How to print lines of two file where column 2 and 3 of File 1 fall in between column 2 and 3 of file 2

Question

[Obex33]

I have a file delimited File 1:

NC_025345       4569   4950   KX838946.2      
NC_025345       16546   17066   KJ641660.1      
NC_025345       11996   12085   KX932454.2

And another File 2:

NC_025345.1     RefSeq  gene    5690    7513    .       +       .       ID=gene-NZ82_gp4;Dbxref=GeneID:20964334;Name=NZ82_gp4;gbkey=Gene;gene_biotype=protein_coding;locus_tag=NZ82_gp4
NC_025345.1     RefSeq  gene    8016    10046   .       +       .       ID=gene-NZ82_gp5;Dbxref=GeneID:20964335;Name=NZ82_gp5;gbkey=Gene;gene_biotype=protein_coding;locus_tag=NZ82_gp5
NC_025345.1     RefSeq  gene    10337   16933   .       +       .       ID=gene-NZ82_gp6;Dbxref=GeneID:20964336;Name=NZ82_gp6;gbkey=Gene;gene_biotype=protein_coding;locus_tag=NZ82_gp6

I want to use each lines of File 1 to search File 2 and print lines where column 2 and 3 of File 1 fall in between column 2 and 3 of File 2 to a new output file. So that I will have a final output file like this:

NC_025345       11996   12085   KX932454.2     NC_025345.1     RefSeq  gene    10337   16933   .       +       .       ID=gene-NZ82_gp6;Dbxref=GeneID:20964336;Name=NZ82_gp6;gbkey=Gene;gene_biotype=protein_coding;locus_tag=NZ82_gp6

Answer 1

[Pierre Lindenbaum]

you're looking for bedtools intersect

[Obex33]

Hi, bedtools intersect does not work for this kind of file entries. Where column1 of file1 macthes column2 of file2 and then column 2 and 3 of file1 is >= and <= column 4 and 5 of file2 respectively, both lines should be printed in new file3. thanks

[Pierre Lindenbaum]

Hi, bedtools intersect does not work for this kind of file entries.

of course it doesn't. You'll first need to move your columns and then apply bedtools.

https://www.google.com/search?q=linux+change+columns+order