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Old 05-07-2015, 07:16 AM   #1
bvk
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Location: czech

Join Date: May 2015
Posts: 65
Default python error in cuffdiff script

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
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