Question: Linux command line use to rename a gff annotation file "Name" attribute
1
gravatar for rob234king
4.8 years ago by
rob234king570
UK/Harpenden/Rothamsted Research
rob234king570 wrote:

I'm having trouble changing a gff file. I think the best way to do this may be the linux command line as I am having a headache getting a script to work correctly. What I would like to do is:

1) remove any text before or after the number of the Name attribute up to the "=" and ";" respectively, highlighted in yellow.

2) for each gene and complementary mRNA with the same name beginning with "fgene" or "augus" or "genema" or "snap" to be changed to a sequential number starting from "20000", so the first gene and mRNA example below would be Name=20000 for both mRNA and gene then the next gene and mRNA would be Name=20001 etc

 

Please note: I have sorted the file by position so each gene and mRNA should be on following lines although with a number of CDS lines following each gene and mRNA.

 

I have this:

Chromosome_2_Copy       maker   gene    60155   61282   .       -       .       Name=mRNAHGSG_07981gene;ID=maker-Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1-gene

Chromosome_2_Copy       maker   mRNA    60155   61282   100.0   -       .       Name=mRNAHGSG_07981;ID=maker-Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1;Parent=maker-Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1-gene

Chromosome_2_Copy       maker   CDS     60743   60970   .       -       .       ID=maker-Chromosome_2Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1

Chromosome_2_Copy       maker   CDS     61019   61282   .       -       .       ID=maker-Chromosome_2Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1

Chromosome_2_Copy       maker   CDS     62547   63546   .       -       .       ID=augustus_masked-Chs_masked-Chromosome_2-processed-gene-0.14-mRNA-1

Chromosome_2_Copy       maker   gene    65607   66745   .       +       .       Name=fgenesh_075_N;ID=fgenesh_masked-Chromosome_2-processed-gene-0.75

Chromosome_2_Copy       maker   mRNA    65607   66745   .       +       .       Name=fgenesh_075_N;ID=fgenesh_masked-Chromosome_2-processed-gene-0.75-mRNA-1;Parent=fgenesh_masked-Chromosome_2-processed-gene-0.75

Chromosome_2_Copy       maker   CDS     65775   65836   .       +       .       ID=fgenesh_masked-Chromosome_2-processed-gene-0.75-mRNA-1:cds;Parent=fgenesh_masked-Chromosome_2-processed-gene-0.75-mRNA-1

 

UPDATE:

 

This is a script I was playing with but I had removed the first part of the Name before the number via the command line to start with before running the script, I still have to work out how I did this and it's not great.

 

#!/usr/bin/perl

#BUG AFTER THE RENAMING FOR SOME REASON THE CDS Name when loaded in geneious becomes "CDS;CDS" but I can't see that I have added anything and the gff file doesn't seem to have checged this part??

use warnings;

my $gffFile = shift;
open (GFF, "<$gffFile");

my $filename = "Chrom1.gff";
open FILE, ">>$filename" or die "Could not open file '$filename' $!";

#counter for new gene names
my $ii=20000;

while (<GFF>) {
    #skip header line
    if ($. < 3) {
            print FILE $_;
        }else{

    #remove return character
    chomp;
    
    #split columns by tabs
    my @col = split /\t/;
        
        #split the last column with the Name attribute in
        my @lastcolumn = split /;/, $col[8];
        
       
        my @Name;
    #ALREADY REMOVED THE STARTING mRNAHGSG_ at command line FORGOTTON COMMAND THOUGH :(
    if($lastcolumn[0] =~ /^Name=[0-9]+gene/){
            
      #get just Name=number
            @Name = split ("gen",$lastcolumn[0]);
    
        ##rename gene names for some
       #   if (($lastcolumn[0] =~ /^Name.augu.*/) || ($lastcolumn[0] =~ /^Name.genema.*/) || ($lastcolumn[0] =~ /^Name.fgene.*/) || ($lastcolumn[0] =~ /^Name.snap.*/)){ 
       
