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Wangen_G418_workflow.py
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Wangen_G418_workflow.py
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__author__ = 'Jamie Wangen'
"""
Workflow for generating figures for G418 paper: https://doi.org/10.1101/798579
### Dependencies:
Python:
matplotlib 2.2.2
numpy 1.14.0
pandas 0.22.0
pysam 0.13
scipy 1.0.1
seaborn 0.9.0
twobitreader 3.1.5
argparse 1.1
multiprocessing 0.70a1
pathos 0.2.1
"""
import sys
import os
import importlib
import argparse
import subprocess
from ftplib import FTP
rootDir = os.path.dirname(os.path.realpath(__file__)) ## add current directory as rootDir
threadNumb = 40
##### 1) Generate Genome Files:
### download hg38 from genecode:
class generateGenomes(object):
### building all files need for downstream analysis
def __init__(self, rootDir, threadNumb):
self.rootDir = rootDir
self.threadNumb = threadNumb
def download_hg38(self):
"""
"""
outfile = "%s/genomes/GRCh38.primary_assembly.genome.fa.gz" % self.rootDir
hg38file = "GRCh38.primary_assembly.genome.fa.gz"
if not os.path.exists("%s/genomes" % rootDir): os.makedirs("%s/genomes" % self.rootDir)
ftp = FTP('ftp.ebi.ac.uk')
ftp.login()
ftp.cwd('pub/databases/gencode/Gencode_human/release_30/')
with open(outfile, 'wb') as fp:
ftp.retrbinary('RETR %s' % hg38file, fp.write)
ftp.quit()
def clean_hg38(self):
GRCh38 = "%s/genomes/GRCh38.primary_assembly.genome.fa.gz" % self.rootDir
# checkCmnd = "zcat %s | grep -in '>' " % GRCh38
# print checkCmnd
# subprocess.check_output(checkCmnd, shell=True)
gunzipCmnd = "gunzip %s" % GRCh38
subprocess.Popen(gunzipCmnd, shell= True).wait()
### 51471479 last line of valid chromosomes
cleanCmnd = "sed -n '1,51471479p' %s/genomes/GRCh38.primary_assembly.genome.fa > %s/genomes/hg38.fa" % (self.rootDir, self.rootDir)
subprocess.Popen(cleanCmnd, shell= True).wait()
indexCmnd = "samtools faidx %s/genomes/hg38.fa" % (self.rootDir)
subprocess.Popen(indexCmnd, shell= True).wait()
TwoBitCmnd = "faToTwoBit %s/genomes/hg38.fa %s/genomes/hg38.2bit" % (self.rootDir, self.rootDir)
subprocess.Popen(TwoBitCmnd, shell= True).wait()
removeGRCh38 = "rm %s/genomes/GRCh38.primary_assembly.genome.fa" % (self.rootDir)
subprocess.Popen(removeGRCh38, shell= True).wait()
def download_Gencode_annotation(self):
outfile = "%s/genomes/gencode.v30.annotation.gtf.gz" % (self.rootDir)
annotationFile = "gencode.v30.annotation.gtf.gz"
outfile_tRNA = "%s/genomes/gencode.v30.tRNAs.gtf.gz" % (self.rootDir)
annotationFiletRNA = "gencode.v30.tRNAs.gtf.gz"
ftp = FTP('ftp.ebi.ac.uk')
ftp.login()
ftp.cwd('pub/databases/gencode/Gencode_human/release_30/')
with open(outfile, 'wb') as fp:
ftp.retrbinary('RETR %s' % annotationFile, fp.write)
with open(outfile_tRNA, 'wb') as fp:
ftp.retrbinary('RETR %s' % annotationFiletRNA, fp.write)
ftp.quit()
def parse_GTF_file(self):
gtfInFile = "%s/genomes/gencode.v30.annotation.gtf.gz" % (self.rootDir)
parseCmnd = "python2 %s/utils/GTF_hg38_protCode_termStop_validUTR.py --gtfInFile %s --rootDir %s" % (
self.rootDir, gtfInFile, self.rootDir)
subprocess.Popen(parseCmnd, shell= True).wait()
def build_annotation_files(self):
gtfInFilePrefix = "%s/genomes/gencodeV30_protCode_TermStopCodon_validUTRs" % (self.rootDir)
twoBitGenome = "%s/genomes/hg38.2bit" % (self.rootDir)
mRNA_cmnd = "python2 %s/utils/mRNA_sequences_from_gtf.py --gtfInFilePrefix %s --rootDir %s --twoBitGenome %s" % (
