awk | update field number after comparing field from other file - awk

Input File1: file1.txt
MH=919767,918975
DL=919922
HR=919891,919394,919812
KR=919999,918888
Input File2: file2.txt
aec,919922783456,a5,b3,,,asf
abc,918975583456,a1,b1,,,abf
aeci,919998546783,a2,b4,,,wsf
Output File
aec,919922783456,a5,b3,DL,,asf
abc,918975583456,a1,b1,MH,,abf
aeci,919998546783,a2,b4,NOMATCH,,wsf
Notes
Need to compare phone number (Input file2.txt - 2nd field - initial 6 digit only) within Input file1.txt - 2nd field with "=" separted). If there is match in intial 6 digit of phone number, then OUTPUT should contain 2 digit code from file (Input file1) into output in 5th field
File1.txt is having single code (for example MH) for mupltiple phone number intials.

If you have GNU awk, try the following. Run like:
awk -f script.awk file1.txt file2.txt
Contents of script.awk:
BEGIN {
FS="[=,]"
OFS=","
}
FNR==NR {
for(i=2;i<=NF;i++) {
a[$1][$i]
}
next
}
{
$5 = "NOMATCH"
for(j in a) {
for (k in a[j]) {
if (substr($2,0,6) == k) {
$5 = j
}
}
}
}1
Alternatively, here's the one-liner:
awk -F "[=,]" 'FNR==NR { for(i=2;i<=NF;i++) a[$1][$i]; next } { $5 = "NOMATCH"; for(j in a) for (k in a[j]) if (substr($2,0,6) == k) $5 = j }1' OFS=, file1.txt file2.txt
Results:
aec,919922783456,a5,b3,DL,,asf
abc,918975583456,a1,b1,MH,,abf
aeci,919998546783,a2,b4,NOMATCH,,wsf
If you have an 'old' awk, try the following. Run like:
awk -f script.awk file1.txt file2.txt
Contents of script.awk:
BEGIN {
# set the field separator to either an equals sign or a comma
FS="[=,]"
# set the output field separator to a comma
OFS=","
}
# for the first file in the arguments list
FNR==NR {
# loop through all the fields, starting at field two
for(i=2;i<=NF;i++) {
# add field one and each field to a pseudo-multidimensional array
a[$1,$i]
}
# skip processing the rest of the code
next
}
# for the second file in the arguments list
{
# set the default value for field 5
$5 = "NOMATCH"
# loop though the array
for(j in a) {
# split the array keys into another array
split(j,b,SUBSEP)
# if the first six digits of field two equal the value stored in this array
if (substr($2,0,6) == b[2]) {
# assign field five
$5 = b[1]
}
}
# return true, therefore print by default
}1
Alternatively, here's the one-liner:
awk -F "[=,]" 'FNR==NR { for(i=2;i<=NF;i++) a[$1,$i]; next } { $5 = "NOMATCH"; for(j in a) { split(j,b,SUBSEP); if (substr($2,0,6) == b[2]) $5 = b[1] } }1' OFS=, file1.txt file2.txt
Results:
aec,919922783456,a5,b3,DL,,asf
abc,918975583456,a1,b1,MH,,abf
aeci,919998546783,a2,b4,NOMATCH,,wsf

Try something like:
awk '
NR==FNR{
for(i=2; i<=NF; i++) A[$i]=$1
next
}
{
$5="NOMATCH"
for(i in A) if ($2~"^" i) $5=A[i]
}
1
' FS='[=,]' file1 FS=, OFS=, file2

Related

Compare multiple columns from one file with multiple columns of another file using awk?

