How to print the lines that contains certain strings by order?

Mike_Brown · 07-04-2016, 08:22 PM

I have two files

file indv

COPDGene_P51515
COPDGene_V67803
COPDGene_Z75868
COPDGene_U48329
COPDGene_R08908
COPDGene_E34944
file data

COPDGene_Z75868 1
COPDGene_A12318 3
COPDGene_R08908 5
COPDGene_P51515 8
COPDGene_U48329 2
COPDGene_V67803 8
COPDGene_E34944 2
COPDGene_D29835 9

I want to print the lines that contains the strings in the `indv` by the order of `indv` like following

COPDGene_P51515 8
COPDGene_V67803 8
COPDGene_Z75868 1
COPDGene_U48329 2
COPDGene_R08908 5
COPDGene_E34944 2

I tried to use

Code:

awk 'NR==FNR{a[$1]++;next} ($1 in a)' indv data

But I got

COPDGene_Z75868 1
COPDGene_R08908 5
COPDGene_P51515 8
COPDGene_U48329 2
COPDGene_V67803 8
COPDGene_E34944 2

which is not the order of `indv`.

syg00 · 07-04-2016, 08:33 PM

Quote:

Originally Posted by awk_manual

By default, the order in which a ‘for (i in array)’ loop scans an array is not defined; it is generally based upon the internal implementation of arrays inside awk.

You will have to design your own solution if neither the index or data is not in some natural order. I have used 2 dimensional array for this sort type of thing.

allend · 07-04-2016, 08:49 PM

Perhaps a simple loop involving grep would work.

Code:

while read aline; do grep "$aline" file.txt; done < indv.txt

Aia · 07-04-2016, 09:06 PM

Code:

awk 'NR==FNR{a[$1]=$2;next} a[$1]{print $1,a[$1]}' data indv

Output:

Code:

COPDGene_P51515 8
COPDGene_V67803 8
COPDGene_Z75868 1
COPDGene_U48329 2
COPDGene_R08908 5
COPDGene_E34944 2

syg00 · 07-04-2016, 09:16 PM

Fragile - what happens when $1 (in data) is not unique ?.

Aia · 07-04-2016, 09:32 PM

Quote:

Originally Posted by syg00

Fragile - what happens when $1 (in data) is not unique ?.

Why to call it fragile when no indication has been made for your requirement? If that were the case a more laborious approach must be taken, since the last entry will have precedence. However, as stand, until that requirement is made my suggestion is perfectly solid and meets the requested output.