Replacing matching entries in one column of a file by another column from a different file Announcing the arrival of Valued Associate #679: Cesar Manara Planned maintenance scheduled April 23, 2019 at 23:30 UTC (7:30pm US/Eastern) 2019 Community Moderator Election Results Why I closed the “Why is Kali so hard” questionMerge two files: two lines, partial line, two lines, partial line, etcFind common elements in a given column from two files and output the column values from each filecompare multiple files(more than two) with two different columnsReplace column in one file with column from another using awk?Joining columns from files if they contain a match in another columnMerging two files, one column at a timeColumn matching in separate filesExtract row if both column values appear in a single column from a separate fileJoining entries based off of column using awk/joinCompare two files by first column. Keep rows if matchingRecursively find and replace contents of one file using a key from another file
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Replacing matching entries in one column of a file by another column from a different file
Announcing the arrival of Valued Associate #679: Cesar Manara
Planned maintenance scheduled April 23, 2019 at 23:30 UTC (7:30pm US/Eastern)
2019 Community Moderator Election Results
Why I closed the “Why is Kali so hard” questionMerge two files: two lines, partial line, two lines, partial line, etcFind common elements in a given column from two files and output the column values from each filecompare multiple files(more than two) with two different columnsReplace column in one file with column from another using awk?Joining columns from files if they contain a match in another columnMerging two files, one column at a timeColumn matching in separate filesExtract row if both column values appear in a single column from a separate fileJoining entries based off of column using awk/joinCompare two files by first column. Keep rows if matchingRecursively find and replace contents of one file using a key from another file
.everyoneloves__top-leaderboard:empty,.everyoneloves__mid-leaderboard:empty,.everyoneloves__bot-mid-leaderboard:empty margin-bottom:0;
7
I have two tab-separated files which look as follows:
file1:
NC_008146.1 WP_011558474.1 1155234 1156286 44173
NC_008146.1 WP_011558475.1 1156298 1156807 12
NC_008146.1 WP_011558476.1 1156804 1157820 -3
NC_008705.1 WP_011558474.1 1159543 1160595 42748
NC_008705.1 WP_011558475.1 1160607 1161116 12
NC_008705.1 WP_011558476.1 1161113 1162129 -3
NC_009077.1 WP_011559727.1 2481079 2481633 8
NC_009077.1 WP_011854835.1 1163068 1164120 42559
NC_009077.1 WP_011854836.1 1164127 1164636 7
file2:
NC_008146.1 GCF_000014165.1_ASM1416v1_protein.faa
NC_008705.1 GCF_000015405.1_ASM1540v1_protein.faa
NC_009077.1 GCF_000016005.1_ASM1600v1_protein.faa
I want to match column 1 of file1 to file2 and replace itself with the respective column 2 entry of file 2.
The output would look like this:
GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7
awk
edited Apr 5 at 12:56
Rui F Ribeiro
42.2k1484143
asked Apr 5 at 12:32
BhushanDhamaleBhushanDhamale
1785
add a comment |
7
I have two tab-separated files which look as follows:
file1:
NC_008146.1 WP_011558474.1 1155234 1156286 44173
NC_008146.1 WP_011558475.1 1156298 1156807 12
NC_008146.1 WP_011558476.1 1156804 1157820 -3
NC_008705.1 WP_011558474.1 1159543 1160595 42748
NC_008705.1 WP_011558475.1 1160607 1161116 12
NC_008705.1 WP_011558476.1 1161113 1162129 -3
NC_009077.1 WP_011559727.1 2481079 2481633 8
NC_009077.1 WP_011854835.1 1163068 1164120 42559
NC_009077.1 WP_011854836.1 1164127 1164636 7
file2:
NC_008146.1 GCF_000014165.1_ASM1416v1_protein.faa
NC_008705.1 GCF_000015405.1_ASM1540v1_protein.faa
NC_009077.1 GCF_000016005.1_ASM1600v1_protein.faa
I want to match column 1 of file1 to file2 and replace itself with the respective column 2 entry of file 2.