self.rootDir, gtfInFilePrefix, self.rootDir, twoBitGenome)
subprocess.Popen(mRNA_cmnd, shell= True).wait()
prot_cmnd = "python2 %s/utils/protein_sequences_from_gtf.py --gtfInFilePrefix %s --rootDir %s --twoBitGenome %s" % (
self.rootDir, gtfInFilePrefix, self.rootDir, twoBitGenome)
subprocess.Popen(prot_cmnd, shell= True).wait()
utrTable_cmnd = "python2 %s/utils/makeUTRtable.py --gtfInFilePrefix %s --rootDir %s --twoBitGenome %s" % (
self.rootDir, gtfInFilePrefix, self.rootDir, twoBitGenome)
subprocess.Popen(utrTable_cmnd, shell= True).wait()
stopFinder_cmnd = "python2 %s/utils/stopcodon_finder.py --gtfInFilePrefix %s --rootDir %s --twoBitGenome %s" % (
self.rootDir, gtfInFilePrefix, self.rootDir, twoBitGenome)
subprocess.Popen(stopFinder_cmnd, shell= True).wait()
stopPositions_cmnd = "python2 %s/utils/utr3_stop_positions.py --gtfInFilePrefix %s --rootDir %s --twoBitGenome %s" % (
self.rootDir, gtfInFilePrefix, self.rootDir, twoBitGenome)
subprocess.Popen(stopPositions_cmnd, shell= True).wait()
uORFs_cmnd = "python2 %s/utils/uORF_finder.py --gtfInFilePrefix %s --rootDir %s --twoBitGenome %s" % (
self.rootDir, gtfInFilePrefix, self.rootDir, twoBitGenome)
subprocess.Popen(uORFs_cmnd, shell= True).wait()
codons_cmnd = "python2 %s/utils/codonFinder.py --gtfInFilePrefix %s --rootDir %s --twoBitGenome %s --threadNumb %s" % (
self.rootDir, gtfInFilePrefix, self.rootDir, twoBitGenome, self.threadNumb)
subprocess.Popen(codons_cmnd, shell= True).wait()
def parse_GTF_allTr(self):
gtfInFile = "%s/genomes/gencode.v30.annotation.gtf.gz" % (self.rootDir)
parseCmnd = "python2 %s/utils/GTF_hg38_all_tr.py --gtfInFile %s --rootDir %s" % (
self.rootDir, gtfInFile, self.rootDir)
subprocess.Popen(parseCmnd, shell= True).wait()
def build_annotation_allTR(self):
gtfInFilePrefix = "%s/genomes/gencodeV30_all_tr" % (self.rootDir)
twoBitGenome = "%s/genomes/hg38.2bit" % (self.rootDir)
utrTable_cmnd = "python2 %s/utils/makeUTRtable.py --gtfInFilePrefix %s --rootDir %s --twoBitGenome %s" % (
self.rootDir, gtfInFilePrefix, self.rootDir, twoBitGenome)
subprocess.Popen(utrTable_cmnd, shell= True).wait()
def build_ncRNA_depletion(self):
gtfInFile = "%s/genomes/gencode.v30.annotation.gtf.gz" % (self.rootDir)
gtfInFileTrna = "%s/genomes/gencode.v30.tRNAs.gtf.gz" % (self.rootDir)
rRNAncbi = "%s/genomes/refseq_human_rRNA_all.fa" % (self.rootDir)
twoBitGenome = "%s/genomes/hg38.2bit" % (self.rootDir)
ncRNA_depletion_cmnd = "python2 %s/utils/rRNA_depletion_hg38.py --gtfInFile %s --gtfInFileTrna %s --rRNAncbi %s --rootDir %s --twoBitGenome %s" % (
self.rootDir, gtfInFile, gtfInFileTrna, rRNAncbi, self.rootDir, twoBitGenome)
subprocess.Popen(ncRNA_depletion_cmnd, shell= True).wait()
def build_STAR_indexes(self):
### ncRNA
ncSparsity = 1
ncGenomeDir = "%s/genomes/star_hg38_ncRNA" % self.rootDir
ncGenomeFasta = "%s/genomes/gencodeV30_ncRNA_all.fa" % self.rootDir
ncSjdbGTF = "0"
ncSAindexNbases = 9
ncRNA_build_STAR_index = "python2 %s/utils/buildStarIndex.py --rootDir %s --threadNumb %s --STARsparsity %s --genomeDir %s --genomeFastaFiles %s --sjdbGTF %s --SAindexNbases %s" % (
self.rootDir, self.rootDir, self.threadNumb, ncSparsity, ncGenomeDir, ncGenomeFasta, ncSjdbGTF, ncSAindexNbases)
subprocess.Popen(ncRNA_build_STAR_index, shell=True).wait()
### hg38
## need to unzip GTF file to work with STAR
unzip_cmnd = "gunzip %s/genomes/gencode.v30.annotation.gtf.gz" % self.rootDir
