convert Trinotate resulte to GFF file
how i can convert Trinotate result to GFF file also how i can replace gene name in gff file by another annotation example thse is the GFF file
MA_CS_1000 transdecoder mRNA 1 3238 . - ID=MA_CS_1000.p1;Parent=GENE.MA_CS_1000~~MA_CS_1000.p1;Name=ORF%20type%3Acomplete%20len%3A560%20%28-%29%2Cscore%3D45.62
and thise is the annotation file
MA_CS_1000.p1 , Zinc finger C2H2-like
i want match those id to the Gff and change Gene_Name by colmne 2 in the Gff file any help !
desired output
MA_CS_1000 transdecoder mRNA 1 3238 . - ID=MA_CS_1000.p1;Parent=GENE.MA_CS_1000~~MA_CS_1000.p1;Name=Zinc%finger%C2H2-like
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Mostafa Mahmoud •
1 answer
Hello Mostafa,
you haven't answer my questions, so I had to make some guesses.
Input files:
$ cat annotation.txt
MA_CS_1000.p1,Zinc finger C2H2-like
$ cat input.gff
MA_CS_1000 transdecoder mRNA 1 3238 . - ID=MA_CS_1000.p1;Parent=GENE.MA_CS_1000~~MA_CS_1000.p1;Name=ORF%20type%3Acomplete%20len%3A560%20%28-%29%2Cscore%3D45.62
Command:
$ awk 'NR==FNR {split($0, ann,","); new[ann[1]]=ann[2]; next;} { match($0, /ID=([^;]+);/, id); if(id[1] in new) {gsub("Name=[^;]*", "Name="new[id[1]])} print}' > output.gff
Output:
$ cat output.gff
MA_CS_1000 transdecoder mRNA 1 3238 . - ID=MA_CS_1000.p1;Parent=GENE.MA_CS_1000~~MA_CS_1000.p1;Name=Zinc finger C2H2-like
fin swimmer
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Hello Mostafa,
please rephrase your question. To me it looks like you're asking two things.
It is very good to always provide an example of the input files and the desired output based on this examples.
In the examples you gave ,above I cannot see any overlap.
Regarding this note makes it much more probably to receive an answer in short time.
Thanks.
fin swimmer
Thanks fin for replay i have just two one tabulated and another is GFF i want replace anntoations in tab file to the GFF file by change the gene name
Hello Mostafa,
better but still many things that are unclear.
In the annotation file the values are comma seperated. Is there a whitespace before the first comma (this is important!)?
The first part in the annotation file (until the comma) should match the value of
IDin the last column of yourgfffile? The value forNamein the last column should be replaced by anything that followed theIDin the annotation file? Why is the comma URL encoded but the whitespace not? Is it necessary?fin swimmer
yes simply match the id and replace.
Please also answer the rest of my questions.
Thats it fin great jop thank you very much.
Please use the
ADD REPLYButton to reply to a comment/answer. Answers are only meant for (full) answers to the original question. So I moved your post to a comment. As you can see this is not perfect.Also note that I changed my command a little bit, to make sure that also line to which no changes where made are printed.
fin swimmer
second question is how to convert Trinotate.xls to gff do you have any idea.
Cite from this post:
Cite from this post:
second question is how to convert Trinotate.xls to gff do you have any idea.
I'm personally not a fan of including these functional annotations in a GFF file format. GFF is messy enough as it is without adding all this data