The output would look like this:
GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7
awk
edited Apr 5 at 12:56
Rui F Ribeiro
42.2k1484143
asked Apr 5 at 12:32
BhushanDhamaleBhushanDhamale
1785
It looks like you might also be interested in our sister site: Bioinformatics.
– terdon♦
Apr 5 at 12:54
Thank you for the link @terdon!
– BhushanDhamale
Apr 5 at 12:57
add a comment |
7
7
7
I have two tab-separated files which look as follows:
file1:
NC_008146.1 WP_011558474.1 1155234 1156286 44173
NC_008146.1 WP_011558475.1 1156298 1156807 12
NC_008146.1 WP_011558476.1 1156804 1157820 -3
NC_008705.1 WP_011558474.1 1159543 1160595 42748
NC_008705.1 WP_011558475.1 1160607 1161116 12
NC_008705.1 WP_011558476.1 1161113 1162129 -3
NC_009077.1 WP_011559727.1 2481079 2481633 8
NC_009077.1 WP_011854835.1 1163068 1164120 42559
NC_009077.1 WP_011854836.1 1164127 1164636 7
file2:
NC_008146.1 GCF_000014165.1_ASM1416v1_protein.faa
NC_008705.1 GCF_000015405.1_ASM1540v1_protein.faa
NC_009077.1 GCF_000016005.1_ASM1600v1_protein.faa
I want to match column 1 of file1 to file2 and replace itself with the respective column 2 entry of file 2.
The output would look like this:
GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7
awk
edited Apr 5 at 12:56
Rui F Ribeiro
42.2k1484143
asked Apr 5 at 12:32
BhushanDhamaleBhushanDhamale
1785
I have two tab-separated files which look as follows:
file1:
NC_008146.1 WP_011558474.1 1155234 1156286 44173
NC_008146.1 WP_011558475.1 1156298 1156807 12
NC_008146.1 WP_011558476.1 1156804 1157820 -3
NC_008705.1 WP_011558474.1 1159543 1160595 42748
NC_008705.1 WP_011558475.1 1160607 1161116 12
NC_008705.1 WP_011558476.1 1161113 1162129 -3
NC_009077.1 WP_011559727.1 2481079 2481633 8
NC_009077.1 WP_011854835.1 1163068 1164120 42559
NC_009077.1 WP_011854836.1 1164127 1164636 7
file2:
NC_008146.1 GCF_000014165.1_ASM1416v1_protein.faa
NC_008705.1 GCF_000015405.1_ASM1540v1_protein.faa
NC_009077.1 GCF_000016005.1_ASM1600v1_protein.faa
I want to match column 1 of file1 to file2 and replace itself with the respective column 2 entry of file 2.
The output would look like this:
GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7
awk
awk
edited Apr 5 at 12:56
Rui F Ribeiro
42.2k1484143
asked Apr 5 at 12:32
BhushanDhamaleBhushanDhamale
1785
edited Apr 5 at 12:56
Rui F Ribeiro
42.2k1484143
asked Apr 5 at 12:32
BhushanDhamaleBhushanDhamale
1785
edited Apr 5 at 12:56
Rui F Ribeiro
42.2k1484143
edited Apr 5 at 12:56
Rui F Ribeiro
42.2k1484143
edited Apr 5 at 12:56
Rui F Ribeiro
42.2k1484143
42.2k1484143
asked Apr 5 at 12:32
BhushanDhamaleBhushanDhamale
1785
asked Apr 5 at 12:32
BhushanDhamaleBhushanDhamale
1785
asked Apr 5 at 12:32
BhushanDhamaleBhushanDhamale
1785
1785
It looks like you might also be interested in our sister site: Bioinformatics.
– terdon♦
Apr 5 at 12:54
Thank you for the link @terdon!
– BhushanDhamale
Apr 5 at 12:57
add a comment |
It looks like you might also be interested in our sister site: Bioinformatics.
