python error in cuffdiff script

[bvk]

I used this in command line:

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

here SRR493359_60_61 is one group and SRR493363_64_65 is the other group. This worked for me.

Now I want to run this from a python script. So, I gave a call in this way.

do.call([cfg.tool_cmd("cuffdiff"), "-p", str(cfg.project["analysis"]["threads"]), "-b", str(cfg.project["genome"]["fasta"]), "-u", cfg.project["samples"][0]["files"]["merging_gtf"], "-L", str(cfg.project["phenotype"][0]), str(cfg.project["phenotype"][1]), "-o", output_folder] + [cfg.project["samples"][0]["files"]["bam"] cfg.project["samples"][1]["files"]["bam"]], cfg.project["analysis"]["log_file"])

here
str(cfg.project["phenotype"][0]) is larval
str(cfg.project["phenotype"][1]) is early

I get an error: invalid syntax. Can anyone please help in this. Thanks in Advance

[rflrob]

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:

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)

[bvk]

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:

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.

[rflrob]

I'm not familiar with this "do" module you seem to be using, but I'm pretty sure that passing a list is the equivalent of spaces on the command line. For instance, in the original cuffdiff call, it's not "cuffdiff, -o, diff_out4, ...". So you can see that the syntax in python isn't exactly the same as the command that gets generated. Thus, you really do want that comma there.

More generally, Python doesn't know how to combine the two variables if there's no comma between them. Depending on the type (which the syntax parser doesn't know in advance), you could want to concatenate them (if strings), multiply them (if they're numbers), or do something else entirely. Recall the Zen of Python: "In the face of ambiguity, refuse the temptation to guess." Since the syntax could be ambiguous, it instead throws a syntax error.