Processing input from one or more files

Perl allows very fine control about how to process and combine input from multiple files. Unfortunately, the code becomes a bit more complexes, pushing it to the limit of one-liners.

1. Add columns with minimum and maximum value for each row in a tab-delimited text file:
   

   perl -MRegexp::Common -F"\t" -lane '@vals = (); foreach (@F) { push @vals, $_ if (/^$RE{num}{real}$/)} @vals = (sort { $a <=> $b } @vals); print "$_\t$vals[0]\t$vals[-1]"' input > output
   
   

2. Report frequency of elements in the third column (index 2) of a tab-delimited text file:
   

   perl -F"\t" -lane '$freq{$F[2]}++; END {foreach (sort keys %freq) {print "$_ -> $freq{$_}";}}' input
   
   

3. Print the different flags set in a BAM file and how many entries are associated with it. This could be used to check if there is an even number of reads mapping to both strands:
   

   samtools view bam_file | perl -lne '@h = split "\t", $_; $f{$h[1]}++; END { foreach (sort keys %f) { print "$_\t$f{$_}";}}'
   
   

4. Read files with gene IDs and report in decreasing order in how many files each ID is found:
   

   perl -e 'foreach (@ARGV) {open (IN, $_); while (<IN>) {chomp; $in{$_}++;}} foreach (sort { $in{$a} <=> $in{$b} } keys %in) { print "$_ -> $in{$_}\n";}' file*
   
   

5. Print the reverse complement of all sequences in a fasta file:
   

   perl -lne 'if (/>/) {$h = $_} else {$in{$h} .= $_;} END { foreach (sort keys %in) { $s = lc reverse $in{$_}; $s =~ tr/acgt/tgca/; print "$_\n$s"}}' input > output
   
   

6. Extract a sub-sequence (50 basepairs at position 1000) from a file with a single fasta sequence:
   

   perl -lne 'next if (/^>/); $s .= $_; END { print(substr $s, 1000-1, 50) }' input
   
   try it out with an example input file
   

7. Report input lines that differ in their first element between two files:
   

   perl -e '$f1 = shift; open (IN, $f1); while (<IN>) {@h = split; $f1{$h[0]}++;} close IN; $f2 = shift; open (IN, $f2); while (<IN>) {@h = split; $f1{$h[0]}--;} foreach (sort keys %f1) { print "$_ -> $f1{$_}\n" if ($f1{$_})}' file1 file2 > diff.txt
   Lines only found in the first file will be printed with a value of 1, lines only in the second with a value of -1.
   
   

8. Use a file of IDs to filter lines from another file and report IDs that were not found:
   

   perl -e '$f = shift; open (IN, $f); while (<IN>) {@h = split; $f{$h[0]}++;} close IN; $f = shift; open (IN, $f); while (<IN>) {chomp; @h = split; if (defined $f{$h[0]}) {print "$_\n"; $f{$h[0]} = 0}} foreach (sort keys %f) {print STDERR "not found: $_\n" if ($f{$_})}' filter_file input > output
   

   
9. Combine two files using IDs from first column as key:
   

   perl -e 'foreach $f (@ARGV) {open (IN, $f); while (<IN>) {chomp; @h = split /\t/, $_; $in{$h[0]}{$f} = $_; } close IN; } foreach (sort keys %in) { print "$in{$_}{$ARGV[0]}\t$in{$_}{$ARGV[1]}\n";}' input1 input2 > combined
   

   
10. Print all palindromes of length 15 found in a sequence file using a sliding window approach:
    

    perl -lne '$in .= $_; END {foreach (0..length($in)-15) { $t = substr $in, $_, 15; print "$i_: $t" if ($t eq reverse($t)) } }' input