Grep only the matched values from the Input - awk

Question

I have a tab limited file as like this
chr20 102 K245 A T 56.0 AC.02 AC=0.1;DC=45;AC_old=452;DP=21;sample=kj;sample_name=DKl;New_sample=rdf
chr10 8742 JH245 G T 86.0 AC.742 AC=2.1;DC=75;AC_old=42;DP=1;sample=KHS;sample_name=WEKl;New_sample=ASEf
chrX 2302 XS245 G A 786.0 AC.452 AC=8;DC=5;AC_old=4A2;DP=5;sample=SED;sample_name=MHNSKl;New_sample=rdf
And Need to extract only AC,DC,sample as like this
chr20 102 K245 A T 56.0 AC.02 AC=0.1 DC=45 sample=kj
chr10 8742 JH245 G T 86.0 AC.742 AC=2.1 DC=75 sample=KHS
chrX 2302 XS245 G A 786.0 AC.452 AC=8 DC=5 sample=SED
I have tried with grep as like this, but not served the purpose
grep -wF "AC|DC|sample" < file.txt

Answer 1

Could you please try following, written and tested with your shown samples only in GNU awk.
awk '
match($0,/AC\.[0-9]+/){
val1=value=""
val1=substr($0,1,RSTART+RLENGTH)
num=split($NF,arr,";")
for(i=1;i<=num;i++){
if(arr[i]~/^(AC=|DC=|sample=)/){
value=(value?value OFS:"")arr[i]
}
}
print val1,value
}
' Input_file
Explanation: Adding detailed explanation for above.
awk ' ##Starting awk program from here.
match($0,/AC\.[0-9]+/){ ##using match function which matches regex AC\.[0-9]+ here.
val1=value="" ##Nullifying val1 and value here.
val1=substr($0,1,RSTART+RLENGTH) ##val1 is having sub string of matched regex.
num=split($NF,arr,";") ##Splitting last field into arr here.
for(i=1;i<=num;i++){ ##Going through all values of last field.
if(arr[i]~/^(AC=|DC=|sample=)/){ ##Checking condition if last field is either AC= OR DC= OR sample= here.
value=(value?value OFS:"")arr[i] ##Create value which has array item value in it.
}
}
print val1,value ##Printing val1 and value here.
}
' Input_file ##mentioning Input_file name here.

Answer 2

You can use
awk -F\; '$1 ~ /AC|DC|sample/{print $1 OFS $2 OFS $5}' file
Here,
-F\; sets the field separator to ;
$1 ~ /AC|DC|sample/ only takes lines having AC, DC or sample in Field 1
{print $1 OFS $2 OFS $5} - prints Field 1, 2 and 5 with spaces as separators.
See the online demo:
s='chr20 102 K245 A T 56.0 AC.02 AC=0.1;DC=45;AC_old=452;DP=21;sample=kj;sample_name=DKl;New_sample=rdf
chr10 8742 JH245 G T 86.0 AC.742 AC=2.1;DC=75;AC_old=42;DP=1;sample=KHS;sample_name=WEKl;New_sample=ASEf
chrX 2302 XS245 G A 786.0 AC.452 AC=8;DC=5;AC_old=4A2;DP=5;sample=SED;sample_name=MHNSKl;New_sample=rdf'
awk -F\; '$1 ~ /AC|DC|sample/{print $1 OFS $2 OFS $5}' <<< "$s"
Output:
chr20 102 K245 A T 56.0 AC.02 AC=0.1 DC=45 sample=kj
chr10 8742 JH245 G T 86.0 AC.742 AC=2.1 DC=75 sample=KHS
chrX 2302 XS245 G A 786.0 AC.452 AC=8 DC=5 sample=SED

Answer 3

You may use this awk:
awk -F '[\t;]+' -v OFS='\t' '{s=""; for (i=1; i<=6; ++i) s = (i == 1 ? "" : s OFS) $i; for (i=6; i<=NF; ++i) if ($i ~ /^([AD]C|sample)[=.]/) s = s OFS $i; print s}' file
chr20 102 K245 A T 56.0 AC.02 AC=0.1 DC=45 sample=kj
chr10 8742 JH245 G T 86.0 AC.742 AC=2.1 DC=75 sample=KHS
chrX 2302 XS245 G A 786.0 AC.452 AC=8 DC=5 sample=SED
A more readable version:
awk -F '[\t;]+' -v OFS='\t' '
{
s = ""
for (i=1; i<=6; ++i)
s = (i == 1 ? "" : s OFS) $i
for (i=6; i<=NF; ++i)
if ($i ~ /^([AD]C|sample)[=.]/)
s = s OFS $i
print s
}' file