Construct a gene arrow map to show the gene features

Question

[utkarsh.sood]

Hello,

I want to generate a gene arrow map showing all the details like gene features, annotation etc. I have the data in the following format:

start   stop    strand  function
208 885 +   Chromosomal replication initiator protein DnaA
1576    1157    -   FIG00958722: hypothetical protein
2174    1578    -   Flavoprotein WrbA
2524    2171    -   Arsenate reductase (EC 1.20.4.1)
2649    3884    +   Inner membrane protein YihY, formerly thought to be RNase BN
4034    4228    +   FIG00956556: hypothetical protein

Please let me know about any software that can convert the above mentioned information to well formatted gene arrow map.

Thanks

Answer 1

[Pierre Lindenbaum]

using awk :-D

 awk -F '\t ' -v chromStart=208.0 -v chromEnd=4228.0 '/^start/{next;} {L=60.0;x1=L*(int($1)-chromStart)/(chromEnd-chromStart);x2=L*(int($2)-chromStart)/(chromEnd-chromStart);if(x1>x2) { t=x1;x1=x2;x2=t;} for(i=0;i<L;++i) {c=" ";if(i>=int(x1) && i<=int(x2)) { c=$3=="+"?">":"<" } ; printf("%c",c);}printf("  %s\n",$4);}' input.tsv


>>>>>>>>>>>                                                   Chromosomal replication initiator protein DnaA
              <<<<<<<                                         FIG00958722: hypothetical protein
                    <<<<<<<<<<                                Flavoprotein WrbA
                             <<<<<<                           Arsenate reductase (EC 1.20.4.1)
                                    >>>>>>>>>>>>>>>>>>>       Inner membrane protein YihY, formerly thought to be RNase BN
                                                         >>>  FIG00956556: hypothetical protein

else see

• Gene Drawing At Scale
• Is There Any Software That Can Be Used To Draw A Gene Order Figure?
• Draw Gene Models From Gff3 File
• ....

[WouterDeCoster]

I'm usually amazed by the elegant awk solutions you offer, but today you took this a step too far o.O

[ivivek_ngs]

he is a master at these , he always amazes me. I have learnt a lot from his blogs and posts here to be honest. Take a bow @Pierre

Answer 2

[n.s.j.vandervelden]

I have made an R package called geneviewer that is designed for drawing gene arrow maps like the example below. Have a look at the package website and github