nested for loop to concatenate fastq files

[lkomo]

My pooled PE RNA-Seq data was demultiplexed by the sequencing facility, so the data I receive is a directory with sub directories for each sample that contain the R1 and R2 fastq files for each lane (i.e., the main directory "FISH_RNA_SEQ" has 96 folders, each labeled by sample-like "SpA.Treatment1.Rep1", etc.). If I am in a sub-directory for a particular sample, I can concatenate across lanes and write to a file in a new directory so I have two files for each sample (R1/R2) using this for loop:

for SUFFIX in R1_001.fastq R2_001.fastq
do
cat *L001_$SUFFIX *L002_$SUFFIX *L003_$SUFFIX > ../test.cat.DDIG/samplename_cat_$SUFFIX
done

However, this requires me to manually run this for each of the 96 samples, going into the sub-directory and typing in the desired output name. Since I will have to repeat this in the future, does anyone have suggestions about how to use a nested for loop (or other way) to do this automatically/iteratively do this from the main directory for all subdirectories, naming the output files with by the subdirectory (i.e. sample name)?

Working from the main directory, I was testing something like:
for dir in *; do
(for SUFFIX in R1_001.fastq R2_001.fastq
do
cat *L001_$SUFFIX *L002_$SUFFIX *L003_$SUFFIX > ../test.cat.DDIG/test_cat_$SUFFIX
done)

But this doesn't seem to work, and it doesn't solve the problem of naming the output files according to the sample names. Any suggestions appreciated!

[dpryan]

Do you just want to use the directory name (e.g., SpA.Treatment1.Rep1) as the prefix, or some variant of whatever the file names are?

[lkomo]

Yes, ideally the directory name would be the file name prefix, so for example a 'Sample1.treatment1.Rep1' directory would produce two output files like: 'Sample1.treatment1.Rep1_cat_R1.001.fastq' and 'Sample1.treatment1.Rep1_cat_R2.001.fastq'

And then the same for all the other directories/samples...
Thank you!

[dpryan]

for dir in `find . -maxdepth 1 -mindepth 1 -type d -printf "%f\n"`
do
    cd $dir
    cat *_L???_R1_*.fastq > $dir_R1.fastq
    cat *_L???_R2_*.fastq > $dir_R2.fastq
    cd ..
done

or something like that.

[lkomo]

thank you! I think I see what each part does except the "%f\n"? my apologies if it's obvious-I'm still fairly new.

[dpryan]

That's just the formatting that the results should be returned in.

[lkomo]

great, thank you so much for the help!