Find string in one file and use it in another file

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In file 1 I need to find lines that contain string hdu in column 2 (or HX* in column 5), and then in file 2 replace the value in the column 2 with value of column 5 from file 1.



file1:



64 ha 1 LIG H64 64 0.000000 12.0100 c 0.637086 12.0100
65 du 1 LIG XX65 65 0.000000 16.0000 o -0.547014 16.0000
66 du 1 LIG XX66 66 0.000000 16.0000 oh -0.611114 16.0000
67 hdu 1 LIG HX67 67 0.000000 1.0080 hc 0.090186 1.0080
68 hdu 1 LIG HX68 68 0.000000 1.0080 hc 0.090186 1.0080


file2:



1LIG H64 64 2.06144000 1.94117000 2.65125000
1LIG XX65 65 2.14737000 1.92392000 2.73722000
1LIG XX66 66 1.98154000 2.05095000 2.64407000
1LIG XX67 67 2.21440000 1.72650000 2.55862000
1LIG XX68 68 2.22046000 1.85502000 2.43909000


In the given case, I need to replace XX67 with HX67, and XX68 with HX68, so that the output is:



1LIG H64 64 2.06144000 1.94117000 2.65125000
1LIG XX65 65 2.14737000 1.92392000 2.73722000
1LIG XX66 66 1.98154000 2.05095000 2.64407000
1LIG HX67 67 2.21440000 1.72650000 2.55862000
1LIG HX68 68 2.22046000 1.85502000 2.43909000


My best guess was command



awk 'FNR==NR && $2=="hdu" x=$1;y=$5 NR!=FNR if ($3==x) $2=y print' file1 file2



but it replaced only last occurrence.






awk







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  • Are the two files the same length?
    – DopeGhoti
    6 mins ago














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In file 1 I need to find lines that contain string hdu in column 2 (or HX* in column 5), and then in file 2 replace the value in the column 2 with value of column 5 from file 1.



file1:



64 ha 1 LIG H64 64 0.000000 12.0100 c 0.637086 12.0100
65 du 1 LIG XX65 65 0.000000 16.0000 o -0.547014 16.0000
66 du 1 LIG XX66 66 0.000000 16.0000 oh -0.611114 16.0000
67 hdu 1 LIG HX67 67 0.000000 1.0080 hc 0.090186 1.0080
68 hdu 1 LIG HX68 68 0.000000 1.0080 hc 0.090186 1.0080


file2:



1LIG H64 64 2.06144000 1.94117000 2.65125000
1LIG XX65 65 2.14737000 1.92392000 2.73722000
1LIG XX66 66 1.98154000 2.05095000 2.64407000
1LIG XX67 67 2.21440000 1.72650000 2.55862000
1LIG XX68 68 2.22046000 1.85502000 2.43909000


In the given case, I need to replace XX67 with HX67, and XX68 with HX68, so that the output is:



1LIG H64 64 2.06144000 1.94117000 2.65125000
1LIG XX65 65 2.14737000 1.92392000 2.73722000
1LIG XX66 66 1.98154000 2.05095000 2.64407000
1LIG HX67 67 2.21440000 1.72650000 2.55862000
1LIG HX68 68 2.22046000 1.85502000 2.43909000


My best guess was command



awk 'FNR==NR && $2=="hdu" x=$1;y=$5 NR!=FNR if ($3==x) $2=y print' file1 file2



but it replaced only last occurrence.






awk







share|improve this question









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user318543 is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.



















  • Are the two files the same length?
    – DopeGhoti
    6 mins ago












up vote
0
down vote

favorite









up vote
0
down vote

favorite











In file 1 I need to find lines that contain string hdu in column 2 (or HX* in column 5), and then in file 2 replace the value in the column 2 with value of column 5 from file 1.



file1:



64 ha 1 LIG H64 64 0.000000 12.0100 c 0.637086 12.0100
65 du 1 LIG XX65 65 0.000000 16.0000 o -0.547014 16.0000
66 du 1 LIG XX66 66 0.000000 16.0000 oh -0.611114 16.0000
67 hdu 1 LIG HX67 67 0.000000 1.0080 hc 0.090186 1.0080
68 hdu 1 LIG HX68 68 0.000000 1.0080 hc 0.090186 1.0080


file2:



1LIG H64 64 2.06144000 1.94117000 2.65125000
1LIG XX65 65 2.14737000 1.92392000 2.73722000
1LIG XX66 66 1.98154000 2.05095000 2.64407000
1LIG XX67 67 2.21440000 1.72650000 2.55862000
1LIG XX68 68 2.22046000 1.85502000 2.43909000


In the given case, I need to replace XX67 with HX67, and XX68 with HX68, so that the output is:



1LIG H64 64 2.06144000 1.94117000 2.65125000
1LIG XX65 65 2.14737000 1.92392000 2.73722000
1LIG XX66 66 1.98154000 2.05095000 2.64407000
1LIG HX67 67 2.21440000 1.72650000 2.55862000
1LIG HX68 68 2.22046000 1.85502000 2.43909000


My best guess was command



awk 'FNR==NR && $2=="hdu" x=$1;y=$5 NR!=FNR if ($3==x) $2=y print' file1 file2



but it replaced only last occurrence.






awk







share|improve this question









New contributor




user318543 is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.











In file 1 I need to find lines that contain string hdu in column 2 (or HX* in column 5), and then in file 2 replace the value in the column 2 with value of column 5 from file 1.



file1:



64 ha 1 LIG H64 64 0.000000 12.0100 c 0.637086 12.0100
65 du 1 LIG XX65 65 0.000000 16.0000 o -0.547014 16.0000
66 du 1 LIG XX66 66 0.000000 16.0000 oh -0.611114 16.0000
67 hdu 1 LIG HX67 67 0.000000 1.0080 hc 0.090186 1.0080
68 hdu 1 LIG HX68 68 0.000000 1.0080 hc 0.090186 1.0080


file2:



1LIG H64 64 2.06144000 1.94117000 2.65125000
1LIG XX65 65 2.14737000 1.92392000 2.73722000
1LIG XX66 66 1.98154000 2.05095000 2.64407000
1LIG XX67 67 2.21440000 1.72650000 2.55862000
1LIG XX68 68 2.22046000 1.85502000 2.43909000


In the given case, I need to replace XX67 with HX67, and XX68 with HX68, so that the output is:



1LIG H64 64 2.06144000 1.94117000 2.65125000
1LIG XX65 65 2.14737000 1.92392000 2.73722000
1LIG XX66 66 1.98154000 2.05095000 2.64407000
1LIG HX67 67 2.21440000 1.72650000 2.55862000
1LIG HX68 68 2.22046000 1.85502000 2.43909000


My best guess was command



awk 'FNR==NR && $2=="hdu" x=$1;y=$5 NR!=FNR if ($3==x) $2=y print' file1 file2



but it replaced only last occurrence.






awk




awk






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user318543 is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.











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Check out our Code of Conduct.









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edited 21 mins ago





















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user318543 is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.






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Check out our Code of Conduct.











  • Are the two files the same length?
    – DopeGhoti
    6 mins ago
















  • Are the two files the same length?
    – DopeGhoti
    6 mins ago















Are the two files the same length?
– DopeGhoti
6 mins ago




Are the two files the same length?
– DopeGhoti
6 mins ago















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