I'm trying to extract the contents of one file (infile.txt) from another file (mainfile.fastq). I'm using the command:

$ grep -f infile.txt mainfile.fastq

In the terminal, the complete contents of mainfile.fastq are shown, with the matching lines from infile.txt highlighted.
If I try to output matching lines, I get the complete contents of mainfile.fastq:

$ grep -f infile.txt mainfile.fastq >out.txt

I'm trying to get this to work so I can use a modified command on a larger file along with -A to extract trailing context as well. The output will be too much to read in the terminal.

Any suggestions?

So what does "infile.txt" exactly contain? I mean how "greedy" (or exact) are your matches?

diff is better suited for this scenario.

unSpawn:

Here are the contents of my infile.txt:
@m130129_192343_42154_c100435262550000001523067002011393_s1_p0/70114/ccs
@m130129_192343_42154_c100435262550000001523067002011393_s1_p0/6850/ccs
@m130129_192343_42154_c100435262550000001523067002011393_s1_p0/22749/ccs

In the terminal window, I get the full mainfile.txt with matching lines highlighted:
@m130129_192343_42154_c100435262550000001523067002011393_s1_p0/49/ccs
@m130129_192343_42154_c100435262550000001523067002011393_s1_p0/2229/ccs
@m130129_192343_42154_c100435262550000001523067002011393_s1_p0/22449/ccs
@m130129_192343_42154_c100435262550000001523067002011393_s1_p0/149/ccs
@m130129_192343_42154_c100435262550000001523067002011393_s1_p0/2802/ccs
@m130129_192343_42154_c100435262550000001523067002011393_s1_p0/20/ccs
@m130129_192343_42154_c100435262550000001523067002011393_s1_p0/749/ccs
@m130129_192343_42154_c100435262550000001523067002011393_s1_p0/70114/ccs
@m130129_192343_42154_c100435262550000001523067002011393_s1_p0/6850/ccs
@m130129_192343_42154_c100435262550000001523067002011393_s1_p0/11523/ccs
@m130129_192343_42154_c100435262550000001523067002011393_s1_p0/81245/ccs
@m130129_192343_42154_c100435262550000001523067002011393_s1_p0/27245/ccs
@m130129_192343_42154_c100435262550000001523067002011393_s1_p0/1634/ccs
@m130129_192343_42154_c100435262550000001523067002011393_s1_p0/959/ccs
@m130129_192343_42154_c100435262550000001523067002011393_s1_p0/15423/ccs
@m130129_192343_42154_c100435262550000001523067002011393_s1_p0/834/ccs

The outfile just duplicates the mainfile.txt

Amani - Would that allow me to output lines that are the same between files? And is there an option for including trailing information, similar to grep -A? My end goal is not just to extract lines that are the same, but to use the infile to extract additional information from a mainfile.

Does infile.txt contain blank lines (maybe at the end)? A blank line would match anything.

Yup, good call! Works perfectly now, even when modified with -A to pull out additional lines from a larger file. Thanks so much!

Is it not possible with the
--LTYPE/GTYPE-line-format=... options?