Extract Intergenic Sequences from GenBank File with Perl

Question

[Diesel]

Hi,

I need help; I need to use perl, possibly Bioperl, to extract the intergenic regions from a genbank file (.gb). The organism is B.subtilis strain 168.

Is there something on Bioperl to do this?

I am competent with R but very rusty with Perl, I would need a bit of advice on how to do this task. I have perl and Bioperl installed.

The genbank file also has the full DNA sequence at the end, after all the information.

Answer 1

[Pierre Lindenbaum]

Extract the gene positions using efetch and eutils, generated a bed file. Something like:

 $ curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_018520.1&rettype=gbwithparts&retmode=txt" |\
    grep "^     gene "  | \
    head -n 50 |\
    sed 's/complement(\([^)]*\))/\1/' |\
    cut -c 22- | sed 's/\.\./ /' |\
    awk '{B=int($1);E=int($2); printf("NC_018520\t%d\t%d\n", (B < E?B:E)-1,(B < E?E:B));}'

    NC_018520   409 1750
            NC_018520   1938    3075
            NC_018520   3205    3421
            NC_018520   3436    4549
            NC_018520   4566    4812
            NC_018520   4866    6783
            NC_018520   6993    9459
            NC_018520   9809    11365
            NC_018520   11463   11540
            NC_018520   11551   11627
            NC_018520   11707   14640
            NC_018520   14691   14807
            NC_018520   14846   15794

Use http://bedtools.readthedocs.io/en/latest/content/tools/complement.html to extract the complement intervals and http://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html to extract the intergenic sequences.

[Diesel]

Thanks for your answer Pierre however I tried using this method but was unable to install bedtools as I have not administrator privileges on the machine I am working on; I have tried using other methods, in R, and Perl, each could not fully get me where I want to; finally I have tried downloading and installing GFF-Ex; it did work, however I am not too happy about the output. Thanks for taking the time.

[Pierre Lindenbaum]

but was unable to install bedtools.

You don't have to be admin. You can install any software in your private directory.

[Diesel]

I will try again tomorrow if that is possible; I read the instruction page and at some point it goes:

"At this point, one should copy the binaries in ./bin/ to either usr/local/bin/ or some other repository for commonly used UNIX tools in your environment. You will typically require administrator (e.g. “root” or “sudo”) privileges to copy to usr/local/bin/."

That is why I tried sorting the problem out differently. I am a beginner and I thought that was not possible, having read that statement about copying binaries.

[Pierre Lindenbaum]

create a bin directory in your home

mkdir -p ${HOME}/bin

copy the binaries in ${HOME}/bin

add ${HOME}/bin to your path:

export PATH=${PATH}:${HOME}/bin

[David]

Pierre, Can you update the curl command, the awk expression is cut !!!!

[David]

My guess is that the awk expression is:

awk '{B=int($1);E=int($2);printf("NC_018520\t%d\t%d\n",B,E)}'