Hello,
I have about 30 VCF files with file names as ID_001.new.vcf. I want to extract only the "ID_001" part from the file name and change it in the header line of the VCF file where "Sample1" is given.
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1
So that the result looks like that:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ID_001
How can I do it ? I tried to use echo in bash and extract the IDs from the Filename but I am unable to iterate it to change inside the file. Thanks for your help.
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written
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Inquisitive8995
In bash this should do.
for i in *.new.vcf
do
ID_NAME=$(basename "$i" .new.vcf)
sed -i "1s|Sample1|$ID_NAME|g" $i
done
Caution: I have used -i with sed. So the actual files will get edited in place.
Now added 1s also as to limit the replacement to first line alone.
This works when all files have Sample1 in the file name. Will that be the case?
Yes all files have Sample1
@Jeffin , Thanks for your response. This line is not the first line within the file. How can I change sed in a way that it find the particular line where Sample1 is there and then change it to $ID_NAME ?
Changing 1s| to simply s| will do replacements for all Sample1 occurrences.
Thanks a lot. This worked !
I think would be better to use 'bcftools view --samples-file` than sed
Hi Pierre, I did not understand. Would bcftools view do any replacement ?
the option sample-file can be used to rename the samples. https://samtools.github.io/bcftools/bcftools.html
This file can also be used to rename samples by giving the new sample name as a second white-space-separated column, like this: "old_name new_name".
If you have GNU parallel installed, you can use it instead of a bash for loop:
parallel 'sed -i "s|Sample1$|{=s/.new.vcf$//=}|"' {} ::: *.new.vcf
Hi Malcom, The suggested command appears to be super efficient, even though I did not understand many of the usages. Can you please explain the {=s/.new.vc$f//=}, {}, ::: etc
Sure.
In general, in your command line:
{} gets replaced with the file being processed.{=perl expression=} gets replaced with the value of a perl expression being evaluated in the context of the perl variable $_ being set to the name of the file being processed.So, in my example, we are using sed to replace the word "Sample1' appearing at the end of line with the result of removing the trailing .new.vcf from each filename.
Documentation for this can be found in parallel's manpage by searching for "{=perl expression=}", and where you can also read
::: arguments
Use arguments from the command line as input source instead of stdin (standard input).
Hi Ole,
Could you please point me to some link or so which would help me understand the {},::: etc.
It is covered in GNU Parallel 2018 chapter 5 (Online https://doi.org/10.5281/zenodo.1146014, printed www.lulu.com/shop/ole-tange/gnu-parallel-2018/paperback/product-23558902.html)
thanks for the fix and the alternate!
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