Dear all,
I have bed file like:
Chr \t start \t stop
And I woud like to add to fourth column information about reference allele from hg19, so output for example should look like:
chr \t start \t stop \t A/A
chr \t start \t stop \t C/C
chr \t start \t stop \t T/T
chr \t start \t stop \t A/A
So create something very similar to gVCF. Reason is, that I need to annotate this output file in VEP.
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written
by
Paul
This should do the trick, let me know if it doesn't :) The script uses as arguments i) the file to add reference nucleotides to ii) a directory containing single chromosome fasta files named like chr1.fa. Obviously you can change this
Let me know if something is not as it should be.
python anotate.py input.tsv path/to/chr/directory
And I have error message:
File "anotate.py", line 57 addrefnucl(key) ^ IndentationError: expected an indented block
Please if you have any idea what I am doing wrong. Thank you so much.
There is a tab error, maybe what I wrote or copy paste. I'm at a conference and will look into this asap.
If that's the complete error message, you did something weird while copying the file. Could you check that the final line is properly indented with a tab (as in my post above). If there is a longer error message, I would like to see that.
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Do you know a bit of Python? I have a script which almost does what you want.
Thank you for reply. I am scripting more in bash and awk.. But maybe I would understand..
How big is your file? Wondering whether to do everything in memory or stream.
It could be about 500000 rows and about 20 MB.