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transrate_reference_trinity_2.2.0.py
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transrate_reference_trinity_2.2.0.py
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import os
import os.path
from os.path import basename
from urllib import urlopen
from urlparse import urlparse
import subprocess
from subprocess import Popen, PIPE
import urllib
import shutil
import glob
import pandas as pd
# custom Lisa module
import clusterfunc
def fix_fasta(trinity_fasta, trinity_dir, sample):
trinity_out = trinity_dir + sample + ".Trinity.fixed.fasta"
if os.path.isfile(trinity_out):
print "Exists:",trinity_out
else:
fix = """
sed 's_|_-_g' {} > {}
""".format(trinity_fasta, trinity_out)
s = subprocess.Popen(fix, shell=True)
print fix
s.wait()
return trinity_out
def transrate(transrate_dir, mmetsp, fixed_fasta, mmetsp_dir, old_assembly):
#sra = old_assembly.split("_")[-1].split(".")[0]
sample = "trinity2.2.0_"+mmetsp+"_trinity2014"
transrate_command = """
transrate -o {}{} \\
--assembly {} \\
--reference {} \\
--threads 8
""".format(transrate_dir, sample, fixed_fasta, old_assembly)
commands = [transrate_command]
process_name = "trans_ref"
module_name_list = ""
filename = mmetsp
#print transrate_command
#s = subprocess.Popen(transrate_command, shell=True)
#s.wait()
#clusterfunc.qsub_file(transrate_dir,process_name,module_name_list,filename,commands)
def transrate_reverse(transrate_dir, mmetsp, fixed_fasta, mmetsp_dir, old_assembly):
#sra = old_assembly.split("_")[-1].split(".")[0]
sample = "reverse_trinity2014_" + mmetsp + "_trinity2.2.0"
transrate_out = transrate_dir + sample + "/" + "assemblies.csv"
transrate_command = """
transrate -o {}{} \\
--assembly {} \\
--reference {} \\
--threads 8
""".format(transrate_dir, sample, old_assembly,fixed_fasta)
print "This is the reverse transrate command:"
commands = [transrate_command]
process_name = "trans_ref_reverse"
module_name_list = ""
filename = sample
#print transrate_command
#s = subprocess.Popen(transrate_command, shell=True)
#s.wait()
#clusterfunc.qsub_file(transrate_dir,process_name,module_name_list,filename,commands)
def parse_transrate_stats(transrate_assemblies,sra,mmetsp):
data = pd.DataFrame.from_csv(transrate_assemblies, header=0, sep=',')
data['SampleName'] = mmetsp
data['Run'] = sra
return data
def build_DataFrame(data_frame, transrate_data):
# columns=["n_bases","gc","gc_skew","mean_orf_percent"]
frames = [data_frame, transrate_data]
data_frame = pd.concat(frames)
return data_frame
def execute(data_frame1,data_frame2,ncgr_dir,trinity_fail, count, basedir):
assemblydir = "/mnt/scratch/ljcohen/mmetsp_assemblies/"
old_files = os.listdir(assemblydir)
id_list = os.listdir(basedir)
for mmetsp in id_list:
if mmetsp != "qsub_files":
alt_mmetsp = mmetsp + "_2"
mmetspdir = basedir + mmetsp + "/"
trinitydir = basedir + mmetsp + "/" + "trinity/"
trinity_files = os.listdir(mmetspdir)
transrate_dir = mmetspdir + "transrate/"
clusterfunc.check_dir(transrate_dir)
trinity_fasta=trinitydir+"trinity_out_2.2.0.Trinity.fasta"
alt_trinity_fasta = "/mnt/home/ljcohen/mmetsp_assemblies_trinity2.2.0/"+mmetsp+".trinity_out_2.2.0.Trinity.fasta"
#trinity_fasta = trinitydir + sample + ".Trinity.fixed.fasta"
clusterfunc.check_dir(trinitydir)
if os.path.isfile(trinity_fasta) == False and os.path.isfile(alt_trinity_fasta) == False:
right = [s for s in trinity_files if s.endswith(".right.fq")][0]
left = [s for s in trinity_files if s.endswith(".left.fq")][0]
right = mmetspdir + right
left = mmetspdir + left
if os.path.isfile(left) and os.path.isfile(right):
#run_trinity(trinitydir,left,right,mmetsp)
print "Trinity not finished:", trinity_fasta
trinity_fail.append(trinitydir)
else:
print "No files:",left
elif os.path.isfile(trinity_fasta) == True:
or os.path.isfile(alt_trinity_fasta) == True:
print "Trinity completed successfully.", trinity_fasta
count += 1
old_assemblies = glob.glob(assemblydir+"*"+mmetsp+"*")
if len(old_assemblies) >= 1:
full_assembly = old_assemblies[0]
else:
print glob.glob(assemblydir + "*" + mmetsp + "*")
#copy_string = "cp " + trinity_fasta + " " + assemblydir
#print copy_string
#s = subprocess.Popen(copy_string, shell=True)
#s.wait()
fixed_fasta = fix_fasta(trinity_fasta,trinitydir,mmetsp)
#sra = old_assembly.split("_")[-1].split(".")[0]
ncgr_assembly = ncgr_dir + mmetsp + ".nt.fa.fixed.fa"
sample = "trinity2.2.0_"+mmetsp+"_trinity2014"
reverse_sample = "reverse_trinity2014_" + mmetsp + "_trinity2.2.0"
transrate_out = transrate_dir + sample + "/" + "assemblies.csv"
transrate_reverse_assemblies = transrate_dir + reverse_sample + "/" + "assemblies.csv"
if os.path.isfile(transrate_out):
print "Transrate completed:",transrate_out
data1 = parse_transrate_stats(transrate_out,mmetsp,mmetsp)
data_frame1 = build_DataFrame(data_frame1,data1)
else:
transrate(transrate_dir, mmetsp, fixed_fasta, mmetspdir, full_assembly)
if os.path.isfile(transrate_reverse_assemblies):
print "Transrate complete:",transrate_reverse_assemblies
data2 = parse_transrate_stats(transrate_reverse_assemblies,mmetsp,mmetsp)
data_frame2 = build_DataFrame(data_frame2,data2)
else:
transrate_reverse(transrate_dir, mmetsp, fixed_fasta, mmetspdir, full_assembly)
print "Number of Trinity de novo transcriptome assemblies:"
print count
print "Number of times Trinity failed:"
print len(trinity_fail)
return data_frame1,data_frame2
basedir = "/mnt/scratch/ljcohen/mmetsp/"
ncgr_dir = "/mnt/research/ged/lisa/mmetsp/imicrobe/nt/"
datafiles = ["SraRunInfo_719.csv"]
data_frame1 = pd.DataFrame()
data_frame2 = pd.DataFrame()
trinity_fail = []
count = 0
data_frame1,data_frame2 = execute(data_frame1,data_frame2,ncgr_dir,trinity_fail, count, basedir)
#data_frame1.to_csv("assembly_evaluation_data/trinity2014_trinity2.2.0_transrate_reference.csv")
#data_frame2.to_csv("assembly_evaluation_data/trinity2014_trinity2.2.0_transrate_reverse.csv")