Extract sequences from a FASTQ file based on another file

[caputcastellae]

I have two files:

file 1: fastaq XXGB file
file 2: list of a few FASTQ ID headers formatted as follows:

@M01032:192:000000000-AAEFT:1:1101:10100:1004 2:N:0:1
@M01032:192:000000000-AAEFT:1:1101:10100:1004 1:N:0:1

Is there an easy way (perl?) to generate a third file with the info (including the ID headers of the targeted sequences (file 2)?

Thanks!

[GenoMax]

There are probably more elegant ways of doing this but you can try this now. With that said (in tcshell and assuming that your sequences do not wrap around)

$ foreach i (`cat ./file_of_ID_you_need`)
foreach? grep ^$i -A 3 your_sequence_file >> new_sequence_file
foreach? end

[gandalf886]

perhaps this?

grep --no-group-separator -A 3 -Fxf file_2 file_1 > output

There are probably more elegant ways of doing this but you can try this now. With that said (in tcshell and assuming that your sequences do not wrap around)

$ foreach i (`cat ./file_of_ID_you_need`)
foreach? grep ^$i -A 3 your_sequence_file >> new_sequence_file
foreach? end

[GenoMax]

If sequence file is compressed then extending gandalf886's suggestion

$ zmore sample.fastq.gz | grep -A 3 -Fxf  file_of_IDs > new_sequence_file

or

$ zcat sample.fastq.gz | grep -A 3 -Fxf  file_of_IDs > new_sequence_file