CR406590
CR406370
CR406126
CR406120
CR406039
CR405999
CR405973
CR405951
CR405934
CR405933
CR405778
CR405740
CR391728
CR391727
CR391713
CR391688
CR391665
CR391596
CR391595
CR391567
CR391552
CR391529
CR391443
CR391410
CR391394
CR391374
CR391364
CR391352
CR391335
CR391234
CR391160
CR391145
CR391079
CR391074
CR391070
CR391068
CR391033
CR391026
CR391013
CR390998
CR390990
CR390921
CR390910
CR390907
CR390906
CR390896
CR390885
CR390868
CR390790
CR390782
CR390770
CR390767
CR390752
CR390624
CR390570
CR390562
CR390554
CR390533
CR390483
CR390333
CR390291
CR390287
CR390250
CR390224
CR390215
CR390211
CR390186
CR390180
CR390179
CR390113
CR390077
CR389968
CR389953
CR389903
CR389894
CR389844
CR389635
CR389625
CR389537
CR389511
CR389461
CR389439
CR389422
CR389401
CR389379
CR389326
CR389310
CR389250
CR389242
CR389202
CR389201
CR389098
CR389046
CR389014
CR389002
CR388980
CR388940
CR388859
CR388850
CR388816
CR388783
CR388753
CR388726
CR338792
CR388609
CR388593
CR388505
CR388494
CR388492
CR388464
CR388462
BX950735
BX950687
BX950619
BX950612
BX950596
BX950568
BX935747
BX934265
BX934260
BX933732
BX931763
BX930278
BX930161
BX929769
CR387909
CR387866
CR387816
CR387802
CR387779
CR387728
CR387571
CR387484
CR387468
CR387381
CR387365
CR387351
CR387320
CR387308
CR387203
CR387193
CR387174
CR387031
CR386884
CR386872
CR386863
CR386839
CR386593
CR386560
CR386517
CR386459
CR386442
CR386435
CR386404
CR386229
CR386036
CR386030
CR385991
CR385931
CR385842
CR385764
CR385632
CR385577
CR385516
CR385511
CR385495
CR385448
CR385390
CR385369
CR385339
CR385310
CR385280
CR385265
CR385258
CR385257
CR385230
CR385225
CR385223
CR385192
CR385181
CR385140
CR385134
CR385129
CR338834
CR338818
CR338754
BX950710
BX936247
BX936030
BX935534
BX935445
BX935420
BX935342
BX935295
BX935087
BX934801
BX934499
BX934437
BX934185
BX934100
BX934068
BX934061
BX933948
BX933634
BX933621
BX933405
BX933289
BX933203
BX933163
BX933071
BX932928
BX932736
BX932128
BX931734
BX931657
BX931481
BX931441
BX931430
BX931347
BX930790
BX930786
BX930725
BX930715
BX930604
BX930588
BX930568
BX930479
BX929948
BX929375
CR354309
CR354246
CR354183
CR354140
CR354066
CR354039
CR353990
CR353980
CR353938
CR353832
CR353813
CR353778
CR353729
CR353683
CR353680
CR353635
CR353611
CR353500
CR353435
CR353424
CR353347
CR353316
CR353267
CR353258
CR353160
CR353010
CR353005
CR352969
CR352967
CR352917
CR352784
CR352721
CR352709
CR352700
CR352662
CR352568
CR352511
CR338886
CR338866
CR338855
CR338849
CR338839
BX950761
BX950302
BX950232
BX936219
BX936011
BX935885
BX935884
BX935880
BX935540
BX935421
BX935344
BX935343
BX935326
BX935278
BX935267
BX935190
BX935053
BX934936
BX934830
BX934559
BX934547
BX934389
BX934266
BX934120
BX934098
BX933874
BX933863
BX933772
BX933760
BX933678
BX933373
BX933243
BX932856
BX932669
BX932662
BX932123
BX932070
BX932067
BX932032
BX931988
BX931981
BX931927
BX931678
BX931569
BX931564
BX931391
BX931304
BX931154
BX931148
BX930913
BX930810
BX930809
BX930793
BX930480
BX930333
BX930293
BX930210
BX930201
BX930189
BX930141
BX929983
BX929914
BX929831
BX929653
BX929633
BX929368
AJ309543
AJ309542
AB120326
D14318
AF435570
AJ301881
Y07588
V00449
X14881
M30355
M30354
M30352
M30351
M30369
M30368
GALGA25_CL10
GALGA25_Ktn6
GALGA25_Ktn9

