How to jvarkit/backlocate multiple mutations using a list file?

The following is a command to query a single mutation in FGFR4 -->"FGFR4\tG388R" using jvarkit

echo -e "FGFR4\tG388R" | java -jar dist/backlocate.jar -R hg19.fa --gtf Homo_sapiens.GRCh37.87.gtf

The output is as follows:

FGFR4   Gly 388 Arg FGFR4   ENST00000292408 +   G   1161    GGG AGG|CGG G   chr5    176520242   ENST00000292408.Exon9   .   .
FGFR4   Gly 388 Arg FGFR4   ENST00000292408 +   G   1162    GGG AGG|CGG G   chr5    176520243   ENST00000292408.Exon9   .   .
FGFR4   Gly 388 Arg FGFR4   ENST00000292408 +   G   1163    GGG AGG|CGG G   chr5    176520244   ENST00000292408.Exon9

. .

I am unable to figure a way to query a long list containing thousands of mutations. Can anyone please suggest a way to query the list (containing ~1000s mutations) (as -i infile) instead of individual mutations? Thanks

java shell echo ubuntu jvarkit

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written 4.1 years ago by TraPS-VarI 0

Here is the solution as suggested by the @lindenb

$ cat input_list.txt | java -jar dist/backlocate.jar -R hg19.fa --gtf Homo_sapiens.GRCh37.87.gtf

where input_list contains

ICOS\tF141X CDH10\tL614X KCNE2\tV49X MMP24\tV603X

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written 4.1 years ago by TraPS-VarI 0

1 answer

\t should be tabulations, not a litteral \ followed by t... of course...

that's why it's echo -e "FGFR4\tG388R" and not just echo "FGFR4\tG388R"

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written 4.1 years ago by Pierre Lindenbaum 17K

Thanks for the solution. It works now.

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written 4.0 years ago by TraPS-VarI 0