How can I extract annotation for genes from a GTF file that are more than 200 bp apart from neighboring genes?

Question

[biplab]

I am new in the field of computational biology. This questions might answered somewhere else but I could not find by searching. How can I extract annotation for genes from a GTF file that are more than 200 bp apart from neighboring genes? I was looking into bedtools for this but most functions in bedtools compare two files but I would like to compare genes within my annotation file. It will very helpful if someone can suggest how can I do this. For example:

Input files:

I   ensembl gene    335 649 .   +   .   gene_id "YAL069W"; gene_source "ensembl"; gene_biotype "protein_coding";
I   ensembl gene    538 792 .   +   .   gene_id "YAL068W-A"; gene_source "ensembl"; gene_biotype "protein_coding";
I   ensembl gene    1807    2169    .   -   .   gene_id "YAL068C"; gene_name "PAU8"; gene_source "ensembl"; gene_biotype "protein_coding";
I   ensembl gene    2480    2707    .   +   .   gene_id "YAL067W-A"; gene_source "ensembl"; gene_biotype "protein_coding";

Output:

I   ensembl gene    1807    2169    .   -   .   gene_id "YAL068C"; gene_name "PAU8"; gene_source "ensembl"; gene_biotype "protein_coding";

Thank you so much.

Answer 1

[Alex Reynolds]

Via BEDOPS gtf2bed and closest-features:

$ gtf2bed < genes.gtf > genes.bed
$ closest-features --no-ref --dist genes.bed genes.bed | awk -v threshold=200 -v FS='|' '{ if (($4>threshold)&&($4!="NA")) { print $3; }}' | uniq > genes_more_than_200_nt_apart.bed

[biplab]

Thank you so much. Very good solution.

Answer 2

[Pierre Lindenbaum]

I was looking into bedtools for this but most functions in bedtools compare two files but I would like to compare genes within my annotation file.

how about using the same file twice ?