When I use printf() in gawk the OFS separates output fields. However,in this script it ignores the OFS so output fields are separated by commas. Reading about the printf() function I don't see how to separate output fields with a pipe, "|".
BEGIN { FS="|", OFS="|" }
{ split ($6, a, "/"); printf "%s,%s,%s,%s,%s,%s-%s-%s,%s\n", $1"|"$2"|"$3"|"$4"|"$5"|" a[3], a[1], a[2]"|"$7; }
Thanks in advance,
Rich
The f in printf stands for "formatting" - you provide all the formatting as the first argument for printf instead of using the defaults like OFS as a separator or OFMT for numeric output as used by print.
When you write:
printf "%s,%s\n", x, y
you're specifically stating that you want a comma between 2 string fields. If you want to use printf but also want whatever value OFS has between the fields then you'd instead write:
printf "%s%s%s\n", x, OFS, y
which is equivalent to:
print x, y
In any case, I think what you're trying to do is:
BEGIN { FS=OFS="|" }
{ split ($6, a, "/"); $6=a[3] "-" a[1] "-" a[2]; print }
Related
I'm processing a Wireshark config file (dfilter_buttons) for display filters and would like to print out the filter of a given name. The content of file is like:
Sample input
"TRUE","test","sip contains \x22Hello, world\x5cx22\x22",""
And the resulting output should have the escape sequences replaced, so I can use them later in my script:
Desired output
sip contains "Hello, world\x22"
My first pass is like this:
Current parser
filter_name=test
awk -v filter_name="$filter_name" 'BEGIN {FS="\",\""} ($2 == filter_name) {print $3}' "$config_file"
And my output is this:
Current output
sip contains \x22Hello, world\x5cx22\x22
I know I can handle these exact two escape sequences by piping to sed and matching those exact two sequences, but is there a generic way to substitutes all escape sequences? Future filters I build may utilize more escape sequences than just " and , and I would like to handle future scenarios.
Using gnu-awk you can do this using split, gensub and strtonum functions:
awk -F '","' -v filt='test' '$2 == filt {n = split($3, subj, /\\x[0-9a-fA-F]{2}/, seps); for (i=1; i<n; ++i) printf "%s%c", subj[i], strtonum("0" substr(seps[i], 2)); print subj[i]}' file
sip contains "Hello, world\x22"
A more readable form:
awk -F '","' -v filt='test' '
$2 == filt {
n = split($3, subj, /\\x[0-9a-fA-F]{2}/, seps)
for (i=1; i<n; ++i)
printf "%s%c", subj[i], strtonum("0" substr(seps[i], 2))
print subj[i]
}' file
Explanation:
Using -F '","' we split input using delimiter ","
$2 == filt we filter input for $2 == "test" condition
Using /\\x[0-9a-fA-F]{2}/ as regex (that matches 2 digit hex strings) we split $3 and save split tokens into array subj and matched separators into array seps
Using substr we remove first char i.e \\ and prepend 0
Using strtonum we convert hex string to equivalent ascii number
Using %c in printf we print corresponding ascii character
Last for loop joins $3 back using subj and seps array elements
Using GNU awk for FPAT, gensub(), strtonum(), and the 3rd arg to match():
$ cat tst.awk
BEGIN { FPAT="([^,]*)|(\"[^\"]*\")"; OFS="," }
$2 == ("\"" filter_name "\"") {
gsub(/^"|"$/,"",$3)
while ( match($3,/(\\x[0-9a-fA-F]{2})(.*)/,a) ) {
printf "%s%c", substr($3,1,RSTART-1), strtonum(gensub(/./,0,1,a[1]))
$3 = a[2]
}
print $3
}
$ awk -v filter_name='test' -f tst.awk file
sip contains "Hello, world\x22"
The above assumes your escape sequences are always \x followed by exactly 2 hex digits. It isolates every \xHH string in the input, replaces \ with 0 in that string so that strtonum() can then convert the string to a number, then uses %c in the printf formatting string to convert that number to a character.
Note that GNU awk has a debugger (see https://www.gnu.org/software/gawk/manual/gawk.html#Debugger) so if you're ever not sure what any part of a program does you can just run it in the debugger (-D) and trace it, e.g. in the following I plant a breakpoint to tell awk to stop at line 1 of the script (b 1), then start running (r) and the step (s) through the script printing the value of $3 (p $3) at each line so I can see how it changes after the gsub():
$ awk -D -v filter_name='test' -f tst.awk file
gawk> b 1
Breakpoint 1 set at file `tst.awk', line 1
gawk> r
Starting program:
Stopping in BEGIN ...