– terdon♦
Apr 5 at 12:54
Thank you for the link @terdon!
– BhushanDhamale
Apr 5 at 12:57
It looks like you might also be interested in our sister site: Bioinformatics.
– terdon♦
Apr 5 at 12:54
It looks like you might also be interested in our sister site: Bioinformatics.
– terdon♦
Apr 5 at 12:54
Thank you for the link @terdon!
– BhushanDhamale
Apr 5 at 12:57
Thank you for the link @terdon!
– BhushanDhamale
Apr 5 at 12:57
add a comment |
3 Answers
3
active
oldest
votes
13
You can do this very easily with awk:
$ awk 'NR==FNRa[$1]=$2; next$1=a[$1]; print' file2 file1
GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7
Or, since that looks like a tab-separated file:
$ awk -vOFS="t" 'NR==FNRa[$1]=$2; next$1=a[$1]; print' file2 file1
GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7
This assumes that every RefSeq (NC_*) id in file1 has a corresponding entry in file2.
Explanation
NR==FNR: NR is the current line number, FNR is the line number of the current file. The two will be identical only while the 1st file (here,file2) is being read.a[$1]=$2; next: if this is the first file (see above), save the 2nd field in an array whose key is the 1st field. Then, move on to thenextline. This ensures the next block isn't executed for the 1st file.$1=a[$1]; print: now, in the second file, set the 1st field to whatever value was saved in the arrayafor the 1st field (so, the associated value fromfile2) and print the resulting line.
answered Apr 5 at 12:38
terdon♦terdon
134k33271450
1
NR == FNRdoesn't work correctly when the first file is empty. See this and the associated answer for a workaround
– iruvar
Apr 5 at 12:44
2
@iruvar nothing will work well if the first file is empty, so I don't really see why that's relevant. The entire point here is to combine the data from the two files. If either file is empty, the whole exercise is pointless.
– terdon♦
Apr 5 at 12:45
sorry I should have said in this particular casefile2and notfile1is empty. Sane behaviour whenfile2is empty is to report the contents offile1. The problem withNR == FNRis that code associated with it executes on the contents offile1whenfile2is empty
– iruvar
Apr 5 at 12:51
2
@iruvar there is no sane behavior here if either file is empty. That's what I'm saying :) So trying to make it deal with that case gracefully is pointless. And, in any case, when either file is empty here, nothing is printed. Which actually seems like the sanest approach, I'd rather get no data than wrong data.
– terdon♦
Apr 5 at 12:54
add a comment |
16
No need for awk, assuming the files are sorted, you can use coreutils join:
join -o '2.2 1.2 1.3 1.4 1.5' file1 file2
Output:
GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7
If your files aren't, sorted, you can either sort them first (sort file1 > file1.sorted; sort file2 > file2.sorted) and then use the command above, or, if your shell supports the <() construct (bash does), you can do:
join -o '2.2 1.2 1.3 1.4 1.5' <(sort file1) <(sort file2)
edited Apr 5 at 13:00
terdon♦
134k33271450
answered Apr 5 at 12:39
ThorThor
12.2k13962
add a comment |
0
Tested with below command and worked fine
for i in `awk 'print $1' f2`; do k=`awk -v i="$i" '$1==i print $2' f2`;sed "/$i/s/$i/$k/g" f1 >f3;done
output
for i in `awk 'print $1' f2`; do k=`awk -v i="$i" '$1==i print $2' f2`;sed "/$i/s/$i/$k/g" f1 >f3;done
GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7
answered Apr 7 at 13:47
Praveen Kumar BSPraveen Kumar BS
1,7691311
add a comment |
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3 Answers
3
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3 Answers
3
active
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active
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13
You can do this very easily with awk:
$ awk 'NR==FNRa[$1]=$2; next$1=a[$1]; print' file2 file1
GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7
Or, since that looks like a tab-separated file:
$ awk -vOFS="t" 'NR==FNRa[$1]=$2; next$1=a[$1]; print' file2 file1
GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7
This assumes that every RefSeq (NC_*) id in file1 has a corresponding entry in file2.
