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get_distance_to_ss_v2.py
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get_distance_to_ss_v2.py
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"""
@authors: Juan L. Trincado
@email: [email protected]
get_distance_to_ss_v2.py: Given the ORFs per transcript, the sequences of each transcript and
the position of the ss, get the relative distance to this ss. Then, take the longest that starts
with the given start codon
"""
import logging, sys, os, re
from copy import deepcopy
from argparse import ArgumentParser, RawTextHelpFormatter
# create logger
logger = logging.getLogger(__name__)
logger.setLevel(logging.INFO)
# create console handler and set level to info
ch = logging.StreamHandler()
ch.setLevel(logging.DEBUG)
# create formatter
formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
# add formatter to ch
ch.setFormatter(formatter)
# add ch to logger
logger.addHandler(ch)
def main():
try:
#
orfs_path = sys.argv[1]
start_codon_user = sys.argv[2]
transcripts_paths = sys.argv[3]
output_path = sys.argv[4]
#
# orfs_path = "/home/shinoda/Desktop/Florida/annotation/MBNL1_possible_ORFs_refseq.fa"
# start_codon_user = "152017982"
# transcripts_paths = "/home/shinoda/Desktop/Florida/annotation/MBNL1_possible_transcripts_refseq.fa.paths"
# output_path = "/home/shinoda/Desktop/Florida/annotation/MBNL1_evaluated_refseq.paths"
# # 1. Extract just the first ORF (the longest) from each transcript
# outFile = open(orfs_path+".unique", 'w')
# with open(orfs_path) as f:
# logger.info("Processing ORFs file...")
# transcript_id, transcript_id_old = "Transcript_0", ""
# for line in f:
# # If its header
# if(re.search(">", line)):
# #If the transcript id changes, output the next 2 lines
# if(not(re.search(transcript_id, line))):
# tokens = line.rstrip().split(":")
# transcript_id = tokens[0][1:]
# pass_flag = False
# outFile.write(line)
# else:
# pass_flag = True
# # If its sequence
# else:
# if(pass_flag):
# pass
# else:
# outFile.write(line)
# outFile.close()
# 1. Using the info in the header of the ORFs file, we can obtain the information of
# whether our stop codon is falling
results = {}
with open(orfs_path + ".unique") as f:
logger.info("Processing ORFs unique file...")
for line in f:
# If its header
if (re.search(">", line)):
# Two things: obtain the differences for each exon associated (with the cordinates)
# and obtain the length of the ORF
tokens = line.rstrip().split(":")
strand = tokens[1]
transcript_id = tokens[0][1:]
exons = tokens[2:-1]
ORF = tokens[-1].split("-")
# Get the difference for each exon. Go substracting the sequences according to the distance
# to the ORF end
first_pos = int(ORF[0])
second_pos = int(ORF[1])
pos = 0
flag_1, flag_2, flag_3 = True, False, False
i = 0
for x in exons:
coords = x.split("_")
length_exon = int(coords[1]) - int(coords[0])
if (flag_1):
# coords = x.split("_")
# length_exon = int(coords[1]) - int(coords[0])
if ((pos + length_exon) < first_pos):
pass
# pos += length_exon
# Reached start codon
else:
offset = first_pos - pos
if(strand=="+"):
start_codon = int(coords[0]) + offset
else:
start_codon = int(coords[1]) - offset
flag_1 = False
flag_2 = True
if ((pos + length_exon) < second_pos):
pass
# pos += length_exon
# Reached stop codon
else:
# offset = second_pos - (pos + length_exon)
offset = second_pos - pos
if (strand == "+"):
stop_codon = int(coords[0]) + offset
else:
stop_codon = int(coords[1]) - offset
flag_2 = False
flag_3 = True
# pos += length_exon
# if (i == len(exons) - 1):
# distance = pos - second_pos
# else:
# pass
if (flag_2):
# coords = x.split("_")
# length_exon = int(coords[1]) - int(coords[0])
if ((pos + length_exon) < second_pos):
pass
# pos += length_exon
# Reached stop codon
else:
offset = second_pos - pos
if (strand == "+"):
stop_codon = int(coords[0]) + offset
else:
stop_codon = int(coords[1]) - offset
flag_2 = False
flag_3 = True
# pos += length_exon
# If reached last exon, the stop codon is in the last exon. Therefore, there won't be NMD
# if (i==len(exons)-1):
# # distance = (pos + length_exon) - second_pos
# distance = 0
# break
# else:
# pass
if (flag_3):
# If not reached last exon, get the distance to the 3'ss
if (i != len(exons) - 1):
# coords = x.split("_")
# length_exon = int(coords[1]) - int(coords[0])
# pos += length_exon
distance = (pos + length_exon) - second_pos
break
# If reached last exon, the stop codon is in the last exon. Therefore, there won't be NMD
else:
distance = 0
break
pos += length_exon
i += 1
results[transcript_id] = [start_codon, stop_codon, distance]
else:
pass
# 2. Get the longer transcript that starts with the given start codon
results_filtered = {}
for key, values in results.items():
transcript_id = "_".join(key.split("_")[0:2])
#Save it if the start_codon coincides with the one that the user specified
if(values[0]==int(start_codon_user)):
if(transcript_id not in results_filtered):
results_filtered[transcript_id] = values
#If there is already a value, get the one with greater distance
else:
if(results_filtered[transcript_id][2]<values[2]):
results_filtered[transcript_id] = values
# 3. Associate the info to the transcripts_paths file
outFile = open(output_path, 'w')
with open(transcripts_paths) as f:
logger.info("Processing transcripts_paths file...")
for line in f:
tokens = line.rstrip().split(":")
transcript_id = tokens[0][1:]
#Get the information from the previous results
if(transcript_id in results_filtered):
info = results_filtered[transcript_id]
outFile.write(":".join(tokens)+"\tStart_codon: "+str(info[0])+
"\tStop_codon: "+str(info[1])+
"\tDistance: "+str(info[2])+"\n")
else:
outFile.write(":".join(tokens)+"\tNo ORF\n")
outFile.close()
logger.info("Saved " + output_path)
logger.info("Done. Exiting program.")
exit(0)
except Exception as error:
logger.error('ERROR: ' + repr(error))
logger.error("Aborting execution")
sys.exit(1)
if __name__ == '__main__':
main()