I want to compare first 2 characters of col1 of file1 with col1 of file2 if col3 of file1 is same as col3 of file2 , provided col4 in file2 equals to TRUE. I tried something :-
awk -F'|' 'BEGIN{OFS=FS};(NR==FNR)
{a[substr($1,1,2),$3]=$1;next}(($1,$3)in a) && $4==TRUE ' file1 file2 > outfield
file 1
AE1267453617238|BIDKFXXXX|United Arab Emirates|
PL76UTYVJDYGHU9|ABSFXXJBW|Poland|
GB76UTRTSCLSKJ|FVDGXXXUY|Russia|
file 2
AE|^AE[0-9]{2}[0-9]{24}|United Arab Emirates|TRUE|
PL|^PL[0-9]{2}[A-Z]{10}[0-9]{4}|Poland|FALSE|
GB|^GB[0-9]{2}[A-Z]{5}[0-9]{3}|Europe|TRUE
expected output :-
AE1267453617238|BIDKFXXXX|United Arab Emirates|
You could just simply cascade the multiple conditions with a && as below. Remember your expected output is on the first file, so you need to process the second file first
awk -F'|' ' FNR == NR {
if ( $4 == "TRUE" ) m[$1] = $3 ; next }{ k = substr($1,1,2) } k in m && m[k] == $3' file2 file1
The part m[$1] = $3 creates a hash-map of the $1 with the value of $3 in the second file, which is then used in the first file to compare against only the first two characters of $1 i.e. substr($1,1,2). To avoid redundant use of substr(..), the value is extracted into a variable k and reused subsequently.
If the matches must be on the same line number in each file:
awk -F \| '
FNR==NR && $4 == "TRUE" {a[NR,1]=$1; a[NR,3]=$3}
FNR!=NR && $3 == a[FNR,3] &&
$1 ~ "^"a[FNR,1]' file2 file1
If the matches can be on any line (every line of file1 is checked against every line of file2, duplicate matches aren't printed):
awk -F \| '
FNR==NR {++l}
FNR==NR && $4 == "TRUE" {a[NR,1]=$1; a[NR,3]=$3}
FNR!=NR {
for (i=1; i<=l; ++i) {
if ($3 == a[i,3] && $1 ~ "^"a[i,1])
c[$0]==0
}
}
END {
for (i in c)
print i
}' file2 file1
Note the order files are given. file2 (which contains TRUE and FALSE), goes first. I also used regex instead of substr, so the characters should be alphanumeric only, if not, go back to substr.
Regarding your code:
awk -F'|' 'BEGIN{OFS=FS};(NR==FNR)
{a[substr($1,1,2),$3]=$1;next}(($1,$3)in a) && $4==TRUE ' file1 file2 > outfield
newlines matter to awk. This:
NR==FNR
{ print }
is not the same as this:
NR==FNR { print }
The first one is actually the same as:
NR==FNR { print }
1 { print }
Also when you want to output the contents of a file (file1 in your case) it's usually better to read the OTHER file into memory and then compare the values from the target file against that so you can just print it as you go. So you should be doing awk 'script' file2 file1, not awk 'script' file1 file2, and writing a script based on that.
Try this:
$ cat tst.awk
BEGIN { FS="|" }
NR==FNR {
if ( $4 == "TRUE" ) {
map[$1] = $3
}
next
}
{ key = substr($1,1,2) }
(key in map) && (map[key] == $3)
$ awk -f tst.awk file2 file1
AE1267453617238|BIDKFXXXX|United Arab Emirates|
awk -F\| '
NR==FNR{
a[$3,1]=$1;
a[$3,4]=$4;
next
}
substr($1,1,2) == a[$3,1] && a[$3,4] == "TRUE" { print }
' file2.txt file1.txt
AE1267453617238|BIDKFXXXX|United Arab Emirates|

Print columns from two files

How to print columns from various files?
I tried according to Awk: extract different columns from many different files
paste <(awk '{printf "%.4f %.5f ", $1, $2}' FILE.R ) <(awk '{printf "%.6f %.0f.\n", $3, $4}' FILE_R )
FILE.R == ARGV[1] { one[FNR]=$1 }
FILE.R == ARGV[2] { two[FNR]=$2 }
FILE_R == ARGV[3] { three[FNR]=$3 }
FILE_R == ARGV[4] { four[FNR]=$4 }
END {
for (i=1; i<=length(one); i++) {
print one[i], two[i], three[i], four[i]
}
}
but I don't understand how to use this script.
FILE.R
56604.6017 2.3893 2.2926 2.2033
56605.1562 2.3138 2.2172 2.2033
FILE_R
56604.6017 2.29259 0.006699 42.
56605.1562 2.21716 0.007504 40.
Output desired
56604.6017 2.3893 0.006699 42.
56605.1562 2.3138 0.007504 40.
Thank you
This is one way:
$ awk -v OFS="\t" 'NR==FNR{a[$1]=$2;next}{print $1,a[$1],$3,$4}' file1 file2
Output:
56604.6017 2.3893 0.006699 42.
56605.1562 2.3138 0.007504 40.
Explained:
$ awk -v OFS="\t" ' # setting the field separator to a tab
NR==FNR { # process the first file
a[$1]=$2 # hash the second field, use first as key
next
}
{
print $1,a[$1],$3,$4 # output
}' file1 file2
If the field spacing with tabs is not enough, use printf with modifiers like in your sample.