subprocess.Popen(unzip_cmnd, shell=True).wait()
hgSparsity = 1
hgGenomeDir = "%s/genomes/star_gtf_gencodeV30annotation" % self.rootDir
hgGenomeFasta = "%s/genomes/hg38.fa" % self.rootDir
hgSjdbGTF = "%s/genomes/gencode.v30.annotation.gtf" % self.rootDir
hgSAindexNbases = 14
hg38_build_STAR_index = "python2 %s/utils/buildStarIndex.py --rootDir %s --threadNumb %s --STARsparsity %s --genomeDir %s --genomeFastaFiles %s --sjdbGTF %s --SAindexNbases %s" % (
self.rootDir, self.rootDir, self.threadNumb, hgSparsity, hgGenomeDir, hgGenomeFasta, hgSjdbGTF, hgSAindexNbases)
subprocess.Popen(hg38_build_STAR_index, shell=True).wait()
gzip_cmnd = "gzip %s/genomes/gencode.v30.annotation.gtf" % self.rootDir
subprocess.Popen(gzip_cmnd, shell=True).wait()
##### 2) Retrieve RawData
class RawData(object):
### building all files need for downstream analysis
def __init__(self, rootDir, threadNumb):
self.rootDir = rootDir
self.threadNumb = threadNumb
def FASTQ_dump_sequences(self):
"""
Download all FASTQ_files in appropriate directories for downstream analysis
"""
fq_dump_cmnd = "python2 %s/utils/fastqDump_G418.py --rootDir %s --threadNumb %s" % (
self.rootDir, self.rootDir, self.threadNumb)
subprocess.Popen(fq_dump_cmnd, shell=True).wait()
def merge_allAG_experiment(self):
"""
merge fastq files from allAG profiling experiment
"""
inputDir = "%s/Data/RPF/FASTQ" % self.rootDir
outputDir = "%s/Data/RPF/FASTQ/allAGmerge" % self.rootDir
if not os.path.exists(outputDir): os.makedirs(outputDir)
mergeFQ_cmnd = "python2 %s/utils/merge_fastq_allAG.py --inputDir %s --outputDir %s" % (
self.rootDir, inputDir, outputDir)
subprocess.Popen(mergeFQ_cmnd, shell=True).wait()
##### 3) Run main analysis pipeline on ribosome profiling data
class RibosomeProfiling_workflow(object):
def __init__(self, rootDir, threadNumb, libSetFile, libSetFileAllTr):
self.rootDir = rootDir
self.threadNumb = threadNumb
self.libSetFile = libSetFile
self.libSetFileAllTr = libSetFileAllTr
def RPexp(self):
"""
run the main ribosome profiling workflow for all samples here
"""
riboseq_cmnd = "python2 %s/riboseq/riboseq_main.py --rootDir %s --libSetFile %s --threadNumb %s" % (
self.rootDir, self.rootDir, self.libSetFile, self.threadNumb)
subprocess.Popen(riboseq_cmnd, shell=True).wait()
def RP_raw_countTables(self):
"""
build raw count tables for RNA seq files
"""
raw_countTables_cmnd = "python2 %s/riboseq/riboseq_build_exp_RAW_countTables.py --rootDir %s --libSetFile %s --threadNumb %s" % (
self.rootDir, self.rootDir, self.libSetFile, self.threadNumb)
subprocess.Popen(raw_countTables_cmnd, shell=True).wait()
def RP_avgene_cdsNorm_start(self):
avgene_cmnd = "python2 %s/riboseq/riboseq_avggene_cdsNorm_start.py --rootDir %s --libSetFile %s --threadNumb %s" % (
self.rootDir, self.rootDir, self.libSetFile, self.threadNumb)
subprocess.Popen(avgene_cmnd, shell=True).wait()
def RP_avgene_cdsNorm_stop(self):
avgene_cmnd = "python2 %s/riboseq/riboseq_avggene_cdsNorm_stop.py --rootDir %s --libSetFile %s --threadNumb %s" % (
self.rootDir, self.rootDir, self.libSetFile, self.threadNumb)
subprocess.Popen(avgene_cmnd, shell=True).wait()
def RP_codon_occ(self):
gtfInFilePrefix = "gencodeV30_protCode_TermStopCodon_validUTRs"
codon_occ_cmnd = "python2 %s/riboseq/riboseq_codon_occ_workflow.py --gtfInFilePrefix %s --rootDir %s --libSetFile %s --threadNumb %s" % (