Breakpoint 1, main() at `tst.awk':1
1 BEGIN { FPAT="([^,]*)|(\"[^\"]*\")"; OFS="," }
gawk> p $3
$3 = uninitialized field
gawk> s
Stopping in Rule ...
2 $2 == "\"" filter_name "\"" {
gawk> p $3
$3 = "\"sip contains \\x22Hello, world\\x5cx22\\x22\""
gawk> s
3 gsub(/^"|"$/,"",$3)
gawk> p $3
$3 = "\"sip contains \\x22Hello, world\\x5cx22\\x22\""
gawk> s
4 while ( match($3,/(\\x[0-9a-fA-F]{2})(.*)/,a) ) {
gawk> p $3
$3 = "sip contains \\x22Hello, world\\x5cx22\\x22"
I have a tab delimited csv file containing summary statistics for object lengths:
sampled. objs. obj. min. len. obj. mean. len. obj. max. len. obj. std.
50 22 60 95 5
I want the information about minimum and maximum lengths by searching matching column headers obj. min. len. and obj. max. len.. I then want to create a new csv file, comma-delimited with new column headers to get the result
object_minimum,object_maximum
22,95
I first print the new headers. Then I tried retrieving the indices of the match and then extracting from the second row using these indices:
#!/bin/awk -f
BEGIN {
cols="object_minimum:object_maximum"
FS="\t"
RS="\n"
col_count=split(cols, col_arr, ":");
for(i=1; i<=col_count; i++) printf col_arr[i] ((i==col_count) ? "\n" : ",");
}
{
for (i=1; i<=NF; i++) {
if(index($i,"obj. min. len.") !=0) {
data["object_minimum"]=i;
}
if(index($i,"obj. max. len.") !=0) {
data["object_maximum"]=i;
}
}
}
END NR==1 {
for (j=1; j<=col_count; j++) printf NF==data[j] ((i==col_count) ? "\n" : ",");
}
There could be more columns and in a different order so it is necessary to do the matching to find the position, and also I may have to select for more columns by changing cols and looking for more matches. I execute by running
awk -f awk_script.awk original.csv > new.csv
With awk:
awk 'BEGIN {FS="\t"; OFS=","}
NR==1 {for (i=1; i<=NF; i++){f[$i] = i}} # fill array with header
NR> 1 {print $(f["obj. min. len."]), $(f["obj. max. len."])}' file
Output:
22,95
Source: https://unix.stackexchange.com/a/359699/74329
See: 8 Powerful Awk Built-in Variables – FS, OFS, RS, ORS, NR, NF, FILENAME, FNR
here is one working prototype, add formatting and error checking...
$ awk -F'\t' -v OFS=, '
NR==1 {for(i=1;i<=NF;i++)
if($i=="obj. min. len.") min=i;
else if($i=="obj. max. len.") max=i;
print "min","max"}
NR==2 {print $min,$max; exit}' file
min,max
22,95
Could you please try following, completely based on your shown samples only, written and tested in GNU awk. Created an awk variable named sep="###" this could be changed as per need too.
awk -v sep="###" '
BEGIN{
OFS=","
}
FNR==1{
while(match($0,/ +obj\./)){
val=substr($0,RSTART,RLENGTH)
sub(/^ +/,"",val)
line=(line?line:"")substr($0,1,RSTART-1)sep val
$0=substr($0,RSTART+RLENGTH)
}
if(substr($0,RSTART+RLENGTH)!=""){
line=line substr($0,RSTART+RLENGTH)
}
num=split(line,arr,sep)
for(i=1;i<=num;i++){
if(arr[i]=="obj. min. len."){ min=i }
if(arr[i]=="obj. max. len."){ max=i }
}
print "object_minimum,object_maximum"
next
}
{
print $min,$max
}
' Input_file
Logical explanation: Working on the very first line of Input_file. Then using awk's match function to look for matches +obj\. in current line. In this creating a variable which has values of matched and before matched values. Once all searching of specific regex is done(means all occurrences of matched regex are found). Then splitting newly created variable(which has value of first line with separators ### assuming these are NOT present in your Input_file else change them to something else) into array. Finally going through all elements of that array and putting condition if a column is obj. min. len. then setting min variable value to that specific index number(which is actually field number for rest of the lines) and if value is obj. max. len. then setting max variable. After processing first line simply printing corresponding fields by doing $min,$max.
