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"
Related
I have this code
BEGIN { FS=OFS=";" }
{ key = $(NF-1) }
NR == FNR {
for (i=1; i<(NF-1); i++) {
if ( !seen[key,$i]++ ) {
map[key] = (key in map ? map[key] OFS : "") $i
}
}
next
}
{ print $0 map[key] }
I use code in this way
awk -f tst.awk 2.txt 1.txt
I have two text files
1.txt
AA;BB;
2.txt
CC;DD;BB;AA;
I try to generate this 3.txt output
AA;BB;CC;DD;
but with this script is not possible because this script return only AA;BB;
logic: The above just uses literal strings in a hash lookup of array indices so it doesn't care what characters you have in your input. However about sample output:if in 2.txt there are common fields also in 1.txt.for example BB;AA; then you need concatenate them in a single row, i.e AA;BB;CC;DD; Ordering is not required, for example is not relevant if output is BB;AA;DD;CC; Only condition that is required is avoid duplicates but my script already does this
Could you please try following, as per OP's comment both files have only 1 line. So using paste command to combine both the files and then processing its output by awk command.
paste -d';' 1.txt 2.txt |
awk '
BEGIN{
FS=OFS=";"
}
{
for(i=1;i<=NF;i++){
if(!seen[$i]++){ val=(val?val OFS:"")$i }
}
print val
delete seen
val=""
}'
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 have a text file that is comma delimited. The first line is a list of field names, and subsequent lines contain data. I'll get new versions of the file, and I want to extract all the values from a particular column by name rather than by column number. (I.e. the column I want may be in different positions in different versions of the file.)
For example, here are two files:
foo,bar,interesting,junk
1,2,gold,ramjet
2,25,diamonds,superfluous
and
foo,bar,baz,interesting,junk,morejunk
5,3,smurf,platinum,garbage,scrap
6,2.5,mushroom,sodium,liverwurst,eew
I'd like a single script that will go through multiple files, extracting the minerals in the "interesting" column. :-)
What I've got so far is something that works on ONE file, but I know that awk is more elegant than this. How do I clean this up and make it work on multiple files at once?
BEGIN {
FS=",";
}
NR == 1 {
for(i=1; i<=NF; i++) {
if($i=="interesting") {
col=i;
}
}
}
NR > 1 {
print $col;
}
You're pretty darn close already. Just use FNR instead of NR, for "File NR".
#!/usr/bin/awk -f
BEGIN { FS="," }
FNR==1 {
for (col=1;col<=NF;col++)
if ($col=="interesting")
next
}
{ print $col }
Or if you like:
#!/usr/bin/awk -f
BEGIN { FS="," }
FNR==1 { for (col=1;$col!="interesting";col++); next }
{ print $col }
Or if you prefer one-liners:
$ awk -F, -v txt="interesting" 'FNR==1{for(c=1;$c!=txt;c++);next} {print $c}' file1 file2
Of course, be careful that you actually have the specified column, or you may find yourself in an endless loop. You can probably figure out the extra condition that saves you from that risk.
Note that in awk, you only need to terminate commands with semicolons if they are followed by another command. Thus, you would do this:
command1; command2
But you can drop the semicolon if you separate commands with newlines:
command1
command2
Do it this way:
$ cat tst.awk
BEGIN { FS=OFS="," }
FNR==1 { for (i=1;i<=NF;i++) f[$i]=i; next }
{ print $(f["interesting"]) }
$ awk -f tst.awk file1 file2
gold
diamonds
platinum
sodium
Creating a name->value array is always the best approach when it's applicable. It keeps every part of the code simple and decoupled from the rest of the code, and it sets you up for doing other things like changing the order of the fields when you output the results, e.g.:
$ cat tst.awk
BEGIN { FS=OFS="," }
FNR==1 { for (i=1;i<=NF;i++) f[$i]=i; next }
{ print $(f["junk"]), $(f["interesting"]), $(f["bar"]) }
$ awk -f tst.awk file1 file2
ramjet,gold,2
superfluous,diamonds,25
garbage,platinum,3
liverwurst,sodium,2.5
I do have a problem that is too difficult for me, but believe it can be solved very easily in awk.
My data looks like this:
8377885 8384365 8385357 8385877 # 8378246 8384786 8385450 8386102
66999065 66999928 67091529 # 66999090 67000051 67091593
It's different lines that that have '#' exactly in the middle of them. I want to:
1.Combine line elements separated with '#' from first to last;
2.Print all combined elements as column.
Preferred output would look like this:
8377885 8378246
8384365 8384786
8385357 8385450
8385877 8386102
8390268 8390996
66999065 66999090
66999928 67000051
67091529 67091593
Hope someone could help me with this.
Here you have a one-liner:
awk 'BEGIN { FS = "[# ]+" } { for (i=1;i<=NF/2;i++) { printf "%s %s\n", $i, $(NF/2+i) } }' infile
That yields:
8377885 8378246
8384365 8384786
8385357 8385450
8385877 8386102
66999065 66999090
66999928 67000051
67091529 67091593
below will work:
awk -F"#" '{n=split($1,a," ");split($2,b," ");for(i=1;i<=n;i++)print a[i],b[i]}' your_file
tested below:
> awk -F"#" '{n=split($1,a," ");split($2,b," ");for(i=1;i<=n;i++)print a[i],b[i]}' temp
8377885 8378246
8384365 8384786
8385357 8385450
8385877 8386102
66999065 66999090
66999928 67000051
67091529 67091593
I am in need of reorganizing a large CSV file. The first column, which is currently a 6 digit number needs to be split up, using commas as the field separator.
For example, I need this:
022250,10:50 AM,274,22,50
022255,11:55 AM,275,22,55
turned into this:
0,2,2,2,5,0,10:50 AM,274,22,50
0,2,2,2,5,5,11:55 AM,275,22,55
Let me know what you think!
Thanks!
It's a lot shorter in perl:
perl -F, -ane '$,=","; 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
}