james.v has asked for the wisdom of the Perl Monks concerning the following question:

Hi all,

I am trying to alter this script:

 perl -lne '/>/ && do {print $c if defined $c; $c = 0; print} || $c++; END {print $c}' input_file > output_file

In order to make the output counts for only unique lines that are between lines starting with '>'

Currently this script works well in generating overall counts of the lines that are between lines that begin with '>'

Example input_file: 
>05143_African_trypanosomiasis
TRINITY_DN26760_c1_g1
18169
42987
42987
>05145_Toxoplasmosis
43736
38319
38320
38320
TRINITY_DN24151_c3_g1
TRINITY_DN25493_c0_g1

[download]
Example of output_file: 
>05143_African_trypanosomiasis
4
>05145_Toxoplasmosis
6

[download]
Example of desired output: 
>05143_African_trypanosomiasis
3
>05145_Toxoplasmosis
5

[download]

I'm also very new to perl so an explanation of the tweaked code would be much appreciated.

-James

Replies are listed 'Best First'.
Re: Getting unique line counts between lines starting with '>'
by choroba (Cardinal) on Oct 19, 2017 at 21:34 UTC
    Use a hash of the lines, keys of a hash are always unique.

    perl -lne 'sub out {print $h, "\n", scalar keys %c if %c }
           />/ and do { out(); %c =(); $h = $_ }
               or $c{$_}++;
           END { out() }' < input-file

    [download]
    ($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,

    [download]
[reply]
[d/l]
[select]

      A quick question. Is there a way to get the keys of the %s hash to be printed in a comma-delimited list?

      For example: 

      >05143_African_trypanosomiasis
3
TRINITY_DN26760_c1_g1, 18169, 42987
>05145_Toxoplasmosis
5
43736, 38319, 38320, TRINITY_DN24151_c3_g1, TRINITY_DN25493_c0_g1

      [download]

      best,

      James

[reply]
[d/l]
        Update: Corrected for Comma-separated numbers. 
        $ perl -lne 'sub prt{@c && print scalar @c,"\n",join ", ",@c;@c=();pri
+nt} />/?prt:push @c,$_}{prt'  TheFileName

        [download]
        output 
        >05143_African_trypanosomiasis
4
TRINITY_DN26760_c1_g1, 18169, 42987, 42987
>05145_Toxoplasmosis
7
43736, 38319, 38320, 38320, TRINITY_DN24151_c3_g1, TRINITY_DN25493_c0_
+g1

        [download]
        For info on "}{", see "Eskimo greeting" in perlsecret.

                        All power corrupts, but we need electricity.

[reply]
[d/l]
[select]

      Thank you for the help Choroba, works like a charm!

      best,

      James

[reply]

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