Perl script for extracting different genes information from gff file

Question

[adeena_hassan]

Assalam o alaikum everyone

I have to write a perl script which extract genes information from annotation files (gff). I have gff files of different genomes downloaded from NCBI and two txt files 1 of them contains full path of gff files and 2nd contains list of genes which information have to extract from annotation files.. Actually i have extracted this information through grep command but now i have to write a perl script for this I'm newin perl kindly guide me how to do so ????

Thanks in advance :)

$ cat annotation_files_path

~/home/usr/NCBI_Mammals_genomes/Nine_banded_armadillo/

~/home/usr/NCBI_Mammals_genomes/Noth_American_deer_mouse/

~/home/usr/NCBI_Mammals_genomes/Northern_mole_vole/

$ cat Genes_list

acmsd

smo

amy2b

[st.ph.n]

Since you say you 'have' to write a perl script, have you tried any code? No one should write something for you if this is homework. That's not the purpose of this site. However, if you post a snippet of your code with an error message that you're having trouble with, someone can give you helpful hints.

[cpad0112]

if you have to write perl code, then below perl code by Alex may work. If you are a bioinformatician, you can use perl module for intersection: http://search.cpan.org/~cjfields/BioPerl-Run/lib/Bio/Tools/Run/BEDTools.pm

Answer 1

[Alex Reynolds]

system("grep -f genes_list.txt some_annotations.gff > answer.gff");

Or:

#
# read genes into array
#
my @genes = [];
my $genesFn = "genes_list.txt";
open my $genesFh, "<", $genesFn or die "could not open genes file handle!\n";
while (<$genesFh>) {
    chomp;
    push @genes, $_;
}
close $genesFh;

#
# build a regular expression pattern from genes
#
my $regex = sprintf('(%s)', join ('|', @genes));

#
# write any matches between annotation line and pattern to results file
#
my $annotationsFn = "some_annotations.gff";
my $resultsFn = "answer.gff";
open my $annotationsFh, "<", $annotationsFn or die "could not open annotations file handle!\n";
open my $resultsFh, ">", $resultsFn or die "could not open handle to results file!\n";
while (<$annotationsFh>) {
    chomp;
    if ($_ =~ /$regex/) {
        print $resultsFh "$_\n";
    }
}
close $resultsFh;
close $annotationsFh;

[adeena_hassan]

Thank u so much ,, its so helpful previously i even don't know the direction ,,,

Actually in the output of this code whole annotation file comes after a small editing it gives genes information in the single file ,,

my $annotationsFn = "GCF_000298275.1_OryAfe1.0_genomic.gff"; my $resultsFn = "answer.gff"; open my $annotationsFh, "<", $annotationsFn or die "could not open annotations file handle!\n"; open my $resultsFh, ">", $resultsFn or die "could not open handle to results file!\n"; while (<$annotationsFh>) { chomp; if ($_ =~ /ACMSD/ || $_ =~ /CRYM/ || $_ =~ /ARID1B/ ) { print $resultsFh " $_\n";

I have two problems now first one is that all genes information come in a single file but i want different output file for different genes ,, for this i tried for loop but it did not work ,,

and second and major problem is that i have to work on about 150 annotation files and in annotation_file_path.txt i gave complete path of all annotation files but failed to execute it because script only work when a single annotation file use as shown above otherwise it print whole annotation _file_path.txt ,,, is there any way to iterate each path of annotation_file.txt one by one ??? kindly guide me ???

p.s i'm a beginner so happy to give me more info ....

[Alex Reynolds]

Look up arrays and looping over elements in an array.