Extract sequence ids from otu map based on representative sequence id

Question

[c.older]

I have an otu map that I would like to extract sequences id corresponding to specific representative sequence ids. For just one representative sequence id I can do

grep "representativesequenceid" otu_map.txt > output.txt

But I would like to do this for a list of ~100 sequence ids, rather than do this 100 times :) Any ideas?

Answer 1

[shenwei356]

grep -f ids_file otu_map.txt > output.txt

ids_file contains list of your representative sequence ids with one id per line.

grep usage:

$ grep --help | grep '\-f' 
  -f, --file=FILE           obtain PATTERN from FILE

[c.older]

Tried it but just got a blank text file. Any idea what I might've done wrong?

[shenwei356]

did you copy and paste your representative sequence ids into the ids_file ?

[c.older]

Yes, it is a tab-delimited file with one representative sequence id per line.

[shenwei356]

Please show several rows

[c.older]

New.CleanUp.ReferenceOTU236161
New.CleanUp.ReferenceOTU307379
New.CleanUp.ReferenceOTU403578
New.CleanUp.ReferenceOTU40971
New.CleanUp.ReferenceOTU128105
138304
New.CleanUp.ReferenceOTU19208
New.CleanUp.ReferenceOTU176865

[shenwei356]

It should be the \r in your IDs file. Did you create that file in Windows?

Run

dos2unix ids_file

And then

grep -f ids_file otu_map.txt > output.txt

This should work.

[c.older]

It worked, thank you!