Question

I want to do some simple database operations on a table without bothering with a database software, e.g., I can use the “filo” package from GitHub to do something similar to “groupby” function. I wonder is there something similar to achieve some simple “join” function? Or can I do it with Python or Bash? Specifically, I have a table like:

Col5a2  NM_007737   chr1    -   45447828    45447829
Slc40a1 NM_016917   chr1    -   45870140    45870141
Gm3852  NM_001177356    chr1    -   45956809    45956810
Slc39a10    NM_172653   chr1    -   46798055    46798056
Obfc2a  NM_028696   chr1    -   51422944    51422945
Myo1b   NM_001161817,NM_010863  chr1    -   51860519    51860520
.
.
.

And I have a list

Slc40a1
Myo1b
Col5a2
Obfc2a
.
.
.

I want to fetch the items in the list from the table, so that I will get:

Slc39a10    NM_172653   chr1    -   46798055    46798056
Myo1b   NM_001161817,NM_010863  chr1    -   51860519    51860520
Col5a2  NM_007737   chr1    -   45447828    45447829
Obfc2a  NM_028696   chr1    -   51422944    51422945
.
.
.

Answer 1

Here’s one way using awk:

awk 'FNR==NR { a[$1]=$0; next } $1 in a { print a[$1] }' table list

or with formatting:

awk 'FNR==NR { a[$1]=$0; next } $1 in a { print a[$1] }' table list | column -t

Results:

Slc40a1  NM_016917               chr1  -  45870140  45870141
Myo1b    NM_001161817,NM_010863  chr1  -  51860519  51860520
Col5a2   NM_007737               chr1  -  45447828  45447829
Obfc2a   NM_028696               chr1  -  51422944  51422945

Explanation:

‘FNR==NR { … }’ is a conditional that is only true for the first file in the argument list.

So for each line in the file called ‘table’, the first column ($1) is added to an array (called ‘a’) and this is assigned the value of the whole line ($0). ‘next’ then skips to remainder of the code and jumps to the next line of input, until all lines in the ‘table’ file have been processed.

‘$1 in a’ is another conditional.

This is asking if column one of the ‘list’ file is a key in the array. If it is, then print out the value of column one that we just stored in the array (a[$1]).