I have multi columns file and i want to extract some info in column 71.
I want to extract using tags which the value can be anything, for example i want to just extract AC=* ; AF=* , where the value can be anything .
I found similar question and gave it a try but it didn't work
Extract columns with values matching a specific pattern
Column 71 looks like this:
AC=14511;AC_AFR=382;AC_AMR=1177;AC_Adj=14343;AC_EAS=5;AC_FIN=427;AC_Het=11813;AC_Hom=1265;AC_NFE=11027;AC_OTH=97;AC_SAS=1228;AF=0.137;AN=106198;AN_AFR=8190;AN_AMR=10424;AN_Adj=99264;AN_EAS=7068;AN_FIN=6414;AN_NFE=51090;AN_OTH=658;AN_SAS=15420;BaseQRankSum=1.73;ClippingRankSum=-1.460e-01;DB;DP=1268322;FS=0.000;GQ_MEAN=190.24;GQ_STDDEV=319.67;Het_AFR=358;Het_AMR=1049;Het_EAS=5;Het_FIN=399;Het_NFE=8799;Het_OTH=83;Het_SAS=1120;Hom_AFR=12;Hom_AMR=64;Hom_EAS=0;Hom_FIN=14;Hom_NFE=1114;Hom_OTH=7;Hom_SAS=54;InbreedingCoeff=0.0478;MQ=60.00;MQ0=0;MQRankSum=0.037;NCC=270;POSITIVE_TRAIN_SITE;QD=21.41;ReadPosRankSum=0.212;VQSLOD=4.79;culprit=MQ;DP_HIST=30|3209|1539|1494|30007|7938|4130|2038|1310|612|334|185|97|60|31|25|9|11|7|33,0|66|339|1048|2096|2665|2626|1832|1210|584|323|179|89|54|31|22|7|9|4|15;GQ_HIST=84|66|56|82|3299|568|617|403|250|319|436|310|28566|2937|827|834|451|186|217|12591,15|15|13|16|25|11|22|28|18|38|52|31|65|76|39|83|93|65|97|12397;CSQ=T|ENSG00000186868|ENST00000334239|Transcript|intron_variant||||||rs754512|1||1|MAPT|HGNC|6893|protein_coding||CCDS11502.1|ENSP00000334886|TAU_HUMAN|B4DSE3_HUMAN|UPI0000000C16||||2/8||ENST00000334239.8:c.134-94A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000570299|Transcript|intron_variant&non_coding_transcript_variant||||||rs754512|1||1|MAPT|HGNC|6893|processed_transcript||||||||||2/6||ENST00000570299.1:n.262-94A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000340799|Transcript|intron_variant||||||rs754512|1||1|MAPT|HGNC|6893|protein_coding||CCDS45716.1|ENSP00000340438|TAU_HUMAN||UPI000004EEE6||||3/10||ENST00000340799.5:c.221-94A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000262410|Transcript|intron_variant||||||rs754512|1||1|MAPT|HGNC|6893|protein_coding||CCDS11501.1|ENSP00000262410|TAU_HUMAN||UPI0000EE80B7||||4/13||ENST00000262410.5:c.308-94A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000446361|Transcript|intron_variant||||||rs754512|1||1|MAPT|HGNC|6893|protein_coding||CCDS11500.1|ENSP00000408975|TAU_HUMAN||UPI000004EEE5||||2/9||ENST00000446361.3:c.134-94A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000574436|Transcript|intron_variant||||||rs754512|1||1|MAPT|HGNC|6893|protein_coding||CCDS11499.1|ENSP00000460965|TAU_HUMAN||UPI000002D754||||3/10||ENST00000574436.1:c.308-94A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000571987|Transcript|intron_variant||||||rs754512|1||1|MAPT|HGNC|6893|protein_coding||CCDS11501.1|ENSP00000458742|TAU_HUMAN||UPI0000EE80B7||||3/12||ENST00000571987.1:c.308-94A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000415613|Transcript|intron_variant||||||rs754512|1||1|MAPT|HGNC|6893|protein_coding||CCDS45715.1|ENSP00000410838|TAU_HUMAN||UPI0001AE66E9||||3/13||ENST00000415613.2:c.308-94A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000571311|Transcript|intron_variant&NMD_transcript_variant||||||rs754512|1||1|MAPT|HGNC|6893|nonsense_mediated_decay|||ENSP00000460048||I3L2Z2_HUMAN|UPI00025A2E6E||||4/4||ENST00000571311.1:c.