self.rootDir, gtfInFilePrefix, self.rootDir, self.libSetFile, self.threadNumb)
subprocess.Popen(codon_occ_cmnd, shell=True).wait()
def densebuild_allTr(self):
dballTr_cmnd = "python2 %s/riboseq/riboseq_allTr_wf.py --rootDir %s --libSetFile %s --threadNumb %s" % (
self.rootDir, self.rootDir, self.libSetFileAllTr, self.threadNumb)
subprocess.Popen(dballTr_cmnd, shell=True).wait()
class RNAseq_workflow(object):
def __init__(self, rootDir, threadNumb, libSetFile):
self.rootDir = rootDir
self.threadNumb = threadNumb
self.libSetFile = libSetFile
def RNAexp(self):
rnaseq_cmnd = "python2 %s/RNAseq/RNAseq_main.py --rootDir %s --libSetFile %s --threadNumb %s" % (
self.rootDir, self.rootDir, self.libSetFile, self.threadNumb)
subprocess.Popen(rnaseq_cmnd, shell=True).wait()
def RNA_raw_countTables(self):
raw_countTables_cmnd = "python2 %s/RNAseq/RNAseq_build_exp_RAW_countTables.py --rootDir %s --libSetFile %s --threadNumb %s" % (
self.rootDir, self.rootDir, self.libSetFile, self.threadNumb)
subprocess.Popen(raw_countTables_cmnd, shell=True).wait()
### plot figures:
class plot_figures(object):
def __init__(self, rootDir, threadNumb,
libSet_RP_allG418, libSet_RP_allAGmerge,
libSet_RNA_HEK293T, libSet_RNA_Calu6,
libSet_RP_allG418_allTr):
self.rootDir = rootDir
self.threadNumb = threadNumb
self.libSet_RP_allG418 = libSet_RP_allG418
self.libSet_RP_allAGmerge = libSet_RP_allAGmerge
self.libSet_RNA_HEK293T = libSet_RNA_HEK293T
self.libSet_RNA_Calu6 = libSet_RNA_Calu6
self.libSet_RP_allG418_allTr = libSet_RP_allG418_allTr
def plot_figure_1(self):
fig_cmnd = "python2 %s/figures/figscripts/plot_figure1.py --rootDir %s --threadNumb %s" % (
rootDir, rootDir, threadNumb)
subprocess.Popen(fig_cmnd, shell=True).wait()
def plot_figure_2(self):
fig_cmnd_AB = "python2 %s/figures/figscripts/plot_figure2AB.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allAGmerge, threadNumb)
subprocess.Popen(fig_cmnd_AB, shell=True).wait()
fig_cmnd_C = "python2 %s/figures/figscripts/plot_figure2C.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_C, shell=True).wait()
fig_cmnd_D = "python2 %s/figures/figscripts/plot_figure2D.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allAGmerge, threadNumb)
subprocess.Popen(fig_cmnd_D, shell=True).wait()
fig_cmnd_S1 = "python2 %s/figures/figscripts/plot_figure2S1.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_S1, shell=True).wait()
fig_cmnd_S2A = "python2 %s/figures/figscripts/plot_figure2S2A.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_S2A, shell=True).wait()
fig_cmnd_S2C = "python2 %s/figures/figscripts/plot_figure2S2C.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_S2C, shell=True).wait()
fig_cmnd_S3A = "python2 %s/figures/figscripts/plot_figure2S3A.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allAGmerge, threadNumb)
subprocess.Popen(fig_cmnd_S3A, shell=True).wait()
fig_cmnd_S3B = "python2 %s/figures/figscripts/plot_figure2S3B.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_S3B, shell=True).wait()
def plot_figure_3(self):
fig_cmnd_A = "python2 %s/figures/figscripts/plot_figure3A.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_A, shell=True).wait()
fig_cmnd_BC = "python2 %s/figures/figscripts/plot_figure3BC.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_BC, shell=True).wait()
fig_cmnd_D = "python2 %s/figures/figscripts/plot_figure3D.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_D, shell=True).wait()
