I have a very large variant calling data. I can not pull out the result I want.
here is an example
bac1 bac2 bac3 bac4
1 0 0 1
Now I want to drop the columns that contain 0 using the ubuntu command-line. The result would be like this
bac1 bac4
1 1
I tried this
awk -F "\t" -v "pat=0\t" 'NR == 2 {for (i=1; i <= NF; i++) Take[i] = (pat != $i)}{for (i =1; i <= NF; i++) if (Take [i]) printf $i FS; print ""}'
And the output is this:
NC_045512.2 18876 NC_045512.2_18876_T_C T C . PASS GT 1
Header of this output is:
#CHROM POS ID REF ALT QUAL FILTER FORMAT EPI_ISL_422804
So the final output had to be like this:
#CHROM POS ID REF ALT QUAL FILTER FORMAT EPI_ISL_422804
NC_045512.2 18876 NC_045512.2_18876_T_C T C . PASS GT 1
The file is not always 2 lines but at most it can be 4 lines.
It does not return the header line that's because I used NR == 2. Is there any way I cant get the header column as well??
If your input file always only has 1 data line as in your example then:
$ cat tst.awk
BEGIN { FS=OFS="\t" }
NR == 1 { split($0,hdr); next }
{
for (i = 1; i <= NF; i++) {
if ($i != 0) {
cols[++nf] = i
}
}
for (i = 1; i <= nf; i++) {
printf "%s%s", hdr[cols[i]], (i<nf ? OFS : ORS)
}
for (i = 1; i <= nf; i++) {
printf "%s%s", $(cols[i]), (i<nf ? OFS : ORS)
}
}
.
$ awk -f tst.awk file
bac1 bac4
1 1
otherwise if your input can have more than 1 data line then you need a 2-pass approach:
$ cat tst.awk
BEGIN { FS=OFS="\t" }
NR == FNR {
if (NR > 1) {
for (i = 1; i <= NF; i++) {
if ($i == 0) {
zeroCols[i]
}
}
}
next
}
FNR == 1 {
for (i = 1; i <= NF; i++) {
if (! (i in zeroCols) ) {
cols[++nf] = i
}
}
}
{
for (i = 1; i <= nf; i++) {
printf "%s%s", $(cols[i]), (i<nf ? OFS : ORS)
}
}
.
$ awk -f tst.awk file file
bac1 bac4
1 1
Long version with if:
awk 'NR==1{
split($0,array,FS)
}
NR==2{
s=0
for(i=1;i<=NF;i++){
if($i!=0){
if(s==0){
s=1
printf("%s",array[i])
}
else{
printf("%s%s",OFS,array[i])
}
}
}
print ""
s=0
for(i=1;i<=NF;i++){
if($i!=0){
if(s==0){
s=1
printf("%s",$i)
}
else{
printf("%s%s",OFS,$i)
}
}
}
print ""
}' FS='\t' OFS="\t" file
One line:
awk 'NR==1{split($0,array,FS)} NR==2{s=0; for(i=1;i<=NF;i++) {if($i!=0) {if(s==0) {s=1; printf("%s",array[i])} else {printf("%s%s",OFS,array[i])}}} print ""; s=0; for(i=1;i<=NF;i++){if($i!=0){if(s==0){s=1; printf("%s",$i)} else {printf("%s%s",OFS,$i)}}} print ""}' FS='\t' OFS="\t" file
Output:
bac1 bac4
1 1
I have my array:
array = [1:"PLCH2", 2:"PLCH1", 3:"PLCH2"]
I want to loop on array to create a new array unique of unique values and obtain:
unique = [1:"PLCH2", 2:"PLCH1"]
how can I achieve that ?
