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There are totally 6 bam files. In that: 1,2,3 are one group 4,5,6 are in other group do.call([cfg.tool_cmd("cuffdiff"), "-p", str(cfg.project["analysis"]["threads"]), "-b", str(cfg.project["genome"]["fasta"]), "-u", cfg.project["experiment"]["merged"], "-L", "%s,%s" % (str(cfg.project["phenotype"][0])[2:8],str(cfg.project["phenotype"][1])[2:7]), "-o", output_folder] + [cfg.project["samples"][0]["files"]["bam"]] + [cfg.project["samples"][1]["files"]["bam"]] In this call: [cfg.project["samples"][0]["files"]["bam"]] should take 1,2,3 (first group) bam files. [cfg.project["samples"][1]["files"]["bam"]] should take 4,5,6 (Second …

analysis: clip_adapters: false differential_expression: comparisons: - condition1: embryo condition2: larva metadata: phenotype metadata: phenotype: embryo: - SAMN00990702-1 - SAMN00990702-2 - SAMN00990702-3 larva: - SAMN00990703-1 - SAMN00990703-2 - SAMN00990703-3 samples: - files: bam: pipeline/SAMN00990702-1/mappings/accepted_hits.bam name: SAMN00990702-1 output_folder: pipeline/SAMN00990702-1 - files: bam: pipeline/SAMN00990702-2/mappings/accepted_hits.bam name: SAMN00990702-2 output_folder: pipeline/SAMN00990702-2 - files: bam: pipeline/SAMN00990702-3/mappings/accepted_hits.bam name: …

In a python script 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["experiment"]["merged"], "-L", "%s,%s" % (str(cfg.project["phenotype"][0])[2:8],str(cfg.project["phenotype"][1])[2:7]), "-o", output_folder] + [cfg.project["samples"][0]["files"]["bam"] + ' ' + cfg.project["samples"][1]["files"]["bam"]], cfg.project["analysis"]["log_file"]) This gives the command: Command '['/usr/local/bin/cuffdiff', '-p', '5', '-b', '/scratchsan/venkatesh/TuxedoProject/data/genome/ce10.fa', '-u', 'pipeline/merging/merged.gtf', '-L', 'embryo,larva', '-o', 'pipeline/degenes', 'pipeline/SAMN00990702-1/mappings/accepted_hits.bam pipeline/SAMN00990702-2/mappings/accepted_hits.bam']' …

I gave a call in this way: print("-L", str(cfg.project["phenotype"][0]), str(cfg.project["phenotype"][1])) This will read the below one phenotype: - embryo: [SAMN00990702-1] - larva: [SAMN00990702-2] And it should give: -L embryo,larva But it is giving like: -L {'embryo': ['SAMN00990702-1']} {'larva': ['SAMN00990702-2']} Can anyone help me in solving this problem. Thank you !!

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"]], …

This is an R script which I used for plotting. Can anyone please give me a python code for this. Thanks in Advance !! setwd("/pipeline/deff") source('http://www.bioconductor.org/biocLite.R') biocLite('cummeRbund') library(cummeRbund) cuff_data <- readCufflinks('deff') pdf("allplots.pdf") #"distbtn of expression levels for each dataset" plot(csDensity(genes(cuff_data))) #"compare the exp of each gene in all the conditions …