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Old 05-07-2015, 11:51 PM   #3
bvk
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Location: czech

Join Date: May 2015
Posts: 65
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Quote:
Originally Posted by rflrob View Post
It looks to me like you're perhaps missing a comma after cfg.project["samples"][0]["files"]["bam"]. As a general debugging strategy, when you have massive blocks of code like that, it's often easier to break it up into component parts, so those could be debugged individually. So something like:

Code:
base_options = [cfg.tool_cmd("cuffdiff"),
                        "-p", str(cfg.project["analysis"]),
                        "etc etc"]

files = [
    cfg.project["samples"][0]["files"]["bam"],
    cfg.project["samples"][1]["files"]["bam"],
    cfg.project["analysis"]["log_file"]
]

do.call(base_options + files)
Thanks for the reply. You may be right in one case. But I want to run this for groups.

cfg.project["samples"][0]["files"]["bam"] is group1
cfg.project["samples"][1]["files"]["bam"] is group2

so it should be group1 vs group2. So, the bam files should be separated with space. And If I run this with space its giving an error. Please tell me how to run this with space between the bam files.
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