    

    print FILE "$col[0]" . "\t" . "$col[1]" . "\t" . "$col[2]" . "\t" . "$col[3]" . "\t" . "$col[4]" . "\t" . "$col[5]" . "\t" . "$col[6]" . "\t" . "$col[7]" . "\t" . $Name[0] . ";";
my $nums = @lastcolumn;

for (my $i=1; $i < $nums; $i++) {
    if ($i+1<$nums) {
        print FILE  "$lastcolumn[$i]" . ";";
    }else{
     print FILE  "$lastcolumn[$i]" . "\n";   
    }
    

}
}else{
      print FILE $_ . "\n";
#      if($data[0] !~ /^Name=[0-9]+gene/){
#      
#    print $data[1] . "\t" . $data[0] . "\n";
#      }
        }

 

        }     
        }
close FILE;

 

 

UPDATE2:

 

The field delimiter seems fine. It only doesn't work for the addition I added the first section of the line with _M in the name gets replaced by an ID=string. 

 

I have this as input:

Chromosome_2_Copy       maker   gene    60155   61282   .       -       .       Name=mRNAHGSG_07981gene;ID=maker-Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1-gene

Chromosome_2_Copy       maker   mRNA    60155   61282   100.0   -       .       Name=mRNAHGSG_07981;ID=maker-Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1;Parent=maker-Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1-gene

Chromosome_2_Copy       maker   CDS     60743   60970   .       -       .       ID=maker-Chromosome_2Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1

Chromosome_2_Copy       maker   CDS     61019   61282   .       -       .       ID=maker-Chromosome_2Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1

Chromosome_2_Copy       maker   CDS     62547   63546   .       -       .       ID=augustus_masked-Chs_masked-Chromosome_2-processed-gene-0.14-mRNA-1

Chromosome_2_Copy       maker   gene    65607   66745   .       +       .       Name=fgenesh_075_N;ID=fgenesh_masked-Chromosome_2-processed-gene-0.75

Chromosome_2_Copy       maker   mRNA    65607   66745   .       +       .       Name=fgenesh_075_N;ID=fgenesh_masked-Chromosome_2-processed-gene-0.75-mRNA-1;Parent=fgenesh_masked-Chromosome_2-processed-gene-0.75

Chromosome_2_Copy       maker   CDS     65775   65836   .       +       .       ID=fgenesh_masked-Chromosome_2-processed-gene-0.75-mRNA-1:cds;Parent=fgenesh_masked-Chromosome_2-processed-gene-0.75-mRNA-1

Chromosome_2_Copy       maker   gene    65707   66845   .       +       .       Name=12345_M;ID=fgenesh_masked-Chromosome_2-processed-gene-0.75

Chromosome_2_Copy       maker   mRNA    65707   66845   .       +       .       Name=12345_M;ID=fgenesh_masked-Chromosome_2-processed-gene-0.75-mRNA-1;Parent=fgenesh_masked-Chromosome_2-processed-gene-0.75

 

 

 

I’m trying this to first sort then do the changes but I need to add something to not change anything if _M in name, any ideas how I can add it to this?

 

sort -t $'\t' -k 4,4 -V Chromosome_1.gff -o Chromosome_1_G.gff

cat Chromosome_1_G.gff | awk 'BEGIN{FS="\t";OFS="\t";id=19999} {if ($3 ~ /gene/ || $3 ~ /mRNA/) {split($9,a,";"); split(a[1],b,"="); if (b[2] ~ /^fgene/ || b[2] ~ /^augus/ || b[2] ~ /^genema/ || b[2] ~ /^snap/){if($3 ~ /gene/){id=id+1}; ss="\\1"id"\\3";} else {ss="\\1\\2\\3"}; s=gensub(/([[:alpha:]]*=)[^[:digit:];]*([[:digit:]]+)[^[:digit:];]*(;.+)/,ss, "g", $9); print $1,$2,$3,$4,$5,$6,$7,$8,s } else {print} }' > Chromosome_1.gff

 

 

Example output that I would like:

Chromosome_2_Copy       maker   gene    60155   61282   .       -       .       Name=07981;ID=maker-Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1-gene

