Selecting a random read from pair of reads in fastq file - bash

Question

I have a question about random selection of a read from a sampled pair-end fastq files. I read some topics regarding this manner but none could solve my problem, which is:
I got two fastq files R1.fastq and R2.fastq. What I want to achieve is to randomly sample those files and from each sampled pair of reads I want to randomly select only one read.
What I did so far is...
I sampled my files using seqtk:
seqtk sample -s100 R1.fastq 10000 > R1_sample.fastq
seqtk sample -s100 R2.fastq 10000 > R2_sample.fastq
then I sorted each file by sequence ID like this:
paste - - - - < R1_sample.fastq | sort -k1 -t " " | tr "\t" "\n" > R1_sample_sorted.fastq
I did the same with R2_sample.fastq. Then I merged both sorted files so that R1 would be in one column and R2 in the second column:
pr -mts R1_sample_sorted.fastq R2_sample_sorted.fastq > merged.fastq
the file looks like this:
#D3YGT8Q1:297:C7T4RACXX:3:1101:1000 #D3YGT8Q1:297:C7T4RACXX:3:1101:1000
TGATGTTTGGATGTAAAGTGAAATATTAGTTGGCG AGCTTTCCTCACTATCTGCTTCATCCGCCAACTAA
+ +
BBBFFFFFFFFFFFIFFIFFIIIIFIIIFIIFIII B0<FFFFFFFFFFIIIIIIIIIIIIIIIIIIIIII
#D3YGT8Q1:297:C7T4RACXX:3:1101:1000 #D3YGT8Q1:297:C7T4RACXX:3:1101:1000
CCTCCTAGGCGACCCAGACAATTATACCCTAGCCA TGTTTAAGGGGTTGGCTAGGGTATAATTGTCTGGG
+ +
BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIII BBBFFFFFFFFFFIIIIIIIIBFFIIIIIIIIIII
#D3YGT8Q1:297:C7T4RACXX:3:1101:1000 #D3YGT8Q1:297:C7T4RACXX:3:1101:1000
TTCTATTTATTACCTCAGAAGTTTTTTTCTTCGCA GTAAAAGGCTCAGAAAAATCCTGCGAAGAAAAAAA
+ +
BBBFFFFFFFFFFIIIIIIIIFIIFIIIFIIIIII BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIII
And now I want to randomly select only one read from each pair. My initial idea was to use shuf to get a random number from range 1-2:
shuf -i1-2 -n1
and then somehow select the read cooresponding to the number I got from shuf. For example in the first iteration I got 1 so I pick the read from column 1, in the socond iteration I got 2 so from the next pair of reads I pick the read in the second column etc.
I got stuck here. So my question is, is there a neat way to do this? Maybe with awk or some other method? Any help will be very appreciated.
Comment to Ashafixs answer:
Thanks for your respond and sorry for the huge delay...!
I've tested your solutions and they both seem to have flaws.
For the first script I constructed test fastq files R1 and R2 each containing 6 reads. After running the script I expect it to output 6 reads as well (24 lines) in the correct order(ID,seq,desc,qual) but as a set of reads randomly selected from R1 or R2 file. What I got from the script is:
#D3YGT8Q1:297:C7T4RACXX:3:1101:10002:27381 2:N:0:ATGCTCGTTCTCTCGT
AGCTTTCCTCACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACATCAAGATC
+
B0<FFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIFIFIIIIIIIIII
#D3YGT8Q1:297:C7T4RACXX:3:1101:10004:50631 2:N:0:ATGCTCGTTCTCTCGT
#D3YGT8Q1:297:C7T4RACXX:3:1101:10007:32152 1:N:0:ATGCTCGTTCTCTCGT
GTAAGGTTAGGAGGGTGTTAATTATTAAAATTAAGGCGAAGTTTATTACTCTTTTTTGAATGTTG
+
BBBFFFFFFFFFFIIBFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFF
You can see that the output is not correct. The second read is missing three lines and there should be six reads in total not three. In addition each time I run the script it outputs different number of reads.
For the second script I input a merged fastq file like described above. The output looks similar to the first script output:
#D3YGT8Q1:297:C7T4RACXX:3:1101:10002:27381 2:N:0:ATGCTCGTTCTCTCGT
AGCTTTCCTCACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACATCAAGATC
+
B0<FFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIFIFIIIIIIIIII
#D3YGT8Q1:297:C7T4RACXX:3:1101:10004:50631 2:N:0:ATGCTCGTTCTCTCGT
#D3YGT8Q1:297:C7T4RACXX:3:1101:10004:50631 2:N:0:ATGCTCGTTCTCTCGT
TGTTTAAGGGGTTGGCTAGGGTATAATTGTCTGGGTCGCCTAGGAGGAGATCGGAAGAGCGTCGT
+
BBBFFFFFFFFFFIIIIIIIIBFFIIIIIIIIIIIFFFIIIIIIFIIIIIFIIIFFFFFFFFFFF
#D3YGT8Q1:297:C7T4RACXX:3:1101:10004:88140 1:N:0:ATGCTCGTTCTCTCGT
ACTGTAACTTAAAAATGATCAAATTATGTTTCCCATGCATCAGGTGCAATGAGAAGCTCTTCATC
+
BBBFFFFFFFFFFIIIIIIIIIIFIIIIIIFIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIIII
#D3YGT8Q1:297:C7T4RACXX:3:1101:10007:32152 2:N:0:ATGCTCGTTCTCTCGT
CTAGTTTTGACAACATTCAAAAAAGAGTAATAAACTTCGCCTTAATTTTAATAATTAACACCCTC
+
BBBFFFFFFFFFFIIIIIIIIIIIIIIFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIII
but this time I always get five reads. Still missing one. And the second and third read headers are the same. This should not happen.

Answer 1

You could try the following script (it also works as one liner). First it gets all the headers from your first fastq file, then it randomly picks a fastq file and returns 4 lines from it.
Please note: This only works if both files have identical headers at identical positions.
#!/bin/bash
headers=$(grep # R1_sample.fastq)
var=1
for line in $headers ; do
r=$(shuf -i1-2 -n1)
tail -n +$var "R$r"_sample.fastq | grep -m 1 -A 4 $line
var=$((var+4))
done
Alternatively you could expand your merge and pick a column approach. cut is used to remove a random column from the merged output.
#!/bin/bash
headers=$(grep # merged.fastq)
var=1
for line in $headers ; do
r=$(shuf -i1-2 -n1)
tail -n +$var merged.fastq | grep -m 1 -A 4 $line | cut -d$'\t' -f$r
var=$((var+4))
done