Mixing
Replace column between patterns in one file from another file
I am trying to write shell script which reads file1, get a specific column from this file. And replace column in file2 with the column extracted from file1 between two patterns .
File1
Line1
Line2
.
LineN
ATOM C1 C2 C3
ATOM P23 HI IKJ
ATOM S23 JSK SN
BOND
Many lines
END
File2
Few Lines
Pattern1
1 C -9.2429 -1.3783 -9.5091 C.3 1 LIG1 0.0555
2 C -10.5865 -0.8658 -8.9679 C.3 1 LIG1 0.0529
3 N -11.3072 -0.5779 -10.1774 N.am 1 LIG1 -0.2940
Patttern2
Lines
I want to get the column $2 from file 1 and replace it the the column $2 in file2 between pattern1 and pattern 2.
Output
Few Lines
Pattern1
1 C1 -9.2429 -1.3783 -9.5091 C.3 1 LIG1 0.0555
2 P23 -10.5865 -0.8658 -8.9679 C.3 1 LIG1 0.0529
3 S23 -11.3072 -0.5779 -10.1774 N.am 1 LIG1 -0.2940
Patttern2
Lines
I have tried few things so far.
awk '($1=="ATOM") {print $2}' file1
awk '/pattern1/{flag=1; next} /pattern2/{flag=0} flag' file2
I can store the column 2 in file1. Also, lines between both the patterns from file2.
I am sure with something like FNR=NR, I should be able to handle both files at the same time. Any help would be great to proceed further.
awk
asked Nov 21 '18 at 19:21
dipak sanapdipak sanap
11
add a comment |
I am trying to write shell script which reads file1, get a specific column from this file. And replace column in file2 with the column extracted from file1 between two patterns .
File1
Line1
Line2
.
LineN
ATOM C1 C2 C3
ATOM P23 HI IKJ
ATOM S23 JSK SN
BOND
Many lines
END
File2
Few Lines
Pattern1
1 C -9.2429 -1.3783 -9.5091 C.3 1 LIG1 0.0555
2 C -10.5865 -0.8658 -8.9679 C.3 1 LIG1 0.0529
3 N -11.3072 -0.5779 -10.1774 N.am 1 LIG1 -0.2940
Patttern2
Lines
I want to get the column $2 from file 1 and replace it the the column $2 in file2 between pattern1 and pattern 2.
Output
Few Lines
Pattern1
1 C1 -9.2429 -1.3783 -9.5091 C.3 1 LIG1 0.0555
2 P23 -10.5865 -0.8658 -8.9679 C.3 1 LIG1 0.0529
3 S23 -11.3072 -0.5779 -10.1774 N.am 1 LIG1 -0.2940
Patttern2
Lines
I have tried few things so far.
awk '($1=="ATOM") {print $2}' file1
awk '/pattern1/{flag=1; next} /pattern2/{flag=0} flag' file2
I can store the column 2 in file1. Also, lines between both the patterns from file2.
I am sure with something like FNR=NR, I should be able to handle both files at the same time. Any help would be great to proceed further.
awk
asked Nov 21 '18 at 19:21
dipak sanapdipak sanap
11
This thread looks like stackoverflow.com/questions/53417240/… so please close another one then if both are same.
– RavinderSingh13
Nov 21 '18 at 19:26
add a comment |
I am trying to write shell script which reads file1, get a specific column from this file. And replace column in file2 with the column extracted from file1 between two patterns .
File1
Line1
Line2
.
LineN
ATOM C1 C2 C3
ATOM P23 HI IKJ
ATOM S23 JSK SN
BOND
Many lines
END
File2
Few Lines
Pattern1
1 C -9.2429 -1.3783 -9.5091 C.3 1 LIG1 0.0555
2 C -10.5865 -0.8658 -8.9679 C.3 1 LIG1 0.0529
3 N -11.3072 -0.5779 -10.1774 N.am 1 LIG1 -0.2940
Patttern2
Lines
I want to get the column $2 from file 1 and replace it the the column $2 in file2 between pattern1 and pattern 2.