awk totally separate duplicate and non-duplicates

If we have an input:
TargetIDs,CPD,Value,SMILES
95,CPD-1111111,-2,c1ccccc1
95,CPD-2222222,-3,c1ccccc1
95,CPD-2222222,-4,c1ccccc1
95,CPD-3333333,-1,c1ccccc1N
Now we would like to separate the duplicates and non-duplicates based on the fourth column (smiles)
duplicate:
95,CPD-1111111,-2,c1ccccc1
95,CPD-2222222,-3,c1ccccc1
95,CPD-2222222,-4,c1ccccc1
non-duplicate
95,CPD-3333333,-1,c1ccccc1N
Now the following attempt could do separate the duplicate without any problem. However, the first occurrence of the duplicate will still be included into the non-duplicate file.
BEGIN { FS = ","; f1="a"; f2="b"}
{
# Keep count of the fields in fourth column
count[$4]++;
# Save the line the first time we encounter a unique field
if (count[$4] == 1)
first[$4] = $0;
# If we encounter the field for the second time, print the
# previously saved line
if (count[$4] == 2)
print first[$4] > f1 ;
# From the second time onward. always print because the field is
# duplicated
if (count[$4] > 1)
print > f1;
if (count[$4] == 1) #if (count[$4] - count[$4] == 0) <= change to this doesn't work
print first[$4] > f2;
duplicate output results from the attempt:
95,CPD-1111111,-2,c1ccccc1
95,CPD-2222222,-3,c1ccccc1
95,CPD-2222222,-4,c1ccccc1
non-duplicate output results from the attempt
TargetIDs,CPD,Value,SMILES
95,CPD-3333333,-1,c1ccccc1N
95,CPD-1111111,-2,c1ccccc1
May I know if any guru might have comments/solutions? Thanks.
I would do this:
awk '
NR==FNR {count[$2] = $1; next}
FNR==1 {FS=","; next}
{
output = (count[$NF] == 1 ? "nondup" : "dup")
print > output
}
' <(cut -d, -f4 input | sort | uniq -c) input
The process substitution will pre-process the file and perform a count on the 4th column. Then, you can process the file and decide if that line is "duplicated".
All in awk: Ed Morton shows a way to collect the data in a single pass. Here's a 2 pass solution that's virtually identical to my example above
awk -F, '
NR==FNR {count[$NF]++; next}
FNR==1 {next}
{
output = (count[$NF] == 1 ? "nondup" : "dup")
print > output
}
' input input
Yes, the input file is given twice.
$ cat tst.awk
BEGIN{ FS="," }
NR>1 {
if (cnt[$4]++) {
dups[$4] = nonDups[$4] dups[$4] $0 ORS
delete nonDups[$4]
}
else {
nonDups[$4] = $0 ORS
}
}
END {
print "Duplicates:"
for (key in dups) {
printf "%s", dups[key]
}
print "\nNon Duplicates:"
for (key in nonDups) {
printf "%s", nonDups[key]
}
}
$ awk -f tst.awk file
Duplicates:
95,CPD-1111111,-2,c1ccccc1
95,CPD-2222222,-3,c1ccccc1
95,CPD-2222222,-4,c1ccccc1
Non Duplicates:
95,CPD-3333333,-1,c1ccccc1N
This solution only works if the duplicates are grouped together.
awk -F, '
function fout( f, i) {
f = (cnt > 1) ? "dups" : "nondups"
for (i = 1; i <= cnt; ++i)
print lines[i] > f
}
NR > 1 && $4 != lastkey { fout(); cnt = 0 }
{ lastkey = $4; lines[++cnt] = $0 }
END { fout() }
' file
Little late
My version in awk
awk -F, 'NR>1{a[$0":"$4];b[$4]++}
END{d="\n\nnondupe";e="dupe"
for(i in a){split(i,c,":");b[c[2]]==1?d=d"\n"i:e=e"\n"i} print e d}' file
Another built similar to glenn jackmans but all in awk
awk -F, 'function r(f) {while((getline <f)>0)a[$4]++;close(f)}
BEGIN{r(ARGV[1])}{output=(a[$4] == 1 ? "nondup" : "dup");print >output} ' file

