How can I find in a tsv file a value and 2 other values corresponding to the same row but in differe-CodePudding

So I have a tsv file that I opened in Numbers (Mac) and it has this aspect:

sequence_id    sequence    v_call        d_call       j_call    sequence alignment    junction_id
TTAATAATGTT    GATCCT...   IGHV1-18*04   IGHD5/OR15   IGHJ3*01  CAGATTCA              CARVVLIYDAFDVW
CTGATACAACA    AGAACT...   IGHV3-72*01   IGHD6-2*01   IGHJ3*01  CTGTGCAG              CARLSQRSDGVDFW
TACATTAGTTA    GACTTT...   IGHV4-28*01   IGHD1-4*01   IGHJ3*02  GCTGCAGA              CARKALTTDAFDIW
TAGCTAGCAAA    TTTCCT...   IGHV3-49*04   IGHD1-6*01   IGHJ3*02  TGGTGGAG              CTRVPISWGSFDIW
...

There are 16 708 lines in the tsv file.

I'm given the sequence alignment and I have to 'grep' this and also the v_call, d_call and j_call to the corresponding sequence alignment.

I've used grep -n "CTRVPISWGSFDIW" for finding the desired sequence but I do not know how to 'grep' v_call and the other two at the same time.

I don't know if I'm explaining what I want but, as example: Given "CTRVPISWGSFDIW ", I want to output "CTRVPISWGSFDIW" junction_id followed by "IGHV3-4904", "IGHD1-601" and "IGHJ3*02", the correspondant v_call, d_call and j_call for CTRVPISWGSFDIW.

CodePudding user response：

Would you please try an awk solution:

awk 'BEGIN {FS=OFS="\t"} $7=="CTRVPISWGSFDIW" {print $7, $3, $4, $5}' file.tsv

The same command with comments:

awk '
    BEGIN {FS=OFS="\t"}                         # initialize input/output field separators to a TAB character
    $7=="CTRVPISWGSFDIW" {print $7, $3, $4, $5} # if the 7th field equals to the string, print the 7th, 3rd, 4th and 5th fields
' file.tsv                                      # input tsv file

Output:

CTRVPISWGSFDIW  IGHV3-49*04     IGHD1-6*01      IGHJ3*02

[Edit]
If you are oblidged to use grep, please try:

grep "CTRVPISWGSFDIW" file.tsv | awk 'BEGIN {FS=OFS="\t"} {print $7, $3, $4, $5}'

which will produce the same result.

CodePudding user response：

Suggesting to user awk script.

Provide matching pattern as argument inp.

Filter only lines matching RexExp provided in inp variable.

Print the fields 7th 3rd 4th 5th.

   awk '$0 ~ inp {print $7, $3, $4, $5}' inp="CTRVPISWGSFDIW" input.tsv

You can insert into inp a bash variable like this:

   awk '$0 ~ inp {print $7, $3, $4, $5}' inp="$variable" input.tsv