Output
Few Lines
Pattern1
1 C1 -9.2429 -1.3783 -9.5091 C.3 1 LIG1 0.0555
2 P23 -10.5865 -0.8658 -8.9679 C.3 1 LIG1 0.0529
3 S23 -11.3072 -0.5779 -10.1774 N.am 1 LIG1 -0.2940
Patttern2
Lines
I have tried few things so far.
awk '($1=="ATOM") {print $2}' file1
awk '/pattern1/{flag=1; next} /pattern2/{flag=0} flag' file2
I can store the column 2 in file1. Also, lines between both the patterns from file2.
I am sure with something like FNR=NR, I should be able to handle both files at the same time. Any help would be great to proceed further.
awk
asked Nov 21 '18 at 19:21
dipak sanapdipak sanap
11
I am trying to write shell script which reads file1, get a specific column from this file. And replace column in file2 with the column extracted from file1 between two patterns .
File1
Line1
Line2
.
LineN
ATOM C1 C2 C3
ATOM P23 HI IKJ
ATOM S23 JSK SN
BOND
Many lines
END
File2
Few Lines
Pattern1
1 C -9.2429 -1.3783 -9.5091 C.3 1 LIG1 0.0555
2 C -10.5865 -0.8658 -8.9679 C.3 1 LIG1 0.0529
3 N -11.3072 -0.5779 -10.1774 N.am 1 LIG1 -0.2940
Patttern2
Lines
I want to get the column $2 from file 1 and replace it the the column $2 in file2 between pattern1 and pattern 2.
Output
Few Lines
Pattern1
1 C1 -9.2429 -1.3783 -9.5091 C.3 1 LIG1 0.0555
2 P23 -10.5865 -0.8658 -8.9679 C.3 1 LIG1 0.0529
3 S23 -11.3072 -0.5779 -10.1774 N.am 1 LIG1 -0.2940
Patttern2
Lines
I have tried few things so far.
awk '($1=="ATOM") {print $2}' file1
awk '/pattern1/{flag=1; next} /pattern2/{flag=0} flag' file2
I can store the column 2 in file1. Also, lines between both the patterns from file2.
I am sure with something like FNR=NR, I should be able to handle both files at the same time. Any help would be great to proceed further.
awk
awk
asked Nov 21 '18 at 19:21
dipak sanapdipak sanap
11
asked Nov 21 '18 at 19:21
dipak sanapdipak sanap
11
asked Nov 21 '18 at 19:21
dipak sanapdipak sanap
11
asked Nov 21 '18 at 19:21
dipak sanapdipak sanap
11
asked Nov 21 '18 at 19:21
dipak sanapdipak sanap
11
11
This thread looks like stackoverflow.com/questions/53417240/… so please close another one then if both are same.
– RavinderSingh13
Nov 21 '18 at 19:26
add a comment |
This thread looks like stackoverflow.com/questions/53417240/… so please close another one then if both are same.
– RavinderSingh13
Nov 21 '18 at 19:26
This thread looks like stackoverflow.com/questions/53417240/… so please close another one then if both are same.
– RavinderSingh13
Nov 21 '18 at 19:26
This thread looks like stackoverflow.com/questions/53417240/… so please close another one then if both are same.
