diff options
Diffstat (limited to 'academic/pyCRAC/GTF2-scripts.patch')
| -rw-r--r-- | academic/pyCRAC/GTF2-scripts.patch | 79 |
1 files changed, 0 insertions, 79 deletions
diff --git a/academic/pyCRAC/GTF2-scripts.patch b/academic/pyCRAC/GTF2-scripts.patch deleted file mode 100644 index 35f9512876..0000000000 --- a/academic/pyCRAC/GTF2-scripts.patch +++ /dev/null @@ -1,79 +0,0 @@ -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 |