Explanation
NR==FNR: NR is the current line number, FNR is the line number of the current file. The two will be identical only while the 1st file (here,file2) is being read.a[$1]=$2; next: if this is the first file (see above), save the 2nd field in an array whose key is the 1st field. Then, move on to thenextline. This ensures the next block isn't executed for the 1st file.$1=a[$1]; print: now, in the second file, set the 1st field to whatever value was saved in the arrayafor the 1st field (so, the associated value fromfile2) and print the resulting line.
answered Apr 5 at 12:38
terdon♦terdon
134k33271450
1
NR == FNRdoesn't work correctly when the first file is empty. See this and the associated answer for a workaround
– iruvar
Apr 5 at 12:44
2
@iruvar nothing will work well if the first file is empty, so I don't really see why that's relevant. The entire point here is to combine the data from the two files. If either file is empty, the whole exercise is pointless.
– terdon♦
Apr 5 at 12:45
sorry I should have said in this particular casefile2and notfile1is empty. Sane behaviour whenfile2is empty is to report the contents offile1. The problem withNR == FNRis that code associated with it executes on the contents offile1whenfile2is empty
– iruvar
Apr 5 at 12:51
2
@iruvar there is no sane behavior here if either file is empty. That's what I'm saying :) So trying to make it deal with that case gracefully is pointless. And, in any case, when either file is empty here, nothing is printed. Which actually seems like the sanest approach, I'd rather get no data than wrong data.
– terdon♦
Apr 5 at 12:54
add a comment |
13
You can do this very easily with awk:
$ awk 'NR==FNRa[$1]=$2; next$1=a[$1]; print' file2 file1
GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7
Or, since that looks like a tab-separated file:
$ awk -vOFS="t" 'NR==FNRa[$1]=$2; next$1=a[$1]; print' file2 file1
GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7
This assumes that every RefSeq (NC_*) id in file1 has a corresponding entry in file2.
Explanation
NR==FNR: NR is the current line number, FNR is the line number of the current file. The two will be identical only while the 1st file (here,file2) is being read.a[$1]=$2; next: if this is the first file (see above), save the 2nd field in an array whose key is the 1st field. Then, move on to thenextline. This ensures the next block isn't executed for the 1st file.$1=a[$1]; print: now, in the second file, set the 1st field to whatever value was saved in the arrayafor the 1st field (so, the associated value fromfile2) and print the resulting line.
answered Apr 5 at 12:38
terdon♦terdon
134k33271450
1
NR == FNRdoesn't work correctly when the first file is empty. See this and the associated answer for a workaround
– iruvar
Apr 5 at 12:44
2
@iruvar nothing will work well if the first file is empty, so I don't really see why that's relevant. The entire point here is to combine the data from the two files. If either file is empty, the whole exercise is pointless.
– terdon♦
Apr 5 at 12:45
sorry I should have said in this particular casefile2and notfile1is empty. Sane behaviour whenfile2is empty is to report the contents offile1. The problem withNR == FNRis that code associated with it executes on the contents offile1whenfile2is empty
– iruvar
Apr 5 at 12:51
2
@iruvar there is no sane behavior here if either file is empty. That's what I'm saying :) So trying to make it deal with that case gracefully is pointless. And, in any case, when either file is empty here, nothing is printed. Which actually seems like the sanest approach, I'd rather get no data than wrong data.
– terdon♦
Apr 5 at 12:54
add a comment |
13
13
13
You can do this very easily with awk:
$ awk 'NR==FNRa[$1]=$2; next$1=a[$1]; print' file2 file1
GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7
Or, since that looks like a tab-separated file:
$ awk -vOFS="t" 'NR==FNRa[$1]=$2; next$1=a[$1]; print' file2 file1
GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7
This assumes that every RefSeq (NC_*) id in file1 has a corresponding entry in file2.