– RavinderSingh13
Nov 21 '18 at 19:26
add a comment |
1 Answer
1
active
oldest
votes
Per Your question and as You mentioning (FNR==NR) solution You can use this AWK:
awk '
( FNR==NR && /^ATOM / ) { atoms[++atomn]=$2; }
( FNR!=NR && /^Patttern2$/ ) { doreplace=0; }
doreplace { $2=atoms[++atomn]; }
( FNR!=NR && /^Pattern1$/ ) { doreplace=1; atomn=0; }
FNR!=NR
' file1 file2
I rather prefer this way when dealing with metafile and datafiles:
awk '
BEGIN {
if ( ARGC != 3 ) exit(1);
while ( getline < ARGV[2] ) if ( $0 ~ /^ATOM / ) atoms[++atomn]=$2;
ARGC=2;
}
/^Patttern2$/ { doreplace=0; }
doreplace { $2=atoms[++atomn]; }
/^Pattern1$/ { doreplace=1; atomn=0; }
1
' file2 file1
Both will work on your provided inputs. Here Output:
Few Lines
Pattern1
1 C1 -9.2429 -1.3783 -9.5091 C.3 1 LIG1 0.0555
2 P23 -10.5865 -0.8658 -8.9679 C.3 1 LIG1 0.0529
3 S23 -11.3072 -0.5779 -10.1774 N.am 1 LIG1 -0.2940
Patttern2
Lines
Both assumes that in metafile (file1) and datafile (file2) you have exactly same number of ATOM and lines between patterns. If You are not able to validate this I would add logic to watch this not to iterate through in-allocated array elements. However in AWK nothing will happen just replacement will be done with empty string instead.
answered Nov 22 '18 at 9:44
KubatorKubator
74911
add a comment |
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1 Answer
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1 Answer
1
active
oldest
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active
oldest
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active
oldest
votes
Per Your question and as You mentioning (FNR==NR) solution You can use this AWK:
awk '
( FNR==NR && /^ATOM / ) { atoms[++atomn]=$2; }
( FNR!=NR && /^Patttern2$/ ) { doreplace=0; }
doreplace { $2=atoms[++atomn]; }
( FNR!=NR && /^Pattern1$/ ) { doreplace=1; atomn=0; }
FNR!=NR
' file1 file2
I rather prefer this way when dealing with metafile and datafiles:
awk '
BEGIN {
if ( ARGC != 3 ) exit(1);
while ( getline < ARGV[2] ) if ( $0 ~ /^ATOM / ) atoms[++atomn]=$2;
ARGC=2;
}
/^Patttern2$/ { doreplace=0; }
doreplace { $2=atoms[++atomn]; }
/^Pattern1$/ { doreplace=1; atomn=0; }
1
' file2 file1
Both will work on your provided inputs. Here Output:
Few Lines
Pattern1
1 C1 -9.2429 -1.3783 -9.5091 C.3 1 LIG1 0.0555
2 P23 -10.5865 -0.8658 -8.9679 C.3 1 LIG1 0.0529
3 S23 -11.3072 -0.5779 -10.1774 N.am 1 LIG1 -0.2940
Patttern2
Lines
Both assumes that in metafile (file1) and datafile (file2) you have exactly same number of ATOM and lines between patterns. If You are not able to validate this I would add logic to watch this not to iterate through in-allocated array elements. However in AWK nothing will happen just replacement will be done with empty string instead.
answered Nov 22 '18 at 9:44
KubatorKubator
74911
add a comment |
Per Your question and as You mentioning (FNR==NR) solution You can use this AWK:
awk '
( FNR==NR && /^ATOM / ) { atoms[++atomn]=$2; }
( FNR!=NR && /^Patttern2$/ ) { doreplace=0; }
doreplace { $2=atoms[++atomn]; }
( FNR!=NR && /^Pattern1$/ ) { doreplace=1; atomn=0; }
FNR!=NR
' file1 file2
I rather prefer this way when dealing with metafile and datafiles:
awk '
BEGIN {
if ( ARGC != 3 ) exit(1);
while ( getline < ARGV[2] ) if ( $0 ~ /^ATOM / ) atoms[++atomn]=$2;
ARGC=2;
}
/^Patttern2$/ { doreplace=0; }
doreplace { $2=atoms[++atomn]; }
/^Pattern1$/ { doreplace=1; atomn=0; }
1
' file2 file1
Both will work on your provided inputs. Here Output:
Few Lines
Pattern1
1 C1 -9.2429 -1.3783 -9.5091 C.3 1 LIG1 0.0555
2 P23 -10.5865 -0.8658 -8.9679 C.3 1 LIG1 0.0529
3 S23 -11.3072 -0.5779 -10.1774 N.am 1 LIG1 -0.2940
Patttern2
Lines
Both assumes that in metafile (file1) and datafile (file2) you have exactly same number of ATOM and lines between patterns. If You are not able to validate this I would add logic to watch this not to iterate through in-allocated array elements. However in AWK nothing will happen just replacement will be done with empty string instead.
