Xargs to call python executable to process multiple bam files
I am running the below loop that to process the 3 bam files (which isn't always the case). A .py executable is then called using | xargs sh to further process. If I just run it with echo the output is fine and expected, however when | xargs sh is added I get the error. I tried adding | xargs python instead, but get a different error where the standard options are not reconized. It seems like the executable is not be called
, but I do not know enough python to troubleshoot. Thank you .
xargs is used to turn a stream on stdin into command line arguments / parameters. sh expects its commands on stdin. Try without xargs, like
Or, use your .py as the xargs' command but make sure it will be interpreted by python (by defining the correct "shebang").
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Hi,
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Hi,
First post here.
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Hi,
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