Explanation
NR==FNR: NR is the current line number, FNR is the line number of the current file. The two will be identical only while the 1st file (here,file2) is being read.a[$1]=$2; next: if this is the first file (see above), save the 2nd field in an array whose key is the 1st field. Then, move on to thenextline. This ensures the next block isn't executed for the 1st file.$1=a[$1]; print: now, in the second file, set the 1st field to whatever value was saved in the arrayafor the 1st field (so, the associated value fromfile2) and print the resulting line.
answered Apr 5 at 12:38
terdon♦terdon
134k33271450
You can do this very easily with awk:
$ awk 'NR==FNRa[$1]=$2; next$1=a[$1]; print' file2 file1
GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7
Or, since that looks like a tab-separated file:
$ awk -vOFS="t" 'NR==FNRa[$1]=$2; next$1=a[$1]; print' file2 file1
GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7
This assumes that every RefSeq (NC_*) id in file1 has a corresponding entry in file2.
Explanation
NR==FNR: NR is the current line number, FNR is the line number of the current file. The two will be identical only while the 1st file (here,file2) is being read.a[$1]=$2; next: if this is the first file (see above), save the 2nd field in an array whose key is the 1st field. Then, move on to thenextline. This ensures the next block isn't executed for the 1st file.$1=a[$1]; print: now, in the second file, set the 1st field to whatever value was saved in the arrayafor the 1st field (so, the associated value fromfile2) and print the resulting line.
answered Apr 5 at 12:38
terdon♦terdon
134k33271450
edited Apr 5 at 12:50
answered Apr 5 at 12:38
terdon♦terdon
134k33271450
answered Apr 5 at 12:38
terdon♦terdon
134k33271450
answered Apr 5 at 12:38
terdon♦terdon
134k33271450
134k33271450
1
NR == FNRdoesn't work correctly when the first file is empty. See this and the associated answer for a workaround
– iruvar
Apr 5 at 12:44
2
@iruvar nothing will work well if the first file is empty, so I don't really see why that's relevant. The entire point here is to combine the data from the two files. If either file is empty, the whole exercise is pointless.
– terdon♦
Apr 5 at 12:45
sorry I should have said in this particular casefile2and notfile1is empty. Sane behaviour whenfile2is empty is to report the contents offile1. The problem withNR == FNRis that code associated with it executes on the contents offile1whenfile2is empty
– iruvar
Apr 5 at 12:51
2
@iruvar there is no sane behavior here if either file is empty. That's what I'm saying :) So trying to make it deal with that case gracefully is pointless. And, in any case, when either file is empty here, nothing is printed. Which actually seems like the sanest approach, I'd rather get no data than wrong data.
– terdon♦
Apr 5 at 12:54
add a comment |
1
NR == FNRdoesn't work correctly when the first file is empty. See this and the associated answer for a workaround
– iruvar
Apr 5 at 12:44
2
@iruvar nothing will work well if the first file is empty, so I don't really see why that's relevant. The entire point here is to combine the data from the two files. If either file is empty, the whole exercise is pointless.
– terdon♦
Apr 5 at 12:45
sorry I should have said in this particular casefile2and notfile1is empty. Sane behaviour whenfile2is empty is to report the contents offile1. The problem withNR == FNRis that code associated with it executes on the contents offile1whenfile2is empty
– iruvar
Apr 5 at 12:51
2
@iruvar there is no sane behavior here if either file is empty. That's what I'm saying :) So trying to make it deal with that case gracefully is pointless. And, in any case, when either file is empty here, nothing is printed. Which actually seems like the sanest approach, I'd rather get no data than wrong data.
– terdon♦
Apr 5 at 12:54
1
1
NR == FNR doesn't work correctly when the first file is empty. See this and the associated answer for a workaround– iruvar
Apr 5 at 12:44
NR == FNR doesn't work correctly when the first file is empty. See this and the associated answer for a workaround– iruvar
Apr 5 at 12:44
2
2
@iruvar nothing will work well if the first file is empty, so I don't really see why that's relevant. The entire point here is to combine the data from the two files. If either file is empty, the whole exercise is pointless.