Chromosome_2_Copy       maker   mRNA    60155   61282   100.0   -       .       Name=07981;ID=maker-Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1;Parent=maker-Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1-gene

Chromosome_2_Copy       maker   CDS     60743   60970   .       -       .       ID=maker-Chromosome_2Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1

Chromosome_2_Copy       maker   CDS     61019   61282   .       -       .       ID=maker-Chromosome_2Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1

Chromosome_2_Copy       maker   CDS     62547   63546   .       -       .       ID=augustus_masked-Chs_masked-Chromosome_2-processed-gene-0.14-mRNA-1

Chromosome_2_Copy       maker   gene    65607   66745   .       +       .       Name=20000;ID=fgenesh_masked-Chromosome_2-processed-gene-0.75

Chromosome_2_Copy       maker   mRNA    65607   66745   .       +       .       Name=20000;ID=fgenesh_masked-Chromosome_2-processed-gene-0.75-mRNA-1;Parent=fgenesh_masked-Chromosome_2-processed-gene-0.75

Chromosome_2_Copy       maker   CDS     65775   65836   .       +       .       ID=fgenesh_masked-Chromosome_2-processed-gene-0.75-mRNA-1:cds;Parent=fgenesh_masked-Chromosome_2-processed-gene-0.75-mRNA-1

Chromosome_2_Copy       maker   gene    65707   66845   .       +       .       Name=12345_M;ID=fgenesh_masked-Chromosome_2-processed-gene-0.75

Chromosome_2_Copy       maker   mRNA    65707   66845   .       +       .       Name=12345_M;ID=fgenesh_masked-Chromosome_2-processed-gene-0.75-mRNA-1;Parent=fgenesh_masked-Chromosome_2-processed-gene-0.75

 

linux gff • 3.2k views
ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by rob234king570

While I'm sure you could put together a very long one-liner, you might as well just write a small perl or python script. If the one you've been working on isn't working, then post it and just say what's not working.
 

ADD REPLYlink written 4.8 years ago by Devon Ryan88k

I updated by create more problems I think.

ADD REPLYlink written 4.8 years ago by rob234king570

Please add some example of result you want. easy to understand.

In addition,  There is no name beginning with "fgene" or "augus" or "genema" or "snap" in  "the first gene and mRNA example" Do you mean mRNAHGSG_07981gene or fgenesh_075_N?

I believe one-liner awk or perl would tackle this. agree with @DevonRyan

 

ADD REPLYlink written 4.8 years ago by Zhilong Jia1.4k
5
gravatar for xb
4.8 years ago by
xb390
Chapel Hill, NC,USA
xb390 wrote:

One of possible solutions


## 1) only

cat <your-file> | awk 'BEGIN{FS="\t";OFS="\t"} {s=gensub(/([[:alpha:]]*=)[^[:digit:];]*([[:digit:]]+)[^[:digit:];]*(;.+)/,"\\1\\2\\3", "g", $9); print $1,$2,$3,$4,$5,$6,$7,$8,s}'

## output

Chromosome_2_Copy       maker   gene    60155   61282   .       -       .       Name=07981;ID=maker-Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1-gene
Chromosome_2_Copy       maker   mRNA    60155   61282   100.0   -       .       Name=07981;ID=maker-Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1;Parent=maker-Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1-gene
Chromosome_2_Copy       maker   CDS     60743   60970   .       -       .       ID=maker-Chromosome_2Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1
Chromosome_2_Copy       maker   CDS     61019   61282   .       -       .       ID=maker-Chromosome_2Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1
Chromosome_2_Copy       maker   CDS     62547   63546   .       -       .       ID=augustus_masked-Chs_masked-Chromosome_2-processed-gene-0.14-mRNA-1
Chromosome_2_Copy       maker   gene    65607   66745   .       +       .       Name=075;ID=fgenesh_masked-Chromosome_2-processed-gene-0.75
Chromosome_2_Copy       maker   mRNA    65607   66745   .       +       .       Name=075;ID=fgenesh_masked-Chromosome_2-processed-gene-0.75-mRNA-1;Parent=fgenesh_masked-Chromosome_2-processed-gene-0.75
Chromosome_2_Copy       maker   CDS     65775   65836   .       +       .       ID=fgenesh_masked-Chromosome_2-processed-gene-0.75-mRNA-1:cds;Parent=fgenesh_masked-Chromosome_2-processed-gene-0.75-mRNA-1

