Sponsored Content
Top Forums UNIX for Beginners Questions & Answers How to count the length of fasta sequences? Post 303033623 by dineshkumarsrk on Tuesday 9th of April 2019 09:04:53 AM
Old 04-09-2019
I have a multi fasta sequences in unique.fasta as given below,
Code:
>seq1
ATGCTA
>seq2
GCTAGTT
>seq3
TAGC

I need to count the length of following header's listed in id.txt as given below,
Code:
seq1
seq2

And the results(length) to be printed in csv file as shown below,
Code:
seq1   6
seq2   7

Moderator's Comments:
Mod Comment Changed QUOTE tags to CODE tags for sample Input_file.

Last edited by RavinderSingh13; 04-09-2019 at 10:16 AM..
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Extract length wise sequences from fastq file

I have a fastq file from small RNA sequencing with sequence lengths between 15 - 30. I wanted to filter sequence lengths between 21-25 and write to another fastq file. how can i do that? (4 Replies)
Discussion started by: empyrean
4 Replies

2. Shell Programming and Scripting

Shell script for changing the accession number of DNA sequences in a FASTA file

Hi, I am having a file of dna sequences in fasta format which look like this: >admin_1_45 atatagcaga >admin_1_46 atatagcagaatatatat with many such thousands of sequences in a single file. I want to the replace the accession Id "admin_1_45" similarly in following sequences to... (5 Replies)
Discussion started by: margarita
5 Replies

3. Shell Programming and Scripting

Extract sequences from a FASTA file based on another file

I have two files. File1 is shown below. >153L:B|PDBID|CHAIN|SEQUENCE RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM DIGTTHDDYANDVVARAQYYKQHGY >16VP:A|PDBID|CHAIN|SEQUENCE... (7 Replies)
Discussion started by: nelsonfrans
7 Replies

4. Shell Programming and Scripting

Count and search by sequence in multiple fasta file

Hello, I have 10 fasta files with sequenced reads information with read sizes from 15 - 35 . I have combined the reads and collapsed in to unique reads and filtered for sizes 18 - 26 bp long unique reads. Now i wanted to count each unique read appearance in all the fasta files and make a table... (5 Replies)
Discussion started by: empyrean
5 Replies

5. Shell Programming and Scripting

Shorten header of protein sequences in fasta file

I have a fasta file as follows >sp|O15090|FABP4_HUMAN Fatty acid-binding protein, adipocyte OS=Homo sapiens GN=FABP4 PE=1 SV=3 MCDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDVITIKSESTFKN TEISFILGQEFDEVTADDRKVKSTITLDGGVLVHVQKWDGKSTTIKRKREDDKLVVECVM KGVTSTRVYERA >sp|L18484|AP2A2_RAT AP-2... (3 Replies)
Discussion started by: alexypaul
3 Replies

6. UNIX for Dummies Questions & Answers

Select distinct sequences from fasta file and list

Hi How can I extract sequences from a fasta file with respect a certain criteria? The beginning of my file (containing in total more than 1000 sequences) looks like this: >H8V34IS02I59VP SDACNDLTIALLQIAREVRVCNPTFSFRWHPQVKDEVMRECFDCIRQGLG YPSMRNDPILIANCMNWHGHPLEEARQWVHQACMSPCPSTKHGFQPFRMA... (6 Replies)
Discussion started by: Marion MPI
6 Replies

7. Shell Programming and Scripting

Getting unique sequences from multiple fasta file

Hi, I have a fasta file with multiple sequences. How can i get only unique sequences from the file. For example my_file.fasta >seq1 TCTCAAAGAAAGCTGTGCTGCATACTGTACAAAACTTTGTCTGGAGAGATGGAGAATCTCATTGACTTTACAGGTGTGGACGGTCTTCAGAGATGGCTCAAGCTAACATTCCCTGACACACCTATAGGGAAAGAGCTAAC >seq2... (3 Replies)
Discussion started by: Ibk
3 Replies

8. Shell Programming and Scripting

Outputting sequences based on length with sed

I have this file: >ID1 AA >ID2 TTTTTT >ID-3 AAAAAAAAA >ID4 TTTTTTGGAGATCAGTAGCAGATGACAG-GGGGG-TGCACCCC Add I am trying to use this script to output sequences longer than 15 characters: sed -r '/^>/N;{/^.{,15}$/d}' The desire output would be this: >ID4... (8 Replies)
Discussion started by: Xterra
8 Replies

9. Shell Programming and Scripting

Shorten header of protein sequences in fasta file to only organism name

I have a fasta file as follows >sp|Q8WWQ8|STAB2_HUMAN Stabilin-2 OS=Homo sapiens OX=9606 GN=STAB2 PE=1 SV=3 MMLQHLVIFCLGLVVQNFCSPAETTGQARRCDRKSLLTIRTECRSCALNLGVKCPDGYTM ITSGSVGVRDCRYTFEVRTYSLSLPGCRHICRKDYLQPRCCPGRWGPDCIECPGGAGSPC NGRGSCAEGMEGNGTCSCQEGFGGTACETCADDNLFGPSCSSVCNCVHGVCNSGLDGDGT... (3 Replies)
Discussion started by: jerrild
3 Replies

10. UNIX for Beginners Questions & Answers

How to add specific bases at the beginning and ending of all the fasta sequences?

Hi, I have to add 7 bases of specific nucleotide at the beginning and ending of all the fasta sequences of a file. For example, I have a multi fasta file namely test.fasta as given below test.fasta >TalAA18_Xoo_CIAT_NZ_CP033194.1:_2936369-2939570:+1... (1 Reply)
Discussion started by: dineshkumarsrk
1 Replies
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 v5.18.2 2006-07-30 Algorithm::DiffOld(3)
All times are GMT -4. The time now is 01:58 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy