How to sort lines in a file based on listing in another file using loop "while read line"

Question

[yreynaud]

Hi, I have a file with sequence ID + metadata that I would like to sort as ID ordered in a second file (corresponding to a phylogenetic tree).

File 1 is like this (header in the first line, then sequence ID + metadata for following lines):

RUN,3.code,SL,SL2
ERR911851,GRL,4.4.1.1,4.4
ERR911854,GRL,4.4.1.1,4.4
ERR911855,GRL,4.4.1.1,4.4
ERR911856,GRL,4.4.1.1,4.4
ERR911859,GRL,4.8,4.8
ERR911860,GRL,4.8,4.8
ERR911862,GRL,4.4.1.1,4.4

etc ........

File 2 is like this:

"ERR163930"
"ERR182011"
"ERR221551"
"ERR221600"
"ERR245800"
"ERR212152"

etc........

Any idea how to proceed? Thanks for your help best Yann

[yreynaud]

Hi, I have a file with sequence ID + metadata that I would like to sort as ID ordered in a second file (corresponding to a phylogenetic tree).

File 1 is like this (header in the first line, then sequence ID + metadata for following lines):

RUN,3.code,SL,SL2

ERR911851,GRL,4.4.1.1,4.4

ERR911854,GRL,4.4.1.1,4.4

ERR911855,GRL,4.4.1.1,4.4

ERR911856,GRL,4.4.1.1,4.4

ERR911859,GRL,4.8,4.8

ERR911860,GRL,4.8,4.8

ERR911862,GRL,4.4.1.1,4.4

etc ........

File 2 is like this:

"ERR163930"

"ERR182011"

"ERR221551"

"ERR221600"

"ERR245800"

"ERR212152"

etc........

Any idea how to proceed? Thanks for your help best Yann

[yreynaud]

Thanks it works perfectly!!!!! best Yann

[GenoMax]

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

[yreynaud]

Sorry I just realized the upvoting stuff and "accept" option, I am new on this website and didnt get the rules. Next time I would do it. Anyway thanks for your help!

Answer 1

[venu]

Not exactly a bioinformatics question but this should work

cat FILE2.txt | while read -r ID; do grep "^$ID" -w FILE1.txt; done

If you have double quotes " in FILE2, try following

cat FILE2.txt | sed 's/"//g' | while read -r ID; do grep "^$ID" -w FILE1.txt; done

[WouterDeCoster]

Marked accepted as answer since OP didn't...

[venu]

Thanks. Some OPs never care about this after finding a working solution. Too bad :(

[WouterDeCoster]

You would think that's the least they can do, in return for us spending our time here. Oh well, good thing we have plenty of nice people here too ;)