Using grep to get lines from a file (.tsv) that contain specific samples listed in a sample file (.tsv)

Question

So I have a file, let's call it pcawg.tsv. It's formatted like the one down below.

Tumor sample ID  Normal sample ID  Mechanism
a                1                 deletion
b                2                 ecDNA
c                3                 ecDNA

I have a file of tumor sample ID's with the ecDNA mechanism called ecDNA_samples.tsv. It's formatted like this:

Tumor sample ID
a
b

To filter and extract the lines of pcawg.tsv that contain the tumor sample ID's in ecDNA_samples.tsv into a new file, I used this line of code below.

grep -f ecDNA_samples.tsv pcawg.tsv > ecDNA.vcf.tsv

Would this be the right code to use?

Answer 1

This may help:

cat ecDNA_samples.tsv | xargs -I % grep '^%\s' pcawg.tsv

The command above executes grep '^<line>\s' pcawg.tsv, for each line of ecDNA_samples.tsv. Which matches the lines taken from ecDNA_samples.tsv to the sequences of characters between line start and a white-space in pcawg.tsv.

Answer 2

Just in case an R solution is acceptable as well, this should be fairly robust code because it properly parses the TSV files and matches up column names:

#!/usr/bin/env Rscript

library(tidyverse)
read_tsv("pcawg.tsv") %>%
   inner_join(read_tsv("ecDNA_samples.tsv")) %>%
   write_tsv("filtered_pcawg.tsv")