Issue with calling subprocess command

[fwzhao]

toolkit/ngs_toolkit/general.py

Lines 1400 to 1408 in 3f828b2

	# shuffle input in no background is provided
	if background_fasta is None:
	shuffled = input_fasta + ".shuffled"
	cmd = """
	fasta-dinucleotide-shuffle -c 1 -f {0} > {1}
	""".format(
	input_fasta, shuffled
	)
	subprocess.call(cmd.split(" "))

The new lines ("\n") and write std_out (">") are causing problems for subprocess.call
I originally encountered this issue when running meme_ame having broken down the command, wehre first there was a Unknown command argument: "\n": "\n", which i was able to trace to the -
"""
cmd
"""
Subsequently after fixing this, subprocess.call does not recognize ">"

The fix:

shuffled = input_fasta + ".shuffled"
file = open(shuffled, "w")
cmd = """fasta-dinucleotide-shuffle -c 1 -f {0}""".format(
    input_fasta
)
subprocess.call(cmd.split(" "), stdout=file)
file.close()

This actually generates the shuffled background. I'm not sure why ">" is not accepted, I did some googling but it was not successful

[afrendeiro]

Hi, thanks for investigating this.
Yeah that does make sense as that is at least missing a shell=True call.

I've recently come up with a improved function to call subprocess.call (https://github.com/ElementoLab/imcpipeline/blob/master/imcpipeline/utils.py#L158) and will likely port that over to ngs_toolkit.

[fwzhao]

Yes, making it shell=True also could work, but the consensus on stackoverflow was that it's a bit riskier to use shell=True (in certain cases, accidental user input can mess things up), hence the stdout file approach.