answered Nov 22 '18 at 9:44
KubatorKubator
74911
add a comment |
Per Your question and as You mentioning (FNR==NR) solution You can use this AWK:
awk '
( FNR==NR && /^ATOM / ) { atoms[++atomn]=$2; }
( FNR!=NR && /^Patttern2$/ ) { doreplace=0; }
doreplace { $2=atoms[++atomn]; }
( FNR!=NR && /^Pattern1$/ ) { doreplace=1; atomn=0; }
FNR!=NR
' file1 file2
I rather prefer this way when dealing with metafile and datafiles:
awk '
BEGIN {
if ( ARGC != 3 ) exit(1);
while ( getline < ARGV[2] ) if ( $0 ~ /^ATOM / ) atoms[++atomn]=$2;
ARGC=2;
}
/^Patttern2$/ { doreplace=0; }
doreplace { $2=atoms[++atomn]; }
/^Pattern1$/ { doreplace=1; atomn=0; }
1
' file2 file1
Both will work on your provided inputs. Here Output:
Few Lines
Pattern1
1 C1 -9.2429 -1.3783 -9.5091 C.3 1 LIG1 0.0555
2 P23 -10.5865 -0.8658 -8.9679 C.3 1 LIG1 0.0529
3 S23 -11.3072 -0.5779 -10.1774 N.am 1 LIG1 -0.2940
Patttern2
Lines
Both assumes that in metafile (file1) and datafile (file2) you have exactly same number of ATOM and lines between patterns. If You are not able to validate this I would add logic to watch this not to iterate through in-allocated array elements. However in AWK nothing will happen just replacement will be done with empty string instead.
answered Nov 22 '18 at 9:44
KubatorKubator
74911
Per Your question and as You mentioning (FNR==NR) solution You can use this AWK:
awk '
( FNR==NR && /^ATOM / ) { atoms[++atomn]=$2; }
( FNR!=NR && /^Patttern2$/ ) { doreplace=0; }
doreplace { $2=atoms[++atomn]; }
( FNR!=NR && /^Pattern1$/ ) { doreplace=1; atomn=0; }
FNR!=NR
' file1 file2
I rather prefer this way when dealing with metafile and datafiles:
awk '
BEGIN {
if ( ARGC != 3 ) exit(1);
while ( getline < ARGV[2] ) if ( $0 ~ /^ATOM / ) atoms[++atomn]=$2;
ARGC=2;
}
/^Patttern2$/ { doreplace=0; }
doreplace { $2=atoms[++atomn]; }
/^Pattern1$/ { doreplace=1; atomn=0; }
1
' file2 file1
Both will work on your provided inputs. Here Output:
Few Lines
Pattern1
1 C1 -9.2429 -1.3783 -9.5091 C.3 1 LIG1 0.0555
2 P23 -10.5865 -0.8658 -8.9679 C.3 1 LIG1 0.0529
3 S23 -11.3072 -0.5779 -10.1774 N.am 1 LIG1 -0.2940
Patttern2
Lines
Both assumes that in metafile (file1) and datafile (file2) you have exactly same number of ATOM and lines between patterns. If You are not able to validate this I would add logic to watch this not to iterate through in-allocated array elements. However in AWK nothing will happen just replacement will be done with empty string instead.
answered Nov 22 '18 at 9:44
KubatorKubator
74911
answered Nov 22 '18 at 9:44
KubatorKubator
74911
answered Nov 22 '18 at 9:44
KubatorKubator
74911
answered Nov 22 '18 at 9:44
KubatorKubator
74911
74911
add a comment |
add a comment |
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This thread looks like stackoverflow.com/questions/53417240/… so please close another one then if both are same.
– RavinderSingh13
Nov 21 '18 at 19:26