Yrurtj

Building on: Extract names from File_B having overlapping intervals with File_A

I want to extract gene names (usually column 10, what's after "Name=") by matching the first column of file_b to file_a, and extracting the gene names if the second column of file_b lies within the gene interval, delineated by columns 4 and 5 of file_b.

There are a few problems with the code I have now.

(1)the way it is set up below, the last row of file_b is lost from the output, although this changes if this row (groupVII 17978350) up the list. I would like it to work the way it is set up.

(2)The names are truncated if they have special characters (eg colons and hyphens). I would like to have the entire name after the equal sign.

(3) I would like to match the entry/row on file_b to the gene hits in the output, such that the first two columns is the entry and the third column is the gene hit.

file_a.tsv

MT  insdc   gene    2851    3825    .   +   .   ID=gene:ENSGACG00000020925  Name=mt-nd1 biotype=protein_coding  description=NADH dehydrogenase 1%2C mitochondrial [Source:ZFIN%3BAcc:ZDB-GENE-011205-7] gene_id=ENSGACG00000020925  logic_name=mt_genbank_import    version=1

MT  insdc   gene    4036    5082    .   +   .   ID=gene:ENSGACG00000020929  Name=mt-nd2 biotype=protein_coding  description=NADH dehydrogenase 2%2C mitochondrial [Source:ZFIN%3BAcc:ZDB-GENE-011205-8] gene_id=ENSGACG00000020929  logic_name=mt_genbank_import    version=1

groupIII    ensembl gene    7332324 7334769 .   -   .   ID=gene:ENSGACG00000015265  Name=si:dkeyp-68b7.10   biotype=protein_coding  description=si:dkeyp-68b7.10 [Source:ZFIN%3BAcc:ZDB-GENE-070912-667]    gene_id=ENSGACG00000015265  logic_name=ensembl  version=1

groupIV ensembl gene    1368026 1374881 .   +   .   ID=gene:ENSGACG00000016447  Name=hnrnpa0b   biotype=protein_coding  description=heterogeneous nuclear ribonucleoprotein A0b [Source:ZFIN%3BAcc:ZDB-GENE-030131-6154]    gene_id=ENSGACG00000016447  logic_name=ensembl  version=1

groupIV ensembl gene    5347339 5349041 .   -   .   ID=gene:ENSGACG00000017010  Name=zgc:153018 biotype=protein_coding  description=zgc:153018 [Source:ZFIN%3BAcc:ZDB-GENE-060929-752]  gene_id=ENSGACG00000017010  logic_name=ensembl  version=1

groupV  ensembl gene    120615  125489  .   +   .   ID=gene:ENSGACG00000002103  Name=zdhhc6 biotype=protein_coding  description=zinc finger%2C DHHC-type containing 6 [Source:ZFIN%3BAcc:ZDB-GENE-030131-3189]  gene_id=ENSGACG00000002103  logic_name=ensembl  version=1

groupVI ensembl gene    11230354    11232784    .   +   .   ID=gene:ENSGACG00000009527  Name=bnip4  biotype=protein_coding  description=BCL2 interacting protein 4 [Source:ZFIN%3BAcc:ZDB-GENE-051113-212]  gene_id=ENSGACG00000009527  logic_name=ensembl  version=1

groupVII    ensembl gene    2271611 2277214 .   +   .   ID=gene:ENSGACG00000019012  Name=sf3b2  biotype=protein_coding  description=splicing factor 3b%2C subunit 2 [Source:ZFIN%3BAcc:ZDB-GENE-070928-1]   gene_id=ENSGACG00000019012  logic_name=ensembl  version=2

groupVII    ensembl gene    15815857    15824549    .   +   .   ID=gene:ENSGACG00000020296  Name=mpp1   biotype=protein_coding  description=membrane protein%2C palmitoylated 1 [Source:ZFIN%3BAcc:ZDB-GENE-031113-4]   gene_id=ENSGACG00000020296  logic_name=ensembl  version=1

groupVII    ensembl gene    17978322    17982388    .   +   .   ID=gene:ENSGACG00000020399  Name=si:ch211-284e13.4  biotype=protein_coding  description=si:ch211-284e13.4 [Source:ZFIN%3BAcc:ZDB-GENE-060526-161]   gene_id=ENSGACG00000020399  logic_name=ensembl  version=1

file_b.tsv

MT  4050

groupIII    7332350

groupIV 5347350

groupVI 11230375

groupVII    17978350

code:

while read -r id pos; do awk -v id="$id" -v pos="$pos" '$1 == id && pos > $4 && pos < $5 { if (gensub(/.*Name=([A-Za-z0-9]*).*/, "\1", 1) !~ /s/) print gensub(/.*Name=([A-Za-z0-9]*).*/, "\1", 1); }' <file_a.tsv; done < file_b.tsv > output.tsv

output.tsv

mt

si

zgc

bnip4

Desired_output

MT  4050    mt-nd1

groupIII    7332350 si:dkeyp-68b7.10

groupIV 5347350 zgc:153018

groupVI 11230375    bnip4

groupVI 11230375    si:ch211-284e13.4

EXTRA (IF POSSIBLE): Some of the entries (of file_b) will not land within a gene but may be close to one, say 100 units away to either side. It would be nice to have seperate code which allows you to specify this proximity, as was attempted here: Extract names from File_B having overlapping intervals with File_A

Any help is VERY much appreciated!