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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

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
python awk bash
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by Obex33 • Obex33

1 answer

you're looking for bedtools intersect

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written by Pierre Lindenbaum Pierre Lindenbaum

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

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written by Obex33 • Obex33

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