 


## 1) + 2)


cat <your-file> | awk 'BEGIN{FS="\t";OFS="\t";id=19999} {if ($3 ~ /gene/ || $3 ~ /mRNA/) {split($9,a,";"); split(a[1],b,"="); if (b[2] ~ /^fgene/ || b[2] ~ /^augus/ || b[2] ~ /^genema/ || b[2] ~ /^snap/){if($3 ~ /gene/){id=id+1}; ss="\\1"id"\\3";} else {ss="\\1\\2\\3"};  s=gensub(/([[:alpha:]]*=)[^[:digit:];]*([[:digit:]]+)[^[:digit:];]*(;.+)/,ss, "g", $9); print $1,$2,$3,$4,$5,$6,$7,$8,s } else {print} }'

## output

Chromosome_2_Copy       maker   gene    60155   61282   .       -       .       Name=07981;ID=maker-Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1-gene
Chromosome_2_Copy       maker   mRNA    60155   61282   100.0   -       .       Name=07981;ID=maker-Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1;Parent=maker-Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1-gene
Chromosome_2_Copy       maker   CDS     60743   60970   .       -       .       ID=maker-Chromosome_2Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1
Chromosome_2_Copy       maker   CDS     61019   61282   .       -       .       ID=maker-Chromosome_2Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1
Chromosome_2_Copy       maker   CDS     62547   63546   .       -       .       ID=augustus_masked-Chs_masked-Chromosome_2-processed-gene-0.14-mRNA-1
Chromosome_2_Copy       maker   gene    65607   66745   .       +       .       Name=20000;ID=fgenesh_masked-Chromosome_2-processed-gene-0.75
Chromosome_2_Copy       maker   mRNA    65607   66745   .       +       .       Name=20000;ID=fgenesh_masked-Chromosome_2-processed-gene-0.75-mRNA-1;Parent=fgenesh_masked-Chromosome_2-processed-gene-0.75
Chromosome_2_Copy       maker   CDS     65775   65836   .       +       .       ID=fgenesh_masked-Chromosome_2-processed-gene-0.75-mRNA-1:cds;Parent=fgenesh_masked-Chromosome_2-processed-gene-0.75-mRNA-1

 

 

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by xb390

worked perfectly, I spent 2 days trying to figure something out. Saved me so much trouble. Thanks very much.

ADD REPLYlink written 4.8 years ago by rob234king570

Just realized that there are some instances in which I don't want to correct the name because they have already been manually changed to include a "_M" for certain models, I'm working out what the AWK command you used does at moment but on the off chance you know of a quick fix to skip when finds a name has the "_M" extension? for instance if finds the Name is "Name=number_M", then skip because doesn't need any correction to these lines.

Chromosome_2_Copy       maker   gene    60155   61282   .       -       .       Name=07981_M;ID=maker-Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1-gene

Chromosome_2_Copy       maker   mRNA    60155   61282   100.0   -       .       Name=07981_M;ID=maker-Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1;Parent=maker-Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1-gene

Chromosome_2_Copy       maker   CDS     60743   60970   .       -       .       ID=maker-Chromosome_2Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1

Chromosome_2_Copy       maker   CDS     61019   61282   .       -       .       ID=maker-Chromosome_2Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1

 

 

 

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by rob234king570

@rob234king You are very welcome! Try this to keep "_M", 
cat <your-file> | awk 'BEGIN{FS="\t";OFS="\t"} {if (gsub(/Name=[0-9]+_M;/,$9)==1) {print} else {s=gensub(/([[:alpha:]]*=)[^[:digit:];]*([[:digit:]]+)[^[:digit:];]*(;.+)/,"\\1\\2\\3\\4", "g", $9); print $1,$2,$3,$4,$5,$6,$7,$8,s} }'

 

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by xb390

Thanks, I tried it but it seems to be not correctly printing for those instances, I combined your commands to keep the renaming but still has the same problem with the _M entries. It seems to print the ID first rather than the first 7 columns, so I think just changing the print command might do it but I'll see how far I get. I'm currently using this:

cat ChromTest.gff | awk 'BEGIN{FS="\t";OFS="\t";id=19999} {if (gsub(/Name=[0-9]+_M;/,$9)==1) {print} else {if ($3 ~ /gene/ || $3 ~ /mRNA/) {split($9,a,";"); split(a[1],b,"="); if (b[2] ~ /^fgene/ || b[2] ~ /^augus/ || b[2] ~ /^genema/ || b[2] ~ /^snap/){if($3 ~ /gene/){id=id+1}; ss="\\1"id"\\3";} else {ss="\\1\\2\\3"}; s=gensub(/([[:alpha:]]*=)[^[:digit:];]*([[:digit:]]+)[^[:digit:];]*(;.+)/,ss, "g", $9); print $1,$2,$3,$4,$5,$6,$7,$8,s } else {print} }}' > test2.gff

 

Before:

Chromosome_1    Geneious        gene    6170    11000   .       -       .       Name=16072_M;ID=rq6L7BqgDRNvsV23NtXQe3jtf8o.1399027473558.764976
Chromosome_1    maker   CDS     6170    6175    .       -       .       ID=fgenesh_masked-Chromosome_1-processed-gene-0.79-mRNA-1:cds;Parent=fgenesh_masked-Chromosome_1-processed-gene-0.79-mRNA-1
Chromosome_1    maker   mRNA    6170    11000   .       -       .       Name=16072_M;ID=fgenesh_masked-Chromosome_1-processed-gene-0.79-mRNA-1

 

 

after:

ID=rq6L7BqgDRNvsV23NtXQe3jtf8o.1399027473558.76497600   .       -       .       Name=16072_M;ID=rq6L7BqgDRNvsV23NtXQe3jtf8o.1399027473558.764976
Chromosome_1    maker   CDS     6170    6175    .       -       .       ID=fgenesh_masked-Chromosome_1-processed-gene-0.79-mRNA-1:cds;Parent=fgenesh_masked-Chromosome_1-processed-gene-0.79-mRNA-1
ID=fgenesh_masked-Chromosome_1-processed-gene-0.79-mRNA-1       .       Name=16072_M;ID=fgenesh_masked-Chromosome_1-processed-gene-0.79-mRNA-1

 

ADD REPLYlink written 4.8 years ago by rob234king570

I tested your command and it works well. One thing to make sure is that the file field delimiter is "\t"instead of space.

ADD REPLYlink written 4.8 years ago by xb390

The field delimiter seems fine. It only doesn't work for the addition I added the first section of the line with _M in the name gets replaced by an ID=string. 

 

I have this as input:

Chromosome_2_Copy       maker   gene    60155   61282   .       -       .       Name=mRNAHGSG_07981gene;ID=maker-Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1-gene

Chromosome_2_Copy       maker   mRNA    60155   61282   100.0   -       .       Name=mRNAHGSG_07981;ID=maker-Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1;Parent=maker-Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1-gene

Chromosome_2_Copy       maker   CDS     60743   60970   .       -       .       ID=maker-Chromosome_2Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1

Chromosome_2_Copy       maker   CDS     61019   61282   .       -       .       ID=maker-Chromosome_2Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1

Chromosome_2_Copy       maker   CDS     62547   63546   .       -       .       ID=augustus_masked-Chs_masked-Chromosome_2-processed-gene-0.14-mRNA-1

Chromosome_2_Copy       maker   gene    65607   66745   .       +       .       Name=fgenesh_075_N;ID=fgenesh_masked-Chromosome_2-processed-gene-0.75

Chromosome_2_Copy       maker   mRNA    65607   66745   .       +       .       Name=fgenesh_075_N;ID=fgenesh_masked-Chromosome_2-processed-gene-0.75-mRNA-1;Parent=fgenesh_masked-Chromosome_2-processed-gene-0.75

Chromosome_2_Copy       maker   CDS     65775   65836   .       +       .       ID=fgenesh_masked-Chromosome_2-processed-gene-0.75-mRNA-1:cds;Parent=fgenesh_masked-Chromosome_2-processed-gene-0.75-mRNA-1

Chromosome_2_Copy       maker   gene    65707   66845   .       +       .       Name=12345_M;ID=fgenesh_masked-Chromosome_2-processed-gene-0.75

Chromosome_2_Copy       maker   mRNA    65707   66845   .       +       .       Name=12345_M;ID=fgenesh_masked-Chromosome_2-processed-gene-0.75-mRNA-1;Parent=fgenesh_masked-Chromosome_2-processed-gene-0.75

 

 

 

I’m trying this to first sort then do the changes but I need to add something to not change anything if _M in name, any ideas how I can add it to this?

 

sort -t $'\t' -k 4,4 -V Chromosome_1.gff -o Chromosome_1_G.gff

cat Chromosome_1_G.gff | awk 'BEGIN{FS="\t";OFS="\t";id=19999} {if ($3 ~ /gene/ || $3 ~ /mRNA/) {split($9,a,";"); split(a[1],b,"="); if (b[2] ~ /^fgene/ || b[2] ~ /^augus/ || b[2] ~ /^genema/ || b[2] ~ /^snap/){if($3 ~ /gene/){id=id+1}; ss="\\1"id"\\3";} else {ss="\\1\\2\\3"}; s=gensub(/([[:alpha:]]*=)[^[:digit:];]*([[:digit:]]+)[^[:digit:];]*(;.+)/,ss, "g", $9); print $1,$2,$3,$4,$5,$6,$7,$8,s } else {print} }' > Chromosome_1.gff

 

 

Example output that I would like:

Chromosome_2_Copy       maker   gene    60155   61282   .       -       .       Name=07981;ID=maker-Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1-gene

Chromosome_2_Copy       maker   mRNA    60155   61282   100.0   -       .       Name=07981;ID=maker-Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1;Parent=maker-Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1-gene

Chromosome_2_Copy       maker   CDS     60743   60970   .       -       .       ID=maker-Chromosome_2Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1

Chromosome_2_Copy       maker   CDS     61019   61282   .       -       .       ID=maker-Chromosome_2Chromosome_2-exonerate_est2genome-gene-0.53-mRNA-1

Chromosome_2_Copy       maker   CDS     62547   63546   .       -       .       ID=augustus_masked-Chs_masked-Chromosome_2-processed-gene-0.14-mRNA-1

Chromosome_2_Copy       maker   gene    65607   66745   .       +       .       Name=20000;ID=fgenesh_masked-Chromosome_2-processed-gene-0.75

Chromosome_2_Copy       maker   mRNA    65607   66745   .       +       .       Name=20000;ID=fgenesh_masked-Chromosome_2-processed-gene-0.75-mRNA-1;Parent=fgenesh_masked-Chromosome_2-processed-gene-0.75

Chromosome_2_Copy       maker   CDS     65775   65836   .       +       .       ID=fgenesh_masked-Chromosome_2-processed-gene-0.75-mRNA-1:cds;Parent=fgenesh_masked-Chromosome_2-processed-gene-0.75-mRNA-1

Chromosome_2_Copy       maker   gene    65707   66845   .       +       .       Name=12345_M;ID=fgenesh_masked-Chromosome_2-processed-gene-0.75

Chromosome_2_Copy       maker   mRNA    65707   66845   .       +       .       Name=12345_M;ID=fgenesh_masked-Chromosome_2-processed-gene-0.75-mRNA-1;Parent=fgenesh_masked-Chromosome_2-processed-gene-0.75

 

ADD REPLYlink written 4.8 years ago by rob234king570
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: 1070 users visited in the last hour