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Top Forums UNIX for Beginners Questions & Answers How to count the length of fasta sequences? Post 303033657 by RudiC on Wednesday 10th of April 2019 03:26:48 AM
Old 04-10-2019
If - as specified - you want the sequences in id.txt ONLY, amend scrutinizer's proposal like
Code:
awk 'FNR == NR {T[$1]; next} $1 in T {print $1, length($2)}' id.txt FS='\n' RS=\> OFS='\t' unique.fasta
seq1    6
seq2    7

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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. perl v5.16.3 2006-07-31 Algorithm::DiffOld(3)
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