script to run CrossMap for a set of bam files

Question

[ifudontmind_plzz]

I was trying to run CrossMap for a set of bam files using this script. But its showing error.

bam_list <- list.files(path = "home_hg19_Bam/", pattern = ".bam$", full.names=T)

for (i in 1:length(bam_list)){
system(paste0("CrossMap.py bam ./hg18ToHg19.over.chain.gz", bam_list[i], folder, "home/SCLC_hg19_Bam/" ,gsub(".bam", "", bam_list[i]), "_hg19.bam"))}

[Pierre Lindenbaum]

why using R ?

[Pierre Lindenbaum]

set the full patch to CrossMap.py, add the python interpreter :" /usr/bin/python /path/to/CrossMap.py ...."

[ifudontmind_plzz]

@Pierre, what would be the best option?

[ifudontmind_plzz]

@Pierre i could not get you

[Pierre Lindenbaum]

a simple bash script...

[ifudontmind_plzz]

Do you mind providing a example?

[Pierre Lindenbaum]

http://tldp.org/HOWTO/Bash-Prog-Intro-HOWTO-7.html