I got the outputfile
Code:
NM_001277933
NM_001277927
GALGA25_CL10

I think the outputfile is wrong, because the line "GALGA25_CL10" is not in file1. Can anybody tell me why this script is failed and what is the alternative solution?
Thank you.
# 2  
Old 10-01-2014
Try

Code:
grep -Fxf file1 file2 
NM_001277933
NM_001277927

Code:
awk 'FNR==NR{A[$0];next}$0 in A' file1 file2

Code:
comm -12 <( sort file1 ) <( sort file2 )

This User Gave Thanks to Akshay Hegde For This Post:
# 3  
Old 10-01-2014
Quote:
Originally Posted by yuejian
I used to use this script to extract the same lines from two files:
Code:
grep -f file1 file2 > outputfile

. . .
I think the outputfile is wrong, because the line "GALGA25_CL10" is not in file1. . . .
It is not, but "GALGA25_CL1" is. That's what is called "false positives". Akshay Hegde already provided you with the -x (exact whole line match) option.
This User Gave Thanks to RudiC For This Post:
# 4  
Old 10-02-2014
Thank you guys, you saved my life.
# 5  
Old 10-03-2014
Hi.

There are utilities that specialize in these kinds of operations, such as combine from moreutils, a package in the Debian repositories, as well as being available via git. Here's an example:
Code:
#!/usr/bin/env bash

# @(#) s1	Demonstrate combine files with boolean operators, package "moreutils".
# combine - combine sets of lines from two files using boolean operations
# For combine, part of moreutils, see:
# http://joeyh.name/code/moreutils/

# Utility functions: print-as-echo, print-line-with-visual-space, debug.
# export PATH="/usr/local/bin:/usr/bin:/bin"
LC_ALL=C ; LANG=C ; export LC_ALL LANG
pe() { for _i;do printf "%s" "$_i";done; printf "\n"; }
pl() { pe;pe "-----" ;pe "$*"; }
db() { ( printf " db, ";for _i;do printf "%s" "$_i";done;printf "\n" ) >&2 ; }
db() { : ; }
C=$HOME/bin/context && [ -f $C ] && $C specimen combine

pl " Input data files:"
specimen data?

pl " Results, combine data1 AND data2:"
combine data1 and data2

pl " Results, combine data2 AND data1:"
combine data2 and data1

exit 0

producing:
Code:
$ ./s1

Environment: LC_ALL = C, LANG = C
(Versions displayed with local utility "version")
OS, ker|rel, machine: Linux, 2.6.26-2-amd64, x86_64
Distribution        : Debian 5.0.8 (lenny, workstation) 
bash GNU bash 3.2.39
specimen (local) 1.17
combine (pm:moreutils) 0.31

-----
 Input data files:
Edges: 5:0:5 of 378 lines in file "data1"
AB029895
AF208401
AF309648
AF526378
AJ444445
   ---
XM_429498
XR_211629
XR_212326
Z97238
Z97296

Edges: 5:0:5 of 820 lines in file "data2"
NM_001128101
NM_205517
NM_204411
AB909129
NM_001205066
   ---
M30369
M30368
GALGA25_CL10
GALGA25_Ktn6
GALGA25_Ktn9

-----
 Results, combine data1 AND data2:
NM_001277927
NM_001277933

-----
 Results, combine data2 AND data1:
NM_001277933
NM_001277927

The documentation explains that for combine, a and b is not always the same as b and a, but they are in this case.

See comments in the script for appropriate links.

Best wishes ... cheers, drl
 
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