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transrate_reference_accessions.py
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import os
import os.path
from os.path import basename
import subprocess
from subprocess import Popen, PIPE
import os
from os import path
# custom Lisa module
import clusterfunc_py3
# Python plotting libraries
import pandas as pd
def transrate(transrate_dir, sample, trinity_fasta, mmetsp_assemblies_dir, filename):
transrate_command = """
transrate -o /tmp/{}_forw \\
--assembly {} \\
--reference {} \\
--threads 8
cp /tmp/{}_forw/assemblies.csv {}{}.assemblies.csv
rm -rf /tmp/{}_forw*
""".format(sample, trinity_fasta, filename,sample,transrate_dir,sample,sample)
commands = [transrate_command]
process_name = "trans_ref"
module_name_list = ""
filename = sample
print(transrate_command)
clusterfunc_py3.qsub_file(mmetsp_assemblies_dir,process_name,module_name_list,filename,commands)
def transrate_reverse(transrate_dir, sample, trinity_fasta, mmetsp_assemblies_dir, filename):
transrate_command = """
transrate -o /tmp/{}_rev \\
--assembly {} \\
--reference {} \\
--threads 8
cp /tmp/{}_rev/assemblies.csv {}{}.assemblies.csv
rm -rf /tmp/{}_rev*
""".format(sample, filename,trinity_fasta,sample,transrate_dir,sample,sample)
#print("This is the reverse transrate command:")
commands = [transrate_command]
process_name = "trans_ref_reverse"
module_name_list = ""
filename = sample
print(transrate_command)
clusterfunc_py3.qsub_file(mmetsp_assemblies_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 get_contigs_data(data_frame, transrate_dir):
listofdirs = os.listdir(transrate_dir)
for dirname in listofdirs:
transrate_dirname = transrate_dir + dirname + "/"
transrate_dirnames = os.listdir(transrate_dirname)
for dirname2 in transrate_dirnames:
if dirname2.endswith(".fixed"):
transrate_contigs = transrate_dirname + dirname2 + "/contigs.csv"
if os.path.isfile(transrate_contigs):
print(transrate_contigs)
data = parse_transrate_stats(transrate_contigs)
data_frame = build_DataFrame(data_frame, data)
else:
print("File missing:", transrate_contigs)
return data_frame
def execute(data_frame1, data_frame2, query_assemblies_dir,reference_assemblies_dir,output_dir1,output_dir2):
assemblies1 = os.listdir(query_assemblies_dir)
assemblies2 = os.listdir(reference_assemblies_dir)
print(assemblies1)
print(assemblies2)
for item in assemblies1:
if item.endswith(".fasta"):
sra_id = item.split(".")[0]
print(sra_id)
reverse_assembly = [s for s in assemblies2 if sra_id in s.split("_") or s.split("_")[-1].startswith(sra_id)]
if len(reverse_assembly)==0:
print("Assembly not present:",sra_id,reference_assemblies_dir)
else:
print(reverse_assembly)
reverse_trinity_fasta = reference_assemblies_dir + reverse_assembly[0]
trinity_fasta = query_assemblies_dir + item
if os.path.isfile(trinity_fasta):
print("SRA assembly found:", trinity_fasta)
transrate_assemblies_ref = output_dir1 + sra_id + ".assemblies.csv"
transrate_reverse_assemblies = output_dir2 + sra_id + ".assemblies.csv"
if os.path.isfile(transrate_assemblies_ref):
print("Finished:",transrate_assemblies_ref)
data1 = parse_transrate_stats(transrate_assemblies_ref,sra_id,sra_id)
data_frame1 = build_DataFrame(data_frame1, data1)
else:
print("Running...")
transrate(output_dir1, sra_id, trinity_fasta, reference_assemblies_dir, reverse_trinity_fasta)
if os.path.isfile(transrate_reverse_assemblies):
print("Finished:",transrate_reverse_assemblies)
data2 = parse_transrate_stats(transrate_reverse_assemblies,sra_id,sra_id)
data_frame2 = build_DataFrame(data_frame2, data2)
else:
print("Running reverse...")
transrate_reverse(output_dir2, sra_id, trinity_fasta, reference_assemblies_dir, reverse_trinity_fasta)
return data_frame1,data_frame2
def get_assemblies_data(data_frame, transrate_dir):
listofdirs = os.listdir(transrate_dir)
for dirname in listofdirs:
transrate_assemblies = transrate_dir + dirname + "/assemblies.csv"
print(transrate_assemblies)
if os.path.isfile(transrate_assemblies):
data = parse_transrate_stats(transrate_assemblies)
data_frame = build_DataFrame(data_frame, data)
else:
print("File missing:", transrate_assemblies)
return data_frame
def get_ref_transrate(transrate_dir):
listdirs = os.listdir(transrate_dir)
print(listdirs)
for dirname in listdirs:
newdir = transrate_dir + dirname + "/"
print(newdir)
newfile = newdir + "assemblies.csv"
if os.path.isfile(newfile):
print("Exists:", newfile)
else:
print("Does not exist:", newfile)
macmanes_assemblies_dir = "/mnt/home/ljcohen/oysterriver_assemblies/MacManes/orthomerged/"
dib_assemblies_dir = "/mnt/home/ljcohen/oysterriver_assemblies/finished/"
output_dir1 = "/mnt/home/ljcohen/oysterriver_assemblies/dib_v_macmanes/"
output_dir2 = "/mnt/home/ljcohen/oysterriver_assemblies/macmanes_v_dib/"
clusterfunc_py3.check_dir(output_dir1)
clusterfunc_py3.check_dir(output_dir2)
data_frame1 = pd.DataFrame()
data_frame2 = pd.DataFrame()
data_frame1, data_frame2 = execute(data_frame1, data_frame2, dib_assemblies_dir,macmanes_assemblies_dir,output_dir1,output_dir2)
data_frame1.to_csv("/mnt/home/ljcohen/oysterriver_assemblies/transrate_reference_dib_v_macmanes.csv")
data_frame2.to_csv("/mnt/home/ljcohen/oysterriver_assemblies/transrate_reverse_ref_macmanes_v_dib.csv")
print("Reference scores written: /mnt/home/ljcohen/oysterriver_assemblies/transrate_reference_dib_v_macmanes.csv")
print("Reverse reference scores written: /mnt/home/ljcohen/oysterriver_assemblies/transrate_reverse_ref_macmanes_v_dib.csv")