system() and "Unterminated quoted string" error

mothur bugs
1

Hi!

I’m using the system() command to run some perl oneliners in between the mothur commands. I noticed that I can’t have commas in the Perl script, or I get the error
sh: 1: Syntax error: Unterminated quoted string

Example:

mothur > system(perl -e 'print "foo bar"')

foo bar

mothur > system(perl -e 'print "foo", "bar"')

sh: 1: Syntax error: Unterminated quoted string

Both versions work fine in bash directly. For now I’m just replacing commas in my Perl with => but that’s kinda ugly…
This is mothur v.1.31.2 running under Ubuntu, same error in bash or zsh.

Cheers,
Till

2

Bumping this because I’m having the same problem in mothur 1.32.1.

I’m trying to reformat a .taxonomy file like such:

cat test.taxonomy | tr ';' '\t' | cut -f 1,3- > test_tax.tsv

Works on the command line, doesn’t inside a system() call.

3

Easy workaround for anyone else hitting this bug: put the commands in a .sh file, then just:

system(bash commands.sh)