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Top Forums UNIX for Beginners Questions & Answers How to count the length of fasta sequences? Post 303033663 by dineshkumarsrk on Wednesday 10th of April 2019 05:43:26 AM
Old 04-10-2019
is it possible to print the order as same as id.txt. The command works fine, but the order has been changed. For example, id.txt file listed the headers as follows,
Code:
seq1
seq2

Where as my unique.fasta file has the sequences in the following order,
Code:
>seq2
ATGCTTA
>seq1
GCTAGT

But, the command print seq2 length first followed by seq1 as shown below.
Code:
seq2     7
seq1      6

Therefore, is it possible to keep the order as same as id.txt.

--- Post updated at 09:43 AM ---

Dear singh,
Is it possible to print the order as same as id.txt. The command works fine, but the order has been changed. For example, id.txt file listed the headers as follows,
Code:
seq1
seq2

Whereas, my unique.fasta file has the sequences in the following order,
Code:
>seq2
ATGCTTA
>seq1
GCTAGT

But, the command print seq2 length first followed by seq1 as shown below.
Code:
seq2     7
seq1    6

Therefore, is it possible to keep the order as same as id.txt.
 

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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 v5.16.2 2006-07-30 Algorithm::DiffOld(3)
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