[Bioperl-l] Very basic Perl/BioPerl Help

Terry Jones tcj25 at cam.ac.uk
Thu Apr 14 11:49:29 EDT 2005

| What I am trying to do is take either A) Two fasta files with
| refseq/genbank data OR B) Two text files with 1 accession# per line
| and compare them, outputting only those fasta seqs or accession #'s
| that are not present in both.
| So is it easier to just use perl somehow to compare the two raw acc#
| text files?

If your files do not contain repeat lines, you can do this from the
raw acc# text files in various ways. If you're using some form of
UNIX, you can do this on the command line:

  $ cat file1 file2 | sort | uniq -c | egrep '^ *1        ' | cut -f2 | sort

Note that there's a TAB in the egrep expression (between the 1 and the ').
Another way is to use comm

  $ sort file1 > file1.sorted
  $ sort file2 > file2.sorted
  $ comm -3 file1.sorted file2.sorted

You can guarantee that your input files do not have duplicates via

$ sort -u -i file1 > file1.sorted

This is all outside perl. In perl you could do something like

open(F1, "file1") || die "could not open file1 ($!)";
open(F2, "file2") || die "could not open file2 ($!)";

my %names;

while (<F1>){

while (<F2>){

close(F1) || die "could not close file1 ($!)";
close(F2) || die "could not close file2 ($!)";

my @not_in_both = grep { $names{$_} == 1 } keys %names;

Again, this relies on names only being present once in each file.  You
could code around this requirement in your perl if you wanted, by
doing more checking of the input.


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