#3.Quantify the TPM of each CDS in each transcriptome using kallisto and use these results as input
#to find differentially expressed genes between the two timepoints (2pi and 6dpi) using the R package sleuth.
#Write the following details for each significant transcript (FDR < 0.05) to your log file, include a header row, and tab-delimit each item: target_id test_stat pval qval

import os

#use kallisto results as input to find differentially expressed genes between the two timepoints (2pi and 6dpi) using the R package sleuth
def run_sleuth():
    sleuth = 'Rscript sleuth.R'
    os.system(sleuth)
    with open('miniProject_Aditi_Patel/sleuth_output.txt') as sleuth_output:
        with open("miniProject.log", "a") as miniProject_log:
            for line in sleuth_output:
                miniProject_log.write(line)


