diff -Naur sgrann-pycrac-8792459eeef7/pyCRAC/scripts/pyGTF2bedGraph.py sgrann-pycrac-8792459eeef7-slack/pyCRAC/scripts/pyGTF2bedGraph.py
--- sgrann-pycrac-8792459eeef7/pyCRAC/scripts/pyGTF2bedGraph.py 2017-09-11 15:11:12.000000000 +0100
+++ sgrann-pycrac-8792459eeef7-slack/pyCRAC/scripts/pyGTF2bedGraph.py 2017-09-10 00:47:13.014633000 +0100
@@ -2,7 +2,7 @@
# not compatible with python 3
__author__ = "Sander Granneman"
__copyright__ = "Copyright 2017"
-__version__ = "0.0.7"
+__version__ = "0.0.6"
__credits__ = ["Sander Granneman"]
__maintainer__ = "Sander Granneman"
__email__ = "sgrannem@staffmail.ed.ac.uk"
@@ -80,14 +80,12 @@
chromdata = processChromFile(chromlengthfile)
###
- normvalue = 1.0
- if permillion and normvalue == 1.0:
- assert data.mapped_reads, "No information on the number of mapped reads could be found in the gtf file. Cannot normalize the data"
- normvalue = float(data.mapped_reads)/1000000.0
-
while True:
lines = data.readLineByLine()
- # to normalize the data to per million reads
+ normvalue = 1.0
+ if permillion and normvalue == 1.0:
+ assert data.mapped_reads, "No information on the number of mapped reads could be found in the gtf file. Cannot normalize the data"
+ normvalue = float(data.mapped_reads)/1000000.0 # to normalize the data to per million reads
if current_chromosome and data.chromosome != current_chromosome or not lines:
for strand in chromdict:
start = 0
diff -Naur sgrann-pycrac-8792459eeef7/pyCRAC/scripts/pyGTF2sgr.py sgrann-pycrac-8792459eeef7-slack/pyCRAC/scripts/pyGTF2sgr.py
--- sgrann-pycrac-8792459eeef7/pyCRAC/scripts/pyGTF2sgr.py 2017-09-11 15:11:12.000000000 +0100
+++ sgrann-pycrac-8792459eeef7-slack/pyCRAC/scripts/pyGTF2sgr.py 2017-09-10 00:47:13.014633000 +0100
@@ -1,8 +1,8 @@
#!/usr/bin/python
# not compatible with python 3
__author__ = "Sander Granneman"
-__copyright__ = "Copyright 2017"
-__version__ = "0.0.6"
+__copyright__ = "Copyright 2015"
+__version__ = "0.0.5"
__credits__ = ["Sander Granneman"]
__maintainer__ = "Sander Granneman"
__email__ = "sgrannem@staffmail.ed.ac.uk"
@@ -13,7 +13,7 @@
# pyGTF2sgr.py
#
#
-# Copyright (c) Sander Granneman 2017
+# Copyright (c) Sander Granneman 2015
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
@@ -73,12 +73,11 @@
###
normvalue = 1.0
- if permillion:
- assert data.mapped_reads, "No information on the number of mapped reads could be found in the gtf file. Cannot normalize the data"
- normvalue = float(data.mapped_reads)/1000000.0
-
while True:
lines = data.readLineByLine()
+ if permillion and normvalue == 1.0:
+ assert data.mapped_reads, "No information on the number of mapped reads could be found in the gtf file. Cannot normalize the data"
+ normvalue = float(data.mapped_reads)/1000000.0
if current_chromosome and data.chromosome != current_chromosome or not lines:
for strand in strands:
if min_cov:
@@ -118,6 +117,8 @@
if data.substitutions: chromdict[data.strand][data.substitutions] += data.number_of_reads
elif type == "deletions":
if data.deletions: chromdict[data.strand][data.deletions] += data.number_of_reads
+ else:
+ break
def gtf2dropoffrates(gtffile,chromosomedata,out_files=[],score=False,log=sys.stdout,zeros=False,min_cov=0):
"""Produces an sgr output file for hits, substitutions and deletions. It requires, besides data a file containing
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