3

I have a large file with the following format tab-separated:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  recombination
chr1    586001  >63041388>63041391      G       A       60      .       AC=80;AF=0.3125;AN=256;AT=>63041388>63041390>63041391,>63041388>63041389>63041391;NS=3;LV=0     GT    1|2|3|

Now, the last column the 10th one appears as many numbers divided by a pipe |; however, what I wish to achieve is the following:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  recombination
chr1    586001  >63041388>63041391      G       A       60      .       AC=80;AF=0.3125;AN=256;AT=>63041388>63041390>63041391,>63041388>63041389>63041391;NS=3;LV=0     GT    1|1    2|2    3|3

I managed to separate the columns with tab by replacing the | symbol, that leaves me with how to duplicate them and add back the | between numbers. I attempted few times with for loops but the best I can do is printing only two columns as such:

1    1
2    2
3    3
...

otherwise with printf I get a one-line output but cannot keep the counter the same value of the initial column... Any help is much appreciated, thanks in advance!

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1
  • Is the column you're trying to modify always the last one? Thx. Commented Feb 2 at 7:47

3 Answers 3

Reset to default
5

This should do it:

awk -F '\t' -v OFS='\t' '
    /^[^#]/{
     gsub("\\|","\t",$10)
     gsub("[0-9]+","&|&\t",$10) 
    }
   1' file.vcf

Explanation

  • awk -F '\t' -v OFS='\t': set the input (-F '\t') and output (-v OFS='\t') field separators to a tab.
  • /^[^#]/{ ... }: on lines that do not start with a #, i.e. non-header lines.
  • gsub("\\|","\t",$10);: replace all | in the 10th field with tabs.
  • gsub("[0-9]+","&|&\t",$10): now replace all sets of digits with themselves (& is replaced by whatever was matched), a | and then themselves again and a tab. /^[^#]/{ ... }1': the default action of awk when something evaluates to true is to print the current record (line), so this 1, which always evaluates to true (non-0) and is outside the /^[^#]/{} conditional, will print every line.

This is what it looks like on your data (showing only the first few fields for clarity):

$ awk -F '\t' -v OFS='\t' '/^[^#]/{gsub("\\|","\t",$10); gsub("[0-9]+","&|&\t",$10) }1' file.vcf | cut -f 1-50
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  recombination
chr1    586001  >63041388>63041391  G   A   60  .   AC=80;AF=0.3125;AN=256;AT=>63041388>63041390>63041391,>63041388>63041389>63041391;NS=3;LV=0 GT  1|1     2|2     3|3     4|4     5|5     6|6     7|7     8|8     9|9     10|10       11|11       12|12       13|13       14|14       15|15       16|16       17|17       18|18       19|19       20|20       21|21

Note that this is not a valid VCF and you will also need to have a sample name on the #CHROM header for each genotype listed so that tools designed to consume VCFs can deal with it correctly.

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2
  • many thanks, I could manage to get to point 3, but I didn't know about that use of gsub and &. Indeed, is very clever and possibly better than a loop; also, thanks a lot for the detailed explanation Commented Nov 25, 2024 at 14:03
  • -F '\t' -v OFS='\t' is not in the code at the top of the answer. Commented Nov 26, 2024 at 15:41
3

Using awk:

$ awk -F '\t' -v OFS='\t' '
          !/^#/{
          split($10,a,/\|/);
          for(i=1;i in a;i++) $10 = (i==1 ? "" : $10 OFS) a[i]"|"a[i]
        }1'
  • Input -Field separator and OFS Output Field Separator are set to \tab.
  • Field $10 is split to array by p|pe as sep.
  • Thereafter $10 is recreated using for loop. There in no need to find number of elements of array i.e.,n=split(..). When for loop is used as for(i=1;i in a;i++) then i in a would take care of number of elements of an array. ( Thanks to @EdMorton).
  • 1 is true always that prints the current record. In fact, anything is truth but empty string or zero.
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0

Using Raku (formerly known as Perl_6)

~$ raku -ne '
   BEGIN  sub infix:<J> ($x,$y) { join "|", $x, $y }  andthen  put get; 
   .flip.split(/ \t /, 2)  andthen  \
   put "{.[1].flip} ", join "\t", [ZJ] .[0].flip.split("|", :skip-empty) xx 2;'  file

Above is an answer written in Raku, a member of the Perl-family of programming languages. Raku limits the number of command line flags, so code you write is more portable to stand-alone scripts. Raku also features real subroutine signatures, so you can define new functions on-the-fly.

Above, the -ne linewise non-autoprinting (awk-like) command line flags are used. We BEGIN (invoke once) by creating a new infix operator J, which joins text on | vertical-bar character. In order to output the header line, we simply put get (get is short for get-line, as opposed to getc for get-character). Note, you could write something like if ++$ == 1 {.put && next}; to output the header line instead.

In the body of the loop, since the column-of-interest is the last one (column 10 of 10), the input line is .flipped and then .split on TAB characters into 2 pieces only. Once this is accomplished we load the line elements into $_ a localized topic variable using andthen, which lets us continue our text manipulation.

We start by outputting columns 1-thru-9 (i.e. .[1] element from the split operation), flipping them back so they read correctly. Finally for column 10 (i.e. .[0] element from the split operation), we .flip back, then .split on | vertical-bar, making sure to :skip-empty strings created. We then xx 2 make two copies, and [ZJ] Zip-join these copies together using the | vertical-bar character, again joining on TAB to complete the manipulation.

Sample Input:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  recombination
chr1    586001  >63041388>63041391  G   A   60  .   AC=80;AF=0.3125;AN=256;AT=>63041388>63041390>63041391,>63041388>63041389>63041391;NS=3;LV=0 GT  1|2|3|

Sample Output:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  recombination
chr1    586001  >63041388>63041391  G   A   60  .   AC=80;AF=0.3125;AN=256;AT=>63041388>63041390>63041391,>63041388>63041389>63041391;NS=3;LV=0 GT  1|1    2|2    3|3

https://raku.org

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