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