– terdon♦
Apr 5 at 12:45
@iruvar nothing will work well if the first file is empty, so I don't really see why that's relevant. The entire point here is to combine the data from the two files. If either file is empty, the whole exercise is pointless.
– terdon♦
Apr 5 at 12:45
sorry I should have said in this particular case
file2 and not file1 is empty. Sane behaviour when file2 is empty is to report the contents of file1. The problem with NR == FNR is that code associated with it executes on the contents of file1 when file2 is empty– iruvar
Apr 5 at 12:51
sorry I should have said in this particular case
file2 and not file1 is empty. Sane behaviour when file2 is empty is to report the contents of file1. The problem with NR == FNR is that code associated with it executes on the contents of file1 when file2 is empty– iruvar
Apr 5 at 12:51
2
2
@iruvar there is no sane behavior here if either file is empty. That's what I'm saying :) So trying to make it deal with that case gracefully is pointless. And, in any case, when either file is empty here, nothing is printed. Which actually seems like the sanest approach, I'd rather get no data than wrong data.
– terdon♦
Apr 5 at 12:54
@iruvar there is no sane behavior here if either file is empty. That's what I'm saying :) So trying to make it deal with that case gracefully is pointless. And, in any case, when either file is empty here, nothing is printed. Which actually seems like the sanest approach, I'd rather get no data than wrong data.
– terdon♦
Apr 5 at 12:54
add a comment |
16
No need for awk, assuming the files are sorted, you can use coreutils join:
join -o '2.2 1.2 1.3 1.4 1.5' file1 file2
Output:
GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7
If your files aren't, sorted, you can either sort them first (sort file1 > file1.sorted; sort file2 > file2.sorted) and then use the command above, or, if your shell supports the <() construct (bash does), you can do:
join -o '2.2 1.2 1.3 1.4 1.5' <(sort file1) <(sort file2)
edited Apr 5 at 13:00
terdon♦
134k33271450
answered Apr 5 at 12:39
ThorThor
12.2k13962
add a comment |
16
No need for awk, assuming the files are sorted, you can use coreutils join:
join -o '2.2 1.2 1.3 1.4 1.5' file1 file2
Output:
GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7
If your files aren't, sorted, you can either sort them first (sort file1 > file1.sorted; sort file2 > file2.sorted) and then use the command above, or, if your shell supports the <() construct (bash does), you can do:
join -o '2.2 1.2 1.3 1.4 1.5' <(sort file1) <(sort file2)
edited Apr 5 at 13:00
terdon♦
134k33271450
answered Apr 5 at 12:39
ThorThor
12.2k13962
add a comment |
16
16
16
No need for awk, assuming the files are sorted, you can use coreutils join:
join -o '2.2 1.2 1.3 1.4 1.5' file1 file2
Output:
GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7
If your files aren't, sorted, you can either sort them first (sort file1 > file1.sorted; sort file2 > file2.sorted) and then use the command above, or, if your shell supports the <() construct (bash does), you can do:
join -o '2.2 1.2 1.3 1.4 1.5' <(sort file1) <(sort file2)
edited Apr 5 at 13:00
terdon♦
134k33271450
answered Apr 5 at 12:39
ThorThor
12.2k13962
No need for awk, assuming the files are sorted, you can use coreutils join:
join -o '2.2 1.2 1.3 1.4 1.5' file1 file2
