CODEWITHSUNDEEP
bashawkgrep
user11005312
user11005312

Reputation:

replace content of a column by the content of a variable

my final goal is to replace, for each line of the GQPDOMB_impute_copie.vcf file, the info column (column 8 of the GQPDOMB_impute_copie.vcf file) by the contents of columns 2 and 3 of the formatting.txt file:

That's my idea:

For each line of the GQPDOMB_impute_copie.vcf file
do 
    the variable rs retrieves the rsID of the current line in column 3 of the GQPDOMB_impute_copie.vcf file
    The variable VAR1 searches for the content of the variable rs in the formatting.txt file for each line
    if the variable is not empty (the content of rs for this line has been found in the formatting.txt file)
    so
        the ra variable recovers the contents of columns 2 and 3 of the formatting.txt file
        The content of column 8 of the current row is replaced by the content of the variable ra (which contains the information contained in columns 2 and 3 of formatting.txt)
    fi
done

GQPDOMB_impute_copie.vcf :

##fileformat=VCFv4.3
1   783071  rs142849724 C   T   .   PASS    TYPED;RefPanelAF=0.018571;AN=80;AC=5;INFO=1 GT  0|0 0|0 1|0 0|0 1|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|1 0|0 0|0 0|0
1   783186  rs141989890 G   C   .   PASS    RefPanelAF=0.000323375;AN=80;AC=0;INFO=1    GT  0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0
1   783632  rs193023236 G   A   .   PASS    RefPanelAF=0.00040037;AN=80;AC=0;INFO=1 GT  0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0

formating.txt : 

rs142849724;ENSG00000228794;ENST00000624927|ENST00000623808|ENST00000445118|ENST00000448975|ENST00000610067|ENST00000608189|ENST00000609139|ENST00000449005|ENST00000416570|ENST00000623070|ENST00000609009|ENST00000622921
rs141989890;ENSG00000228794;ENST00000624927|ENST00000623808|ENST00000445118|ENST00000448975|ENST00000610067|ENST00000608189|ENST00000609139|ENST00000449005|ENST00000416570|ENST00000623070|ENST00000609009|ENST00000622921
rs193023236;ENSG00000228794;ENST00000624927|ENST00000623808|ENST00000445118|ENST00000448975|ENST00000610067|ENST00000608189|ENST00000609139|ENST00000449005|ENST00000416570|ENST00000623070|ENST00000609009|ENST00000622921

After a lot of research on the internet, here is the code I can offer you:

#!/bin/bash

while read line
do
   rs=$(awk -F '\t' '{print $3}' GQPDOMB_impute_copie.vcf)     #recovery rsID
   VAR1=$(grep "${rs}" formating.txt)      #we check if the rsID of the current line is found in the file formatting.txt
   if [ -n "$VAR1" ] ;     #if the rsID of the current line has been found
   then
       ra=$(grep "${rs}" formating.txt | awk -F ';' '{print $2,";",$3}')   #recovery of the contents of columns 2 and 3 of the formating.txt file in the same vaiable  
       awk -F '\t' -v t="\"$ra\"" '{$8=t; print }' OFS='\t' GQPDOMB_impute_copie.vcf   #replace the content of the column 8 (info) with the content of the prévious var
   fi
done < GQPDOMB_impute_copie.vcf

However, I think the program does not read the vcf file line by line and does not succeed in creating the variable VAR1. Here is the error that was returned to me:

./script-info.sh: line 16: /usr/bin/grep: Argument list too long
./script-info.sh: line 16: /usr/bin/grep: Argument list too long
./script-info.sh: line 16: /usr/bin/grep: Argument list too long

How to succeed in creating this script and if possible as efficiently as possible?

I thank you for that.

Edit : As you wish, here is how I would like to recover my output file :

##fileformat=VCFv4.3
1   783071  rs142849724 C   T   .   PASS    ENSG00000228794;ENST00000624927|ENST00000623808|ENST00000445118|ENST00000448975|ENST00000610067|ENST00000608189|ENST00000609139|ENST00000449005|ENST00000416570|ENST00000623070|ENST00000609009|ENST00000622921
 GT  0|0 0|0 1|0 0|0 1|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|1 0|0 0|0 0|0 0|1 0|0 0|0 0|0
1   783186  rs141989890 G   C   .   PASS    ENSG00000228794;ENST00000624927|ENST00000623808|ENST00000445118|ENST00000448975|ENST00000610067|ENST00000608189|ENST00000609139|ENST00000449005|ENST00000416570|ENST00000623070|ENST00000609009|ENST00000622921    GT  0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0
1   783632  rs193023236 G   A   .   PASS    ENSG00000228794;ENST00000624927|ENST00000623808|ENST00000445118|ENST00000448975|ENST00000610067|ENST00000608189|ENST00000609139|ENST00000449005|ENST00000416570|ENST00000623070|ENST00000609009|ENST00000622921 GT  0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0

Upvotes: 0

Views: 239

Answers (1)

Ed Morton
Ed Morton

Reputation: 203645

Without showing us the expected output we're guessing at what you want but maybe this is it:

$ cat tst.awk
BEGIN   { FS=";" }
NR==FNR { val[$1] = $2 FS $3; next }
FNR==1  { FS=OFS="\t"; $0=$0 }
!/^#/   { $8 = ($3 in val ? val[$3] : $8) }
{ print }

$ awk -f tst.awk formatting.txt GQPDOMB_impute_copie.vcf
##fileformat=VCFv4.3
1       783071  rs142849724     C       T       .       PASS    ENSG00000228794;ENST00000624927|ENST00000623808|ENST00000445118|ENST00000448975|ENST00000610067|ENST00000608189|ENST00000609139|ENST00000449005|ENST00000416570|ENST00000623070|ENST00000609009|ENST00000622921 GT      0|0     0|0     1|0     0|0     1|0     0|0     0|0     0|0     0|0     0|1     0|0     0|00|0      0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|00|0      0|0     0|0     0|0     0|1     0|0     0|0     0|0     0|1     0|0     0|0     0|0
1       783186  rs141989890     G       C       .       PASS    ENSG00000228794;ENST00000624927|ENST00000623808|ENST00000445118|ENST00000448975|ENST00000610067|ENST00000608189|ENST00000609139|ENST00000449005|ENST00000416570|ENST00000623070|ENST00000609009|ENST00000622921 GT      0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|00|0      0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|00|0      0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0
1       783632  rs193023236     G       A       .       PASS    ENSG00000228794;ENST00000624927|ENST00000623808|ENST00000445118|ENST00000448975|ENST00000610067|ENST00000608189|ENST00000609139|ENST00000449005|ENST00000416570|ENST00000623070|ENST00000609009|ENST00000622921 GT      0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|00|0      0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|00|0      0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0

Upvotes: 2

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