How to match the regex for the below pattern? - regex

Question

I am trying to write a script which should work out like this below but somehow am not able to get the write way to put the syntax.
I have folders like S_12_O_319_K4me1.
While the contents are S_12_O_319_K4me1_S12816.sorted.bam in each folder.
So I wanted to write a script where my my script goes into my folder of the same name in a loop and then identifies the *.bam file and perform the operation, but I am unable to put the regex. This is what I tried:
#!/bin/bash
#$ -S /bin/bash
spp_run=/path/phantompeakqualtools/run_spp.R
bam_loc=/path/ChIP-Seq/output
samples="S_12_O_319_K27me3
S_12_O_319_K4me1
S_12_O_319_K4me3
S_12_O_319_K27ac"
for s in $samples; do
echo "Running SPP on $s ..."
Rscript $spp_run -c=$bam_loc/$s/${s}_S[[0-9]+\.sorted.bam -savp -out=$bam_loc/$s/${s}".run_spp.out"
done
I am not being able to recognize the digits with the above regex match.
Where am I getting it wrong?
Edit:
I tried below still it does not work, problem with parsing in the Rscript, but why will this be a problem
#!/bin/bash
#$ -S /bin/bash
spp_run=/path/tools/phantompeakqualtools/run_spp.R
bam_loc=/path/ChIP-Seq/output
samples="S_12_O_319_K27me3
S_12_O_319_K4me1
S_12_O_319_K4me3"
for s in $samples; do
echo "Running SPP on $s ..."
echo $bam_loc/$s/${s}_S*.sorted.bam
inbam=$bam_loc/$s/${s}_S*.sorted.bam
echo $inbam
Rscript $spp_run -c=$inbam -savp -out=$bam_loc/$s/${s}".run_spp.out"
done
echo "done"
Error
Error in parse.arguments(args) :
ChIP File:/path/ChIP-Seq/output/S_12_O_319_K27me3/S_12_O_319_K27me3_S*.sorted.bam does not exist
Execution halted
Does not recognize the file even though $inbam value is /path/ChIP-Seq/output/S_12_O_319_K27me3/S_12_O_319_K27me3_S12815.sorted.bam

Answer 1

You can use a regex in a find command :
export spp_run=/path/phantompeakqualtools/run_spp.R
export bam_loc=/path/ChIP-Seq/output
export dir
samples=(S_12_O_319_K27me3 S_12_O_319_K4me1 S_12_O_319_K4me3 S_12_O_319_K27ac)
for dir in ${samples[#]}; do
find . -type f -regex ".*/*${dir}_S[0-9]+\.sorted\.bam" \
-exec bash -c 'echo Rscript $spp_run -c=$bam_loc/${dir}/${1##*/} -savp -out=$bam_loc/${dir}/${dir}".run_spp.out"' _ {} \;
done
Note : just remove the echo before the Rscript if the output meets your needs.

Answer 2

I found answer to my query and below is the code. Not an elegant one but it works. I realized that the Rscript requires full name and full path so I just initialized the output of the echo command to a variable and passed it to the Rscript as input file argument and it gets a full path with full filename so now it recognizes the input file.
Not an elegant way but still it works for me.
#!/bin/bash
#$ -S /bin/bash
spp_run=/path/tools/phantompeakqualtools/run_spp.R
bam_loc=/path/ChIP-Seq/output
samples="S_12_O_319_K27me3
S_12_O_319_K4me1
S_12_O_319_K4me3"
for s in $samples; do
echo "Running SPP on $s ..."
echo $bam_loc/$s/${s}_S*.sorted.bam
inbam=$bam_loc/$s/${s}_S*.sorted.bam
echo $inbam
infile=`echo $inbam`
Rscript $spp_run -c=$infile -savp -out=$bam_loc/$s/${s}".run_spp.out"
done
echo "done"
Thanks everyone for the suggestions and comments. My code is not elegant but it is working so I put the answer here.