EDIT: as per #Ed Morton request, I show below how my array is populated. In fact, this post is the key solution to my previous post.
in my file.txt, I have:
PLCH2:A1007int&PLCH1:D987int&PLCH2:P977L
INTS11:P446P&INTS11:P449P&INTS11:P518P&INTS11:P547P&INTS11:P553P
I use split to obtain array:
awk '{
split($0,a,"&")
for ( i in a ) {
split(a[i], b, ":");
array[i] = b[1];
}
}' file.txt
This might be what you're trying to do:
$ cat tst.awk
BEGIN {
split("PLCH2 PLCH1 PLCH2",array)
printf "array ="
for (i=1; i in array; i++) {
printf " %s:\"%s\"", i, array[i]
}
print ""
for (i=1; i in array; i++) {
if ( !seen[array[i]]++ ) {
unique[++j] = array[i]
}
}
printf "unique ="
for (i=1; i in unique; i++) {
printf " %s:\"%s\"", i, unique[i]
}
print ""
}
$ awk -f tst.awk
array = 1:"PLCH2" 2:"PLCH1" 3:"PLCH2"
unique = 1:"PLCH2" 2:"PLCH1"
EDIT: given your updated question, here's how I'd really approach that:
$ cat tst.awk
BEGIN { FS="[:&]" }
{
numVals=0
for (i=1; i<NF; i+=2) {
vals[++numVals] = $i
}
print "vals =" arr2str(vals)
delete seen
numUniq=0
for (i=1; i<=numVals; i++) {
if ( !seen[vals[i]]++ ) {
uniq[++numUniq] = vals[i]
}
}
print "uniq =" arr2str(uniq)
}
function arr2str(arr, str, i) {
for (i=1; i in arr; i++) {
str = str sprintf(" %s:\"%s\"", i, arr[i])
}
return str
}
$ awk -f tst.awk file
vals = 1:"PLCH2" 2:"PLCH1" 3:"PLCH2"
uniq = 1:"PLCH2" 2:"PLCH1"
vals = 1:"INTS11" 2:"INTS11" 3:"INTS11" 4:"INTS11" 5:"INTS11"
uniq = 1:"INTS11" 2:"PLCH1"
I have these two csv files:
File A:
veículo;carro;sust
automóvel;carro;sust
viatura;carro;sust
breve;rápido;adj
excepcional;excelente;adj
maravilhoso;excelente;adj
amistoso;simpático;adj
amigável;simpático;adj
...
File B:
"A001","carro","sust","excelente","adj","ocorrer","adv","bom","adj"
...
In the file A, $1(word) is synonym for $2(word) and $3(word) the part of speech.
In the lines of the file B we can skip $1,the remaining columns are words and their part of speech.
What I need to to do is to look line by line each pair (word-pos) in the file A and generate a line for each synonym. It is difficult to explain.
Desired Output:
"A001","carro","sust","excelente","adj","ocorrer","adv","bom","adj"
"A001","viatura","sust","excelente","adj","ocorrer","adv","bom","adj"
"A001","veículo","sust","excelente","adj","ocorrer","adv","bom","adj"
"A001","automóvel","sust","excelente","adj","ocorrer","adv","bom","adj"
"A001","carro","sust","excepcional","adj","ocorrer","adv","bom","adj"
"A001","viatura","sust","excepcional","adj","ocorrer","adv","bom","adj"
"A001","veículo","sust","excepcional","adj","ocorrer","adv","bom","adj"
"A001","automóvel","sust","excepcional","adj","ocorrer","adv","bom","adj"
"A001","carro","sust","maravilhoso","adj","ocorrer","adv","bom","adj"
"A001","viatura","sust","maravilhoso","adj","ocorrer","adv","bom","adj"
"A001","veículo","sust","maravilhoso","adj","ocorrer","adv","bom","adj"
"A001","automóvel","sust","maravilhoso","adj","ocorrer","adv","bom","adj"
Done:
BEGIN {
FS="[,;]";
OFS=";";
}
FNR==NR{
sinonim[$1","$2","$3]++;
next;
}
{
s1=split($0,AX,"\n");
for (i=1;i<=s1;i++)
{
s2=split(AX[i],BX,",");
for (j=2;j<=NF;j+=2)
{
lineX=BX[j]","BX[j+1];
gsub(/\"/,"",lineX);
for (item in sinonim)
{
s3=split(item,CX,",");
lineS=CX[2]","CX[3];
if (lineX == lineS)
{
BX[j]=CX[1];
lineD=""
for (t=1;t<=s2;t++)
{
lineD=lineD BX[t]",";
}
lineF=lineF lineD"\n";
}
}
}
}
print lineF
}
$ cat tst.awk
BEGIN { FS=";" }
NR==FNR { synonyms[$2,$3][$2]; synonyms[$2,$3][$1]; next }
FNR==1 { FS=OFS="\",\""; $0=$0 }
{
gsub(/^"|"$/,"")
for (i=2;i<NF;i+=2) {
if ( ($i,$(i+1)) in synonyms) {
for (synonym in synonyms[$i,$(i+1)]) {
$i = synonym
for (j=2;j<NF;j+=2) {
if ( ($j,$(j+1)) in synonyms) {
for (synonym in synonyms[$j,$(j+1)]) {
orig = $0
$j = synonym
if (!seen[$0]++) {
print "\"" $0 "\""
}
$0 = orig
}
}
}
}
}
}
}
.
