How is possible that 'delta_oligo_combined.bedgraph' file is in the directory and can't be seen by cat command? OSX typo?
$ type=oligo
$ file_type=combined
$ ls delta_oligo_combined.bedgraph
delta_oligo_combined.bedgraph
$ cat delta_$(type)_$(file_type).bedgraph
-bash: file_type: command not found
cat: delta__.bedgraph: No such file or directory
You're looking to include variable values in a (path) string:
${varName} is how you reference a variable named varName - note the delimiters, { and } (which aren't always needed).
By contrast, you mistakenly used syntax $(...), which is meant for for embedding the output from commands in a string.
Therefore, tokens type and file_type were interpreted as commands and executed:
type happens to be the name of a builtin utility that outputs nothing when called without parameters.
file_type, on the other hand, is not the name of any existing command, which is why Bash complained (command not found).
The resulting file path - after the command substitutions were performed - was delta__.bedgraph (both command substitutions expanded to the empty string), causing cat to report a non-existent file (No such file or directory).
See man bash for more.
