Hi,
I have gtf files for a list of organisms. I want to extract only the intergenic sequences for each of their corresponding fasta files. Currently, I have been able to use grep -o '^..........' ecoli.fa > 10.txt to grep out the first 10 characters if the first gene starts at pos 11.
I now need to find a way to automate the process for the remaining regions, as manual inspection is impossible. How can I do the same for a huge file, for example -
Gene Start End
Gene1 11 157
Gene2 2878 8548
Gene3 11254 12124
The process might require file handling to subtract End of a row from the Start of the next row, and that value could be coupled with grep to give a command like grep -o '^{2877.}' ecoli.gtf | tail -f 2720 > 2720.txt
P.S. I could make the gtf file containing the intergenic lengths, but I do need help with the file handling.
Thanks in advance
1 answer
Hello again,
this doesn't look like a proper gtf file. Nevertheless here is a python script that should create a bed file for the intergenic regions. It asumes the columns you gave, that your file is sorted by coordinates and that there is header line.
Run it like this:
$ python intergenic.py genes.gtf > intergenic.bed
Hello,
than you are using python2. Add this line at the beginning of the python script and run again:
from __future__ import print_function
fin swimmer
You're welcome.
I moved my post to an answer.
fin swimmer
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Hello,
you could first create a
bedfile containing the coordinates for each intergenic regions with the language of your choice. Than you can use thisbedfile together with bedtools getfasta to get the sequences.fin swimmer
Thanks for the advice. It would certainly help, but to do the same, I first need to employ file handling to select the
StartandEndcoordinates of the annotated genes. Would you happen to have a code to create the bed file?Thanks.
How does your file with gene coordinates looks like? In your first post you've said you have a
gtffile. But the example you have posted doesn't looks like one.fin swimmer
Sorry for the confusion on my part. I only showed the relevant columns, but it is a proper gtf file.
Hello vinayjrao!
We believe that this post does not fit the main topic of this site.
Answer accepted
For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
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Why this should not be a bioinformatic topic?
Is the closing of this topic a mistake?
And why is the OP closing his own topic with this reason?
Strange ...
fin swimmer
I'm sorry. I closed it because the answer was accepted. The message of this not being a bioinformatic topic is automated. I'll revert it.
@ Pierre Lindenbaum , Devon Ryan , genomax , WouterDeCoster
What happens to that thread? Who closes it and why?
fin swimmer
Only mods
closethreads when they are off-topic/spam etc. Users should justacceptanswers that are correct. That provides proper closure for the thread.Hello,
I have a GFF3 file. How can I get the intergenic regions and its positive and negative chain information?
Thank.
This is an unrelated question and should have been posted as a new thread. Also provide clear objective of what you are trying to achieve.