Question: Construct a gene arrow map to show the gene features
0
gravatar for utkarsh.sood
2.8 years ago by
utkarsh.sood30
India
utkarsh.sood30 wrote:

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

ADD COMMENTlink modified 2.8 years ago by Pierre Lindenbaum125k • written 2.8 years ago by utkarsh.sood30

I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

101010 Button

ADD REPLYlink written 2.8 years ago by WouterDeCoster42k
3
gravatar for Pierre Lindenbaum
2.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum125k wrote:

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

ADD COMMENTlink written 2.8 years ago by Pierre Lindenbaum125k
2

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

ADD REPLYlink written 2.8 years ago by WouterDeCoster42k
1

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

ADD REPLYlink written 2.8 years ago by ivivek_ngs4.9k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1762 users visited in the last hour