Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Renaming fasta headers - string within a string issue

    Hi Everyone,

    I am in the midst of renaming some fasta headers to include the chromosomes they have been mapped to (from a tab delimited txt file). I don't have any problems setting up the hash for the scaffold and chromosome locations...the problem is that I have some short strings contained in longer strings (scaffold1 and scaffold10 and scaffold100). Usually I would add "$" to the end of my search term (/scaffold1$/) and thereby indicate the end of the search string, but I'm not sure how to make use of this when the search term is a variable ($hash{$scaff/$/}). Advice?

    Below is my script so far...and TIA!

    Code:
    #!/bin/bash/perl
    #mod-header2include-chrom.pl
    #This script is intended to read in a fasta file and a tab-delimited file and use the information from the tab-delimited file to modify the header.
    #In this case, we are appending to the header (e.g. "scaffold671") the chromosome to which it has been mapped and the number of genes on this scaffold.
    
    use strict;
    use warnings;
    
    open (DATA, "<genome-assoc-chromosomes.txt") or die "Could not open genome chromosome mapping data: $!\n";
    open (FASTA, "<scafSeq.FG.fill") or die "Could not open Fasta file: $!\n";
    
    my %hash;
    
    while (<DATA>)
    {
    chomp;
    if ($_ =~ "scafold"){ #skip header - scafold is spelled incorrectly on purpose;
    next;
    }
    else {
    my ($key, $chrom, $len, $gene) = split /\t/;
    $hash{$key} = $chrom;
    }
    }
    
    while (<FASTA>){
    
    my $line = $_;
    chomp ($line);
    if ( defined $hash{$line} ) {
    print "$line-$hash{$line}";
    }
    else { print $line; }
    
    }

  • #2
    Hi,
    Kindly upload a sample of both files (scafSeq.FG.fill and genome-assoc-chromosomes.txt). Without the fasta file, I am wondering how the following:
    while (<FASTA>){
    my $line = $_;
    chomp ($line);
    if ( defined $hash{$line} ) {


    reads in the header line with ">" from "<scafSeq.FG.fill"

    does the variable $key in "$hash{$key} = $chrom;" contain ">"?

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM
    • seqadmin
      Techniques and Challenges in Conservation Genomics
      by seqadmin



      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

      Avian Conservation
      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
      03-08-2024, 10:41 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 06:37 PM
    0 responses
    11 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    51 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    67 views
    0 likes
    Last Post seqadmin  
    Working...
    X