Awk merge the results of processing two files into a single file

I use awk to extract and calculate information from two different files and I want to merge the results into a single file in columns ( for example, the output of first file in columns 1 and 2 and the output of the second one in 3 and 4 ).
The input files contain:
file1
SRR513804.1218581HWI-ST695_116193610:4:1307:17513:49120 SRR513804.16872HWI ST695_116193610:4:1101:7150:72196 SRR513804.2106179HWI-
ST695_116193610:4:2206:10596:165949 SRR513804.1710546HWI-ST695_116193610:4:2107:13906:128004 SRR513804.544253
file2
>SRR513804.1218581HWI-ST695_116193610:4:1307:17513:49120
TTTTGTTTTTTCTATATTTGAAAAAGAAATATGAAAACTTCATTTATATTTTCCACAAAG
AATGATTCAGCATCCTTCAAAGAAATTCAATATGTATAAAACGGTAATTCTAAATTTTAT
ACATATTGAATTTCTTTGAAGGATGCTGAATCATTCTTTGTGGAAAATATAAATGAAGTT
TTCATATTTCTTTTTCAAAT
To parse the first file I do this:
awk '
{
s = NF
center = $1
}
{
printf "%s\t %d\n", center, s
}
' file1
To parse the second file I do this:
awk '
/^>/ {
if (count != "")
printf "%s\t %d\n", seq_id, count
count = 0
seq_id = $0
next
}
NF {
long = length($0)
count = count+long
}
END{
if (count != "")
printf "%s\t %d\n", seq_id, count
}
' file2
My provisional solution is create one temporal and overwrite in the second step. There is a more "elegant" way to get this output?
I am not fully clear on the requirement and if you can update the question may be we can help improvise the answer. However, from what I have gathered is that you would like to summarize the output from both files. I have made an assumption that content in both files are in sequential order. If that is not the case, then we will have to add additional checks while printing the summary.
Content of script.awk (re-using most of your existing code):
NR==FNR {
s[NR] = NF
center[NR] = $1
next
}
/^>/ {
seq_id[++y] = $0
++i
next
}
NF {
long[i] += length($0)
}
END {
for(x=1;x<=length(s);x++) {
printf "%s\t %d\t %d\n", center[x], s[x], long[x]
}
}
Test:
$ cat file1
SRR513804.1218581HWI-ST695_116193610:4:1307:17513:49120 SRR513804.16872HWI ST695_116193610:4:1101:7150:72196 SRR513804.2106179HWI-
ST695_116193610:4:2206:10596:165949 SRR513804.1710546HWI-ST695_116193610:4:2107:13906:128004 SRR513804.544253
$ cat file2
>SRR513804.1218581HWI-ST695_116193610:4:1307:17513:49120
TTTTGTTTTTTCTATATTTGAAAAAGAAATATGAAAACTTCATTTATATTTTCCACAAAG
AATGATTCAGCATCCTTCAAAGAAATTCAATATGTATAAAACGGTAATTCTAAATTTTAT
ACATATTGAATTTCTTTGAAGGATGCTGAATCATTCTTTGTGGAAAATATAAATGAAGTT
TTCATATTTCTTTTTCAAAT
$ awk -f script.awk file1 file2
SRR513804.1218581HWI-ST695_116193610:4:1307:17513:49120 4 200
ST695_116193610:4:2206:10596:165949 3 0

awk transpose column to line and adjust field width [duplicate]

With this script every field is printed out according to the longest word of the current file, but needs to have a line break every file. How can this be achieved?
awk 'BEGIN{ORS="\n"}FNR=NR{a[i++]=$0; if(length($0) > length(max)) max=$0;l=length(max)} END{ for(j=1; j<=i;j++) printf("%-"(l+1)"s,",a[j-1])}' file1 file2 >outfile
file1
HELLO
WORLD
SOUTH IS
WARM
NORTH IS
COLD
file2
HELLO
WORLD
SOUTH
WARM
NORTH
COLD
output
HELLO ,WORLD ,SOUTH IS ,WARM ,NORTH IS ,COLD
HELLO ,WORLD ,SOUTH ,WARM ,NORTH ,COLD
It's not entirely clear what you are asking for, but perhaps you just want:
FNR==1 {print "\n"}
Which will print a newline whenever it starts reading the first line of a file. Make sure this pattern/action is before any others so that the newline prints before any other action prints anything for the first line of the current file. (This does not appear to apply in your case, since no such action exists.)
Took me some time, got it solved with this script.
awk '{ NR>1 && FNR==1 ? l=length($0) && a[i++]= "\n" $0 : a[i++]=$0 }
{if(NR>1 && FNR==1) for(e=(i-c);e<=(i-1);e++) b[e]=d ;c=FNR; d=l }
{ if( length($0) > l) l=length($0)+1 }
END{for(e=(i-c+1);e<=i;e++) b[e]=d; for(j=1;j<=i;j++) printf("%-"b[j]"s,",a[j-1] )}' infiles* >outfile
#!/usr/bin/awk -f
function beginfile (file) {
split("", a)
max = 0
delim = ""
}
function endfile (file) {
for (i = 1; i <= lines; i++) {
printf "%s%-*s", delim, max, a[i]
delim = " ,"
}
printf "\n"
}
FILENAME != _oldfilename \
{
if (_oldfilename != "")
endfile(_oldfilename)
_oldfilename = FILENAME
beginfile(FILENAME)
}
END { endfile(FILENAME) }
{
len = length($0)
if (len > max) {
max = len
}
a[FNR] = $0
lines = FNR
}
To run it:
chmod u+x filename
./filename file1 file2
Note that in gawk you can do delete a instead of split("", a). GAWK 4 has builtin BEGINFILE and ENDFILE.