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psiCalculator.py
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psiCalculator.py
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# -*- coding: utf-8 -*-
"""
Created on Tue May 6 12:19:45 2014
@author: Gael P Alamancos
@email: gael.perez[at]upf.edu
"""
import sys
import logging
import numpy as np
from argparse import ArgumentParser, RawTextHelpFormatter
from lib.tools import *
description = \
"Description:\n\n" + \
"This tool reads an ioe file and a transcript expression file and calculates\n" + \
"the Percentage of Sliced In (PSI)\n"
parser = ArgumentParser(description=description, formatter_class=RawTextHelpFormatter,
add_help=False)
parser.add_argument("-i", "--ioe-file", help="Input file with the event-transcripts equivalence (.ioe format).", required=True)
parser.add_argument("-e", "--expression-file", required=True,
help="Input transcript expression file.")
parser.add_argument("-o", "--output-file", required=True,
help="Output psi file.")
parser.add_argument("-f", "--total-filter", type=float, default=0,
help="Minimum total expression of the transcripts involved in the event.")
parser.add_argument('-s', '--save_tpm_events',
action="store_true",
default=False,
help="Boolean. If True, save the TPM of the events in an external file (Default: False).")
parser.add_argument("-m", "--mode", default="INFO",
help="to choose from DEBUG, INFO, WARNING, ERROR and CRITICAL")
def main():
args = parser.parse_args()
#Parsing arguments
mode = "logging." + args.mode
#Setting logging preferences
logger = logging.getLogger(__name__)
logger.setLevel(eval(mode))
# Setting the level of the loggers in lib
setToolsLoggerLevel(mode)
output_file = args.output_file
total_filter = args.total_filter
expression_file = args.expression_file
expression_dictionary = {} # to store transcript expression [transcript_id] = {[colId] = expression}
psi_dictionary = {} # to store the psi values calculated [event_id] = {[colId] = expression}
expression_dictionary_events = {} # to store the expression values calculated [event_id] = {[colId] = expression}
col_ids = [] # to store all the column_id for the expression fields
try:
#Buffering EXPRESSION FILE
factory = FactoryReader()
r = factory.getReader("expression")
r.openFile(expression_file)
logger.info("Buffering transcript expression levels.")
line = r.readLine()
try:
while True:
try:
arguments = nextel(line)
col_ids = arguments["colIds"]
expression_dictionary[arguments["transcript_id"]] = {}
# Assign per each colId the expression [colId] = expression
for key, value in arguments["expression"].items():
expression_dictionary[arguments["transcript_id"]][key] = float(value)
except ValueError:
logger.error("%s expression is not a float. Skipping..." % arguments["transcript_id"])
continue
except StopIteration:
if not expression_dictionary:
logger.error("No expression values have been buffered.")
sys.exit(1)
#Buffering IOE and calculating PSI
factory = FactoryReader()
r = factory.getReader("ioe")
# r.openFile(args.ioe_file)
r.openFile(args.ioe_file)
logger.info("Calculating PSI from the ioe file.")
line = r.readLine()
try:
while True:
alternative_transcripts = {}
total_transcripts = {}
arguments = nextel(line)
if psi_dictionary.get(arguments["event_id"]):
logger.error("Duplicated event %s. Skipping line..." %
arguments["event_id"])
continue
skip = False # to avoid checking total_iso if event == "NA"
psi_dictionary[arguments["event_id"]] = {}
expression_dictionary_events[arguments["event_id"]] = {}
for x in col_ids:
#set to 0 all the cumulative expression values
alternative_transcripts[x] = 0
total_transcripts[x] = 0
#Add all the expression values of the alternative transcripts
for tr in arguments["alt_iso"].rstrip("\n").split(","):
try:
for x in col_ids:
alternative_transcripts[x] += \
expression_dictionary[tr][x]
except KeyError:
logger.error(
"transcript %s not found in the \"expression file\"." %
tr)
logger.error("PSI not calculated for event %s." %
arguments["event_id"])
for x in col_ids:
psi_dictionary[arguments["event_id"]][x] = "NA"
expression_dictionary_events[arguments["event_id"]][x] = "NA"
skip = True
# Add all the expression values of the total transcripts
if not skip:
for tr in arguments["total_iso"].rstrip("\n").split(","):
try:
for x in col_ids:
total_transcripts[x] += \
expression_dictionary[tr][x]
except KeyError:
logger.error(
"transcript %s not found in the \"expression file\"." %
tr)
logger.error("PSI not calculated for event %s." %
arguments["event_id"])
for x in col_ids:
psi_dictionary[arguments["event_id"]][x] = "NA"
expression_dictionary_events[arguments["event_id"]][x] = "NA"
skip = True
for x in col_ids:
#If it passes the filter and skip == False
if total_transcripts[x] >= total_filter and not skip:
try:
psi_dictionary[arguments["event_id"]][x] = (
alternative_transcripts[x]/total_transcripts[x])
expression_dictionary_events[arguments["event_id"]][x] = total_transcripts[x]
except ZeroDivisionError:
logger.debug("Zero division for event %s.(psi= nan)." % arguments["event_id"])
psi_dictionary[arguments["event_id"]][x] = np.nan
expression_dictionary_events[arguments["event_id"]][x] = total_transcripts[x]
#If it passes the filter but skip == True
elif not skip:
#for x in col_ids:
psi_dictionary[arguments["event_id"]][x] = np.nan
expression_dictionary_events[arguments["event_id"]][x] = total_transcripts[x]
except StopIteration:
writer = Writer.getWriter("PSI")
logger.info("Generating output %s" % (output_file + ".psi"))
writer.openFile(output_file)
writer.writeLine("\t".join(col_ids), False)
for key, value in sorted(psi_dictionary.items()):
logger.debug("Calculating psi for %s" % key)
psi_line = PsiWriter.lineGenerator(key, value, col_ids)
writer.writeLine("\t".join(psi_line))
writer.closeFile()
if (args.save_tpm_events == True):
#Save the expression of the events
writer = Writer.getWriter("TPM")
logger.info("Generating output %s" % (output_file + ".tpm"))
writer.openFile(output_file)
writer.writeLine("\t".join(col_ids), False)
for key, value in sorted(expression_dictionary_events.items()):
logger.debug("Calculating tpm for %s" % key)
tpm_line = TpmWriter.lineGenerator(key, value, col_ids)
writer.writeLine("\t".join(tpm_line))
writer.closeFile()
except BaseException:
logger.error("Unknown error: %s" % sys.exc_info()[1].args[0])
sys.exit(1)
logger.info("Done")
if __name__ == '__main__':
main()