$ awk -f tst.awk fileA fileB
"A001","carro","sust","excelente","adj","ocorrer","adv","bom","adj"
"A001","veículo","sust","excelente","adj","ocorrer","adv","bom","adj"
"A001","automóvel","sust","excelente","adj","ocorrer","adv","bom","adj"
"A001","viatura","sust","excelente","adj","ocorrer","adv","bom","adj"
"A001","carro","sust","maravilhoso","adj","ocorrer","adv","bom","adj"
"A001","carro","sust","excepcional","adj","ocorrer","adv","bom","adj"
"A001","veículo","sust","maravilhoso","adj","ocorrer","adv","bom","adj"
"A001","veículo","sust","excepcional","adj","ocorrer","adv","bom","adj"
"A001","automóvel","sust","maravilhoso","adj","ocorrer","adv","bom","adj"
"A001","automóvel","sust","excepcional","adj","ocorrer","adv","bom","adj"
"A001","viatura","sust","maravilhoso","adj","ocorrer","adv","bom","adj"
"A001","viatura","sust","excepcional","adj","ocorrer","adv","bom","adj"
The above uses GNU awk for multi-dimensional arrays, with other awks it's a simple tweak to use synonyms[$2,$3] = synonyms[$2,$3] " " $2 etc. or similar and then split() later instead of synonyms[$2,$3][$2] and in.
BEGIN { FS="[,;]"; OFS="," }
NR == FNR { key = "\"" $2 "\""; synonym[key] = synonym[key] "," $1; next }
{
print;
if ($2 in synonym) {
count = split(substr(synonym[$2], 2), choices)
for (i = 1; i <= count; i++) {
$2 = "\"" choices[i] "\""
print
}
}
}
How do I use the awk range pattern '/begin regex/,/end regex/' within a self-contained awk script?
To clarify, given program csv.awk:
#!/usr/bin/awk -f
BEGIN {
FS = "\""
}
/TREE/,/^$/
{
line="";
for (i=1; i<=NF; i++) {
if (i != 2) line=line $i;
}
split(line, v, ",");
if (v[5] ~ "FOAM") {
print NR, v[5];
}
}
and file chunk:
TREE
10362900,A,INSTL - SEAL,Revise
,10362901,A,ASSY / DETAIL - PANEL,Revise
,,-203,ASSY - PANEL,Qty -,Add
,,,-309,PANEL,Qty 1,Add
,,,,"FABRICATE FROM TEKLAM NE1G1-02-250 PER TPS-CN-500, TYPE A"
,,,-311,PANEL,Qty 1,Add
,,,,"FABRICATE FROM TEKLAM NE1G1-02-750 PER TPS-CN-500, TYPE A"
,,,-313,FOAM SEAL,1.00 X 20.21 X .50 THK,Qty 1,Add
,,,,"BMS1-68, GRADE B, FORM II, COLOR BAC706 (BLACK)"
,,,-315,FOAM SEAL,1.50 X 8.00 X .25 THK,Qty 1,Add
,,,,"BMS1-68, GRADE B, FORM II, COLOR BAC706 (BLACK)"
,PN HERE,Dual Lock,Add
,
10442900,IR,INSTL - SEAL,Update (not released)
,10362901,A,ASSY / DETAIL - PANEL,Revise
,PN HERE,Dual Lock,Add
I want to have this output:
27 FOAM SEAL
29 FOAM SEAL
What is the syntax for adding the command line form '/begin regex/,/end regex/' to the script to operate on those lines only? All my attempts lead to syntax errors and googling only gives me the cli form.