Output:
GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7
If your files aren't, sorted, you can either sort them first (sort file1 > file1.sorted; sort file2 > file2.sorted) and then use the command above, or, if your shell supports the <() construct (bash does), you can do:
join -o '2.2 1.2 1.3 1.4 1.5' <(sort file1) <(sort file2)
edited Apr 5 at 13:00
terdon♦
134k33271450
answered Apr 5 at 12:39
ThorThor
12.2k13962
edited Apr 5 at 13:00
terdon♦
134k33271450
edited Apr 5 at 13:00
terdon♦
134k33271450
edited Apr 5 at 13:00
terdon♦
134k33271450
134k33271450
answered Apr 5 at 12:39
ThorThor
12.2k13962
answered Apr 5 at 12:39
ThorThor
12.2k13962
answered Apr 5 at 12:39
ThorThor
12.2k13962
12.2k13962
add a comment |
add a comment |
0
Tested with below command and worked fine
for i in `awk 'print $1' f2`; do k=`awk -v i="$i" '$1==i print $2' f2`;sed "/$i/s/$i/$k/g" f1 >f3;done
output
for i in `awk 'print $1' f2`; do k=`awk -v i="$i" '$1==i print $2' f2`;sed "/$i/s/$i/$k/g" f1 >f3;done
GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7
answered Apr 7 at 13:47
Praveen Kumar BSPraveen Kumar BS
1,7691311
add a comment |
0
Tested with below command and worked fine
for i in `awk 'print $1' f2`; do k=`awk -v i="$i" '$1==i print $2' f2`;sed "/$i/s/$i/$k/g" f1 >f3;done
output
for i in `awk 'print $1' f2`; do k=`awk -v i="$i" '$1==i print $2' f2`;sed "/$i/s/$i/$k/g" f1 >f3;done
GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7
answered Apr 7 at 13:47
Praveen Kumar BSPraveen Kumar BS
1,7691311
add a comment |
0
0
0
Tested with below command and worked fine
for i in `awk 'print $1' f2`; do k=`awk -v i="$i" '$1==i print $2' f2`;sed "/$i/s/$i/$k/g" f1 >f3;done
output
for i in `awk 'print $1' f2`; do k=`awk -v i="$i" '$1==i print $2' f2`;sed "/$i/s/$i/$k/g" f1 >f3;done
GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7
answered Apr 7 at 13:47
Praveen Kumar BSPraveen Kumar BS
1,7691311
Tested with below command and worked fine
for i in `awk 'print $1' f2`; do k=`awk -v i="$i" '$1==i print $2' f2`;sed "/$i/s/$i/$k/g" f1 >f3;done
output
for i in `awk 'print $1' f2`; do k=`awk -v i="$i" '$1==i print $2' f2`;sed "/$i/s/$i/$k/g" f1 >f3;done
GCF_000014165.1_ASM1416v1_protein.faa WP_011558474.1 1155234 1156286 44173
GCF_000014165.1_ASM1416v1_protein.faa WP_011558475.1 1156298 1156807 12
GCF_000014165.1_ASM1416v1_protein.faa WP_011558476.1 1156804 1157820 -3
GCF_000015405.1_ASM1540v1_protein.faa WP_011558474.1 1159543 1160595 42748
GCF_000015405.1_ASM1540v1_protein.faa WP_011558475.1 1160607 1161116 12
GCF_000015405.1_ASM1540v1_protein.faa WP_011558476.1 1161113 1162129 -3
GCF_000016005.1_ASM1600v1_protein.faa WP_011559727.1 2481079 2481633 8
GCF_000016005.1_ASM1600v1_protein.faa WP_011854835.1 1163068 1164120 42559
GCF_000016005.1_ASM1600v1_protein.faa WP_011854836.1 1164127 1164636 7
answered Apr 7 at 13:47
Praveen Kumar BSPraveen Kumar BS
1,7691311
answered Apr 7 at 13:47
Praveen Kumar BSPraveen Kumar BS
1,7691311
answered Apr 7 at 13:47
Praveen Kumar BSPraveen Kumar BS
1,7691311
answered Apr 7 at 13:47
Praveen Kumar BSPraveen Kumar BS
1,7691311
1,7691311
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It looks like you might also be interested in our sister site: Bioinformatics.
– terdon♦
Apr 5 at 12:54
Thank you for the link @terdon!
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