BP_SEQRET(1p) User Contributed Perl Documentation BP_SEQRET(1p)NAME
bp_seqret - bioperl implementation of sequence fetch from local db (like EMBOSS seqret)
USAGE
bp_seqret [-f/--format outputformat] [-o/--out/--outfile outfile] [-d/--db dbname] [-i/--id/-s/--seqname seqname1]
Example usage:
bp_seqret -f fasta -db db.fa -i seq1 -i seq2 > output.fas
bp_seqret db.fa:seq1 output.fas
bp_seqret db.fa:seq1 -o output.fas
bp_seqret -db db.fa -o output.fas seq1 seq2 seq3
bp_seqret -db db.fa seq1 seq2 seq3 output.fas
bp_seqret -db db.fa seq1 seq2 seq3 - > output.fas
The DB is expected to be a Fasta formatted sequence file with multiple sequences.
Output format is Fasta by default.
If no output filename is provided then output is written to STDOUT. Providing '-' as the output filename will accomplish the same thing.
AUTHOR
Jason Stajich jason_AT_bioperl-dot-org
perl v5.14.2 2012-03-02 BP_SEQRET(1p)
Check Out this Related Man Page
Algorithm::DiffOld(3) User Contributed Perl Documentation Algorithm::DiffOld(3)NAME
Algorithm::DiffOld - Compute `intelligent' differences between two files / lists but use the old (<=0.59) interface.
NOTE
This has been provided as part of the Algorithm::Diff package by Ned Konz. This particular module is ONLY for people who HAVE to have the
old interface, which uses a comparison function rather than a key generating function.
Because each of the lines in one array have to be compared with each of the lines in the other array, this does M*N comparisions. This can
be very slow. I clocked it at taking 18 times as long as the stock version of Algorithm::Diff for a 4000-line file. It will get worse
quadratically as array sizes increase.
SYNOPSIS
use Algorithm::DiffOld qw(diff LCS traverse_sequences);
@lcs = LCS( @seq1, @seq2, $comparison_function );
$lcsref = LCS( @seq1, @seq2, $comparison_function );
@diffs = diff( @seq1, @seq2, $comparison_function );
traverse_sequences( @seq1, @seq2,
{ MATCH => $callback,
DISCARD_A => $callback,
DISCARD_B => $callback,
},
$comparison_function );
COMPARISON FUNCTIONS
Each of the main routines should be passed a comparison function. If you aren't passing one in, use Algorithm::Diff instead.
These functions should return a true value when two items should compare as equal.
For instance,
@lcs = LCS( @seq1, @seq2, sub { my ($a, $b) = @_; $a eq $b } );
but if that is all you're doing with your comparison function, just use Algorithm::Diff and let it do this (this is its default).
Or:
sub someFunkyComparisonFunction
{
my ($a, $b) = @_;
$a =~ m{$b};
}
@diffs = diff( @lines, @patterns, &someFunkyComparisonFunction );
which would allow you to diff an array @lines which consists of text lines with an array @patterns which consists of regular expressions.
This is actually the reason I wrote this version -- there is no way to do this with a key generation function as in the stock
Algorithm::Diff.
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