Extracting features from a file from another file with an ID list

Question

[ljohanam]

Guys,

I need to extract some features from a DEG file like a Log2 Fold change from an ID gene list. I'm trying with python but I haven't enough experience with programming, this task is resulting complex. I don't know if this is the best way or is better to construct a database using SQlite. What is your advice or somebody have already one script for python or R.....

From already thank you very much.

Answer 1

[Ashutosh Pandey]

I may be wrong but I assume you want to print or extract lines from a file using some patterns or id stored in another file. If this is the case try "grep -F -f file1(with geneids) file2 (big file with expression information)"

[ljohanam]

Ashutosh Pandey I try with this: grep -F -f thatineed.txt searchhere.txt but is not work, I don't receive any result... these are my example files:

thatineed.txt

evm.TU.supercontig_32.161
evm.TU.supercontig_19.58
evm.TU.supercontig_125.26
evm.TU.supercontig_27.252

searchhere.txt

evm.TU.supercontig_32.161    -3,9
evm.TU.supercontig_19.58    -3,9
evm.TU.supercontig_125.26    -3,8
evm.TU.supercontig_27.252    -3,8
evm.TU.supercontig_7.165    -3,6
evm.TU.supercontig_112.75    -3,5
evm.TU.supercontig_81.9    -3,5
evm.TU.supercontig_91.13    -3,5
evm.TU.supercontig_23.147    -3,4
evm.TU.supercontig_190.11    -3,4
evm.TU.supercontig_2.268    -3,4
evm.TU.supercontig_53.153    -3,4
evm.TU.supercontig_131.79    -3,3
evm.TU.supercontig_19.175    -3,3
evm.TU.supercontig_146.42    -3,3
evm.TU.supercontig_95.62    -3,3

What I would expect:

evm.TU.supercontig_32.161    -3,9
evm.TU.supercontig_19.58    -3,9
evm.TU.supercontig_125.26    -3,8
evm.TU.supercontig_27.252    -3,8

Thank you again :)

[Ashutosh Pandey]

I copied your example and it worked for me. I assume you are using UNIX to do this. In your case the command would be

grep -F -f thatineed.txt searchhere.txt

What error are you getting or the command doesn't print anything in your case?

[ljohanam]

Not, I'm using Linux (ubuntu) and yes, doesn't print anything.... I think for Linux is the same command or doesn't?

[Phil S.]

Hi,

I checked it on CentOS like that:

$ grep -wFf thatineed.txt searchhere.txt

and what I got is:

evm.TU.supercontig_32.161    -3,9
evm.TU.supercontig_19.58    -3,9
evm.TU.supercontig_125.26    -3,8
evm.TU.supercontig_27.252    -3,8

If that does not work for you maybe something is strange with your POSIX?

[ljohanam]

I don't know what happen I did everything... and when I try with a word it work:

grep -F 'evm.TU.supercontig_32.161' searchhere.txt > results.txt
evm.TU.supercontig_32.161    -3,9

but when I try with a file it returns me an empty file:

bioinformatica@bioinformatica2:~/Área de Trabalho$ grep -F -f thatineed.txt searchhere.txt
bioinformatica@bioinformatica2:~/Área de Trabalho$

I think grep is perfect for my task if it get work :D.

Really, thank you for your patience.

[sisod]

I had the exact same problem and want to share the solution for future readers: check the line-endings in your files (files created in windows use '\r\n', while linux expects '\n'). You can find-and-replace with almost any text-editor.