3

I have a very similar problem to this question, but have no idea how to adapt the answer to my own issue.

I have a tab-sep file with 2nd column containing comma-sep list, such as:

TRINITY_DN1_c0_g1   DN1_c0_g1   GO:0000166,GO:0003674,GO:0005488,GO:0005515,GO:0005524,GO:0005575
TRINITY_DN1_c0_g3   DN1_c0_g3   GO:0005829,GO:0006457,GO:0006458,GO:0006950,GO:0008134
TRINITY_DN10_c0_g1  DN10_c0_g1  GO:0050896,GO:0051082,GO:0051084,GO:0051085

I want to get it to this:

TRINITY_DN1_c0_g1   DN1_c0_g1   GO:0000166
TRINITY_DN1_c0_g1   DN1_c0_g1   GO:0003674
TRINITY_DN1_c0_g1   DN1_c0_g1   GO:0005488
TRINITY_DN1_c0_g1   DN1_c0_g1   GO:0005515
TRINITY_DN1_c0_g1   DN1_c0_g1   GO:0005524
TRINITY_DN1_c0_g1   DN1_c0_g1   GO:0005575
TRINITY_DN1_c0_g3   DN1_c0_g3   GO:0005829
TRINITY_DN1_c0_g3   DN1_c0_g3   GO:0006457
TRINITY_DN1_c0_g3   DN1_c0_g3   GO:0006458
TRINITY_DN1_c0_g3   DN1_c0_g3   GO:0006950
TRINITY_DN1_c0_g3   DN1_c0_g3   GO:0008134
TRINITY_DN10_c0_g1  DN10_c0_g1  GO:0050896
TRINITY_DN10_c0_g1  DN10_c0_g1  GO:0051082
TRINITY_DN10_c0_g1  DN10_c0_g1  GO:0051084
TRINITY_DN10_c0_g1  DN10_c0_g1  GO:0051085

There is a variable number of terms in the 3rd column. I need a separate line for each with it's associated 1st and 2nd column.

If any help, the starting one liner from above questions is:

perl -lne 'if(/^(.*?: )(.*?)(\W*)$/){print"$1$_$3"for split/, /,$2}'

But I have no idea which bits needs to be changed to work for my issue!

Many thanks in advance for help.

2
  • Are you positive there are tabs in your input file, and not sequences of spaces? – glenn jackman Apr 13 at 16:15
  • 1
    Can you provide us the output of the command: cat -A yourfile ? That will show what kind of line ndings are there. – guest_7 Apr 13 at 16:26
3

This awk command is quite readable:

awk '
  BEGIN {FS = "[,\t]"; OFS = "\t"}
  {for (i=3; i<=NF; i++) print $1, $2, $i}
' file

In perl, this is

perl -F'[,\t]' -lane 'print join "\t", @F[0,1], $F[$_] for 2..$#F' file
# or
perl -F'[,\t]' -slane 'print @F[0,1], $F[$_] for 2..$#F' -- -,=$'\t' file

If you're not sure you have actual tab characters:

  • awk: FS = ",|[[:blank:]]+"
  • perl: -F',|\s+'

And for fun, bash

while IFS= read -r line; do
    prefix=${line%%GO:*}
    IFS=, read -ra gos <<< "${line#$prefix}"
    for go in "${gos[@]}"; do echo "$prefix$go"; done
done < file

This version doesn't care about spaces versus tabs, but it will be much slower than perl or awk.

3
  • Thanks @glenn-jackman but both is giving 3 GO:xxx columns, the first two are repeats of first 2 terms in comma-sep list and 3rd is working way through rest. I need each line to only have one GO:xxx. Definitely tab-separated columns. – AmyE Apr 13 at 16:17
  • I don't know what to tell you except I don't believe you have tabs in the input file. I can reproduce what you're seeing with expand file | awk ... – glenn jackman Apr 13 at 16:22
  • 1
    Oh damn... you were right. Mi real (very big) file is tab-delim. My mocked up one to test your answers was not. My sincere apologies for wasting your time - it works like a charm! – AmyE Apr 13 at 16:24
3

Use the -a switch to get each line split into the @F array on whitespace.

perl -lane 'print join "\t", @F[0, 1], $_ for split /,/, $F[2]'
4
  • Thanks for speedy reply! But this outputting nothing :( – AmyE Apr 13 at 16:18
  • It works for me. Did you provide the input file as the last argument? – choroba Apr 13 at 16:19
  • As above, my mistake in test file I was using was not actually tab-delim. Sorry this works too! – AmyE Apr 13 at 16:27
  • 1
    The -a splits on any whitespace, tabs or spaces. – choroba Apr 13 at 16:30
1

Another option here is the nest --explode action of Miller

mlr --nidx --fs tab nest --explode --values --across-records --nested-fs ',' -f 3 file

or using the shorthand nest specifier

mlr --nidx --fs tab nest --evar ',' -f 3 file
0

Using GNU sed which has [\n\t] regex features we can do as shown:

sed -n '
  y/,/\n/
  :a
      P; s/\t[^\n\t]*\n/\t/
  ta
'  file

You can do it using perl also

perl -F'(\t)' -pale '$"="";
  $_ = pop(@F) =~ tr/,/\n/r =~ s/^/@F/mgr;
' file

One method with Perl is shown here. $a scalar holds the first two fields and then the search begins in the while loop from where it was left off due to the /c modifier.

perl -lne '
  my($a) = /^((?:.*?\t){2})/gc;
  print $a, $1 while /\G([^,]+)(?:,|$)/g;
' file

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