why not use 2 steps:
% awk '/start/,/end/' < input.csv | awk csv.awk
Simply do:
#!/usr/bin/awk -f
BEGIN {
FS = "\""
}
/from/,/to/ {
line="";
for (i=1; i<=NF; i++) {
if (i != 2) line=line $i;
}
split(line, v, ",");
if (v[5] ~ "FOAM") {
print NR, v[5];
}
}
If the from to regexes are dynamic:
#!/usr/bin/awk -f
BEGIN {
FS = "\""
FROM=ARGV[1]
TO=ARGV[2]
if (ARGC == 4) { # the pattern was the only thing, so force read from standard input
ARGV[1] = "-"
} else {
ARGV[1] = ARGV[3]
}
}
{ if ($0 ~ FROM) { p = 1 ; l = 0} }
{ if ($0 ~ TO) { p = 0 ; l = 1} }
{
if (p == 1 || l == 1) {
line="";
for (i=1; i<=NF; i++) {
if (i != 2) line=line $i;
}
split(line, v, ",");
if (v[5] ~ "FOAM") {
print NR, v[5];
}
l = 0 }
}
Now you have to call it like: ./scriptname.awk "FROM_REGEX" "TO_REGEX" INPUTFILE. The last param is optional, if missing STDIN can be used.
HTH
You need to show us what you have tried. Is there something about /begin regex/ or /end regex/ you're not telling us, other wise your script with the additions should work, i.e.
#!/usr/bin/awk -f
BEGIN {
FS = "\""
}
/begin regex/,/end regex/{
line="";
for (i=1; i<=NF; i++) {
if (i != 2) line=line $i;
}
split(line, v, ",");
if (v[5] ~ "FOAM") {
print NR, v[5];
}
}
OR are you using an old Unix, where there is old awk as /usr/bin/awk and New awk as /usr/bin/nawk. Also see if you have /usr/xpg4/bin/awk or gawk (path could be anything).
Finally, show us the error messages you are getting.
I hope this helps.
If I had a string with escaped commas like so:
a,b,{c\,d\,e},f,g
How might I use awk to parse that into the following items?
a
b
{c\,d\,e}
f
g
{
split($0, a, /,/)
j=1
for(i=1; i<=length(a); ++i) {
if(match(b[j], /\\$/)) {
b[j]=b[j] "," a[i]
} else {
b[++j] = a[i]
}
}
for(k=2; k<=length(b); ++k) {
print b[k]
}
}
Split into array a, using ',' as delimiter
Build array b from a, merging lines that end in '\'
Print array b (Note: Starts at 2 since first item is blank)
This solution presumes (for now) that ',' is the only character that is ever escaped with '\'--that is, there is no need to handle any \\ in the input, nor weird combinations such as \\\,\\,\\\\,,\,.
{
gsub("\\\\,", "!Q!")
n = split($0, a, ",")
for (i = 1; i <= n; ++i) {
gsub("!Q!", "\\,", a[i])
print a[i]
}
}
I don't think awk has any built-in support for something like this. Here's a solution that's not nearly as short as DigitalRoss's, but should have no danger of ever accidentally hitting your made-up string (!Q!). Since it tests with an if, you could also extend it to be careful about whether you actually have \\, at the end of your string, which should be an escaped slash, not comma.
BEGIN {
FS = ","
}
{
curfield=1
for (i=1; i<=NF; i++) {
if (substr($i,length($i)) == "\\") {
fields[curfield] = fields[curfield] substr($i,1,length($i)-1) FS
} else {
fields[curfield] = fields[curfield] $i
curfield++
}
}
nf = curfield - 1
for (i=1; i<=nf; i++) {
printf("%d: %s ",i,fields[i])
}
printf("\n")
}