fig_cmnd_E = "python2 %s/figures/figscripts/plot_figure3E.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_E, shell=True).wait()
fig_cmnd_S1A = "python2 %s/figures/figscripts/plot_figure3S1A.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_S1A, shell=True).wait()
fig_cmnd_S1B = "python2 %s/figures/figscripts/plot_figure3S1B.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_S1B, shell=True).wait()
fig_cmnd_S1C = "python2 %s/figures/figscripts/plot_figure3S1C.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_S1C, shell=True).wait()
fig_cmnd_S2 = "python2 %s/figures/figscripts/plot_figure3S2.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_S2, shell=True).wait()
def plot_figure_4(self):
fig_cmnd_A = "python2 %s/figures/figscripts/plot_figure4A.py --rootDir %s --threadNumb %s" % (
rootDir, rootDir, threadNumb)
subprocess.Popen(fig_cmnd_A, shell=True).wait()
fig_cmnd_B = "python2 %s/figures/figscripts/plot_figure4B.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_B, shell=True).wait()
fig_cmnd_C = "python2 %s/figures/figscripts/plot_figure4C.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_C, shell=True).wait()
fig_cmnd_D = "python2 %s/figures/figscripts/plot_figure4D.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_D, shell=True).wait()
fig_cmnd_S1A = "python2 %s/figures/figscripts/plot_figure4S1A.py --rootDir %s --threadNumb %s" % (
rootDir, rootDir, threadNumb)
subprocess.Popen(fig_cmnd_S1A, shell=True).wait()
fig_cmnd_S1B = "python2 %s/figures/figscripts/plot_figure4S1B.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_S1B, shell=True).wait()
def plot_figure_5(self):
fig_cmnd_A = "python2 %s/figures/figscripts/plot_figure5A.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_A, shell=True).wait()
fig_cmnd_B = "python2 %s/figures/figscripts/plot_figure5B.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_B, shell=True).wait()
fig_cmnd_C = "python2 %s/figures/figscripts/plot_figure5C.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_C, shell=True).wait()
fig_cmnd_D = "python2 %s/figures/figscripts/plot_figure5D.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_D, shell=True).wait()
fig_cmnd_S1A = "python2 %s/figures/figscripts/plot_figure5S1A.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_S1A, shell=True).wait()
fig_cmnd_S1B = "python2 %s/figures/figscripts/plot_figure5S1B.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_S1B, shell=True).wait()
fig_cmnd_S2 = "python2 %s/figures/figscripts/plot_figure5S2.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_S2, shell=True).wait()
def plot_figure_6(self):
fig_cmnd_B = "python2 %s/figures/figscripts/plot_figure6B.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RNA_Calu6, threadNumb)
subprocess.Popen(fig_cmnd_B, shell=True).wait()
fig_cmnd_C = "python2 %s/figures/figscripts/plot_figure6C.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418_allTr, threadNumb)
subprocess.Popen(fig_cmnd_C, shell=True).wait()
fig_cmnd_S1 = "python2 %s/figures/figscripts/plot_figure6S1.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_S1, shell=True).wait()
def plot_figure_7(self):
libSetPathForR = "%s/RNAseq/libsettings/%s.py" % (rootDir, self.libSet_RNA_HEK293T)
# print libSetPathForR
fig_cmnd_AB_1 = "Rscript %s/figures/figscripts/plot_figure7AB.R %s %s" % (
rootDir, libSetPathForR, rootDir)
subprocess.Popen(fig_cmnd_AB_1, shell=True).wait()