*176-94A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000535772|Transcript|intron_variant||||||rs754512|1||1|MAPT|HGNC|6893|protein_coding||CCDS56033.1|ENSP00000443028|TAU_HUMAN|B4DSE3_HUMAN|UPI000004EEE4||||4/10||ENST00000535772.1:c.308-94A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000576518|Transcript|stop_gained|5499|7|3|K/*|Aag/Tag|rs754512|1||1|MAPT|HGNC|6893|protein_coding|||ENSP00000458621||I3L170_HUMAN&B4DSE3_HUMAN|UPI0001639A7C|||1/7|||ENST00000576518.1:c.7A>T|ENSP00000458621.1:p.Lys3Ter|T:0.1171|||||||||15792962|||||POSITION:0.00682261208576998&ANN_ORF:-255.6993&MAX_ORF:-255.6993|PHYLOCSF_WEAK|ANC_ALLELE|LC,T|ENSG00000186868|ENST00000420682|Transcript|intron_variant||||||rs754512|1||1|MAPT|HGNC|6893|protein_coding||CCDS45716.1|ENSP00000413056|TAU_HUMAN||UPI000004EEE6||||2/9||ENST00000420682.2:c.221-94A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000572440|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2790|||||rs754512|1||1|MAPT|HGNC|6893|retained_intron|||||||||1/1|||ENST00000572440.1:n.2790A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000351559|Transcript|intron_variant||||||rs754512|1||1|MAPT|HGNC|6893|protein_coding||CCDS11499.1|ENSP00000303214|TAU_HUMAN||UPI000002D754||||4/11||ENST00000351559.5:c.308-94A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000344290|Transcript|intron_variant||||||rs754512|1||1|MAPT|HGNC|6893|protein_coding|YES|CCDS45715.1|ENSP00000340820|TAU_HUMAN||UPI0001AE66E9||||4/14||ENST00000344290.5:c.308-94A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000347967|Transcript|intron_variant||||||rs754512|1||1|MAPT|HGNC|6893|protein_coding|||ENSP00000302706|TAU_HUMAN|B4DSE3_HUMAN|UPI0000173D91||||4/10||ENST00000347967.5:c.32-100A>T||T:0.1171|||||||||15792962||||||||,T|ENSG00000186868|ENST00000431008|Transcript|intron_variant||||||rs754512|1||1|MAPT|HGNC|6893|protein_coding||CCDS56033.1|ENSP00000389250|TAU_HUMAN|B4DSE3_HUMAN|UPI000004EEE4||||3/9||ENST00000431008.3:c.308-94A>T||T:0.1171|||||||||15792962||||||||
The code that i tried:
awk '{
for (i = 1; i <= NF; i++) {
if ($i ~ /AC|AF/) {
printf "%s %s ", $i, $(i + 1)
}
}
print ""
}'
I keep getting syntax error.
output wanted :
AC=14511;AF=0.137
Whenever you have name=value pairs, it's usually simplest to first create an array that maps names to values (n2v[] below) and then you can just access the values by their names.
$ cat file
AC=1;AC_AFR=2;AF=3 AC=4;AC_AFR=5;AF=6
$ cat tst.awk
{
delete n2v
split($2,tmp,/[;=]/)
for (i=1; i in tmp; i+=2) {
n2v[tmp[i]] = tmp[i+1]
}
prt("AC")
prt("AF")
}
function prt(name) { print name, "=", n2v[name] }
$ awk -f tst.awk file
AC = 4
AF = 6
Just change $2 to $71 for your real input.
Something like this should do it (in Gnu awk due to switch):
$ awk '{split($71,a,";");for(i in a )if(a[i]~/^AF/) print a[i]}' foo
AF=0.137
You split the field $71 by ;s, loop thru the array you split to looking for desired match. For multiple matches use switch:
$ awk '{
split($0,a,";");
for(i in a )
switch(a[i]) {
case /^AF=/:
b=b a[i] OFS;
break;
case /^AC=/:
b=b a[i] OFS;
break
}
sub(/.$/,"\n",b);
printf b
}' foo
AC=14511 AF=0.137
EDIT: Now it buffers output to a variable and prints it in the end. You can control the separator with OFS.
