I run a command on command line like :
cuffdiff -o diff_out4 -b ../genome/ce10.fa -p 2 -L larval,early -u merged_asm/merged.gtf ../tophat/em/SRR493359_60_61_thout/accepted_hits.bam ../tophat/em/SRR493363_64_65_thout/accepted_hits.bam
Both bam files are separated with "space".
Now the same command I gave a call in python script:
do.call([cfg.tool_cmd("cuffdiff"),
"-b", str(cfg.project["genome"]["fasta"]),
"-u", cfg.project["experiment"]["merged"],
"-o", output_folder] + [cfg.project["samples"][0]["files"]["bam"]
cfg.project["samples"][1]["files"]["bam"]],
cfg.project["analysis"]["log_file"])
It gave me a syntax error because of the space. Can anyone help me how to use this.