fig_cmnd_AB_2 = "python2 %s/figures/figscripts/plot_figure7AB.py --rootDir %s --threadNumb %s" % (
rootDir, rootDir, threadNumb)
subprocess.Popen(fig_cmnd_AB_2, shell=True).wait()
fig_cmnd_Cl = "python2 %s/figures/figscripts/plot_figure7C_left.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allAGmerge, threadNumb)
subprocess.Popen(fig_cmnd_Cl, shell=True).wait()
fig_cmnd_Cr = "python2 %s/figures/figscripts/plot_figure7C_right.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allAGmerge, threadNumb)
subprocess.Popen(fig_cmnd_Cr, shell=True).wait()
fig_cmnd_Dl = "python2 %s/figures/figscripts/plot_figure7D_left.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418_allTr, threadNumb)
subprocess.Popen(fig_cmnd_Dl, shell=True).wait()
fig_cmnd_Dr = "python2 %s/figures/figscripts/plot_figure7D_right.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418_allTr, threadNumb)
subprocess.Popen(fig_cmnd_Dr, shell=True).wait()
fig_cmnd_El = "python2 %s/figures/figscripts/plot_figure7E_left.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_El, shell=True).wait()
fig_cmnd_Er = "python2 %s/figures/figscripts/plot_figure7E_right.py --rootDir %s --libSetFile %s --threadNumb %s" % (
rootDir, rootDir, self.libSet_RP_allG418, threadNumb)
subprocess.Popen(fig_cmnd_Er, shell=True).wait()
fig_cmnd_S1B = "python2 %s/figures/figscripts/plot_figure7S1B.py --rootDir %s --threadNumb %s" % (
rootDir, rootDir, threadNumb)
subprocess.Popen(fig_cmnd_S1B, shell=True).wait()
##### MAIN #####
def main():
### 1) Generate Genome Files
genomeGen = generateGenomes(rootDir, threadNumb)
genomeGen.download_hg38()
genomeGen.clean_hg38()
genomeGen.download_Gencode_annotation()
genomeGen.parse_GTF_file() ## this takes awhile
genomeGen.build_annotation_files()
genomeGen.parse_GTF_allTr() ## this takes a very long time
genomeGen.build_annotation_allTR()
genomeGen.build_ncRNA_depletion()
genomeGen.build_STAR_indexes()
### 2) Process Raw Data
rawData = RawData(rootDir, threadNumb)
rawData.FASTQ_dump_sequences()
rawData.merge_allAG_experiment()
### 3) Run Ribosome Profiling analysis pipeline
RP = RibosomeProfiling_workflow(rootDir, threadNumb,
libSetFile="riboseq_libsettings_allG418",
libSetFileAllTr="riboseq_libsettings_allG418_allTr")
RP.RPexp()
RP.RP_raw_countTables()
RP.RP_avgene_cdsNorm_stop()
RP.RP_codon_occ()
RP.densebuild_allTr()
RP2 = RibosomeProfiling_workflow(rootDir, threadNumb,
libSetFile="riboseq_libsettings_allAGmerge",
libSetFileAllTr="riboseq_libsettings_allAGmerge_allTr")
RP2.RPexp()
RP2.RP_raw_countTables()
RP2.RP_avgene_cdsNorm_start()
RP2.RP_avgene_cdsNorm_stop()
### 4) Run RNAseq analysis pipeline
RNA = RNAseq_workflow(rootDir, threadNumb, libSetFile='RNAseq_libsettings_HEK293T')
RNA.RNAexp()
RNA.RNA_raw_countTables()
RNA2 = RNAseq_workflow(rootDir, threadNumb, libSetFile='RNAseq_libsettings_Calu6')
RNA2.RNAexp()
RNA2.RNA_raw_countTables()
### 5) Plot Figures
pltFig = plot_figures(rootDir, threadNumb,
libSet_RP_allG418 = 'riboseq_libsettings_allG418',
libSet_RP_allAGmerge = 'riboseq_libsettings_allAGmerge',
libSet_RNA_HEK293T = 'RNAseq_libsettings_HEK293T',
libSet_RNA_Calu6 = 'RNAseq_libsettings_Calu6',
libSet_RP_allG418_allTr = 'riboseq_libsettings_allG418_allTr')
pltFig.plot_figure_1()
pltFig.plot_figure_2()
pltFig.plot_figure_3()
pltFig.plot_figure_4()
pltFig.plot_figure_5()
pltFig.plot_figure_6()
pltFig.plot_figure_7()
if __name__ == '__main__':
main()