I was wondering if I can make lists having left characters OR right characters after splitting with '=', and finally each character also get splitted with another '|' and ','. I have tried but failed because the number of lists are not fixed. Even C16 can be shown up, then it will be 16 item in the input.
Can you give me any hint?
Input
C1=34,C2=35,C3="99"
Output
C1|C2|C3#34,35,"99"
You can pass multiple characters as the delimiter when using -F. The command could look like this:
awk -F'[,=]' '{printf "%s|%s|%s#%s,%s,%s", $1,$3,$5,$2,$4,$6}' input.txt
I'm using , and = as the delimiter. This makes it simple to access individual values and reassemble them using printf.
If the number of columns is unknown, you need to loop over the columns. First over the odd columns which are the names, then over the even columns which are the values. I suggest to put it into a script:
test.awk
BEGIN {
FS="[,=]"
}
{
for(i=1;i<=NF;i+=2){
if(i>=NF-1){
fmt="%s"
}else{
fmt="%s|"
}
printf fmt,$i
}
printf "#"
for(i=2;i<=NF;i+=2){
if(i>=NF-1){
fmt="%s"
}else{
fmt="%s,"
}
printf fmt,$i
}
}
Then execute it like this:
awk -f test.awk input.txt
awk -F'[=,]' '
{
for (i=1;i<=NF;i+=2) {
printf "%s%s", $i, (i<(NF-1)?"|":"#")
}
for (i=2;i<=NF;i+=2) {
printf "%s%s", $i, (i<NF?",":ORS)
}
}
' file
C1|C2|C3#34,35,"99"
awk '{sub(/C1=34,C2=35,C3="99"/,"C1|C2|C3#34,35,\"99\"")}1' file
C1|C2|C3#34,35,"99"
I am in need of reorganizing a large CSV file. The first column, which is currently a 6 digit number needs to be split up, using commas as the field separator.
For example, I need this:
022250,10:50 AM,274,22,50
022255,11:55 AM,275,22,55
turned into this:
0,2,2,2,5,0,10:50 AM,274,22,50
0,2,2,2,5,5,11:55 AM,275,22,55
Let me know what you think!
Thanks!
It's a lot shorter in perl:
perl -F, -ane '$,=","; print split("",$F[0]), #F[1..$#F]' <file>
Since you don't know perl, a quick explanation. -F, indicates the input field separator is the comma (like awk). -a activates auto-split (into the array #F), -n implicitly wraps the code in a while (<>) { ... } loop, which reads input line-by-line. -e indicates the next argument is the script to run. $, is the output field separator (it gets set iteration of the loop this way, but oh well). split has obvious purpose, and you can see how the array is indexed/sliced. print, when lists as arguments like this, uses the output field separator and prints all their fields.
In awk:
awk -F, '{n=split($1,a,""); for (i=1;i<=n;i++) {printf("%s,",a[i])}; for (i=2;i<NF;i++) {printf("%s,",$i)}; print $NF}' <file>
I think this might work. The split function (at least in the version I am running) splits the value into individual characters if the third parameter is an empty string.
BEGIN{ FS="," }
{
n = split( $1, a, "" );
for ( i = 1; i <= n; i++ )
printf("%s,", a[i] );
sep = "";
for ( i = 2; i <= NF; i++ )
{
printf( "%s%s", sep, $i );
sep = ",";
}
printf("\n");
}
here's another way in awk
$ awk -F"," '{gsub(".",",&",$1);sub("^,","",$1)}1' OFS="," file
0,2,2,2,5,0,10:50 AM,274,22,50
0,2,2,2,5,5,11:55 AM,275,22,55
Here's a variation on a theme. One thing to note is it prints the remaining fields without using a loop. Another is that since you're looping over the characters in the first field anyway, why not just do it without using the null-delimiter feature of split() (which may not be present in some versions of AWK):
awk -F, 'BEGIN{OFS=","} {len=length($1); for (i=1;i<len; i++) {printf "%s,", substr($1,i,1)}; printf "%s", substr($1,len,1);$1=""; print $0}' filename
As a script:
BEGIN {FS = OFS = ","}
{
len = length($1);
for (i=1; i<len; i++)
{printf "%s,", substr($1, i, 1)};
printf "%s", substr($1, len, 1)
$1 = "";
print $0
}