Merge pull request #26 from jpiper/0.2.6

0.2.6 updates

.travis.yml

@@ -5,6 +5,7 @@ python:
     - "3.3"
     - "3.4"
     - "3.5"
+    - "3.6"
 addons:
   apt:
     packages:

CHANGES

@@ -1,3 +1,10 @@
+0.2.6 - 2018-01-27
+==================
+* ENHANCEMENT: License changed to MIT
+* BUGFIX: Scripts should now all work for Python 3
+* BUGFIX: Empty lines in BED files are now ignored
+* BUGFIX: Fix issue with passing values to the "-pv" argument on `wellington_footprints.py`
+
 0.2.5 - 2016-07-23
 ==================
 * IMPORTANT: Python 2.6 and 3.2 support dropped. 2.7, 3.3, 3.4, and 3.5 are where it's at.

README.rst

@@ -61,4 +61,4 @@ Reference
 License
 -------
 
-Copyright (C) 2015 Jason Piper. This work is licensed under the GNU GPLv3 license, see ``LICENCE.TXT`` for details. If you require the use of this software under a difference license (e.g. for commercial purposes), please email me at `j.piper@me.com`.
+Copyright (C) 2015 Jason Piper. This work is licensed under the MIT license, see ``LICENCE.TXT`` for details. If you require the use of this software under a difference license, please email me at `j.piper@me.com`.

examples/footprinttest.py

@@ -1,18 +1,3 @@
-# Copyright (C) 2016 Jason Piper - j.piper@me.com
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
 import matplotlib.pyplot as plt
 import pyDNase
 from pyDNase.footprinting import wellington

pyDNase/__init__.py

@@ -1,18 +1,3 @@
-# Copyright (C) 2016 Jason Piper - j.piper@me.com
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
 from . import _version
 __version__ = _version.__version__
 
@@ -277,11 +262,12 @@ def loadBEDFile(self,filename):
         records = []
 
         intervalCount = max(enumerate(open(filename)))[0] + 1
-        for _ in progress.bar(range(intervalCount)):
+        for _ in progress.bar(list(range(intervalCount))):
             line    = BEDfile.readline()
-            #Skip lines in the bed files which are UCSC track metadata or comments
-            if not self.__isBEDHeader(line):
-                records.append(self.__parseBEDString(line))
+            if line:
+                #Skip lines in the bed files which are UCSC track metadata or comments
+                if not self.__isBEDHeader(line):
+                    records.append(self.__parseBEDString(line))
 
         for i in records:
             self.__addInterval(GenomicInterval(i[0], i[1], i[2], i[3], i[4], i[5]))
@@ -372,22 +358,22 @@ def __len__(self):
         Return the number of intervals in the set
         """
         intervals = 0
-        for each in self.intervals.values():
+        for each in list(self.intervals.values()):
             intervals += len(each)
         return intervals
 
     def __iter__(self):
         """
         Iterates over the intervals in the order that the intervals were generated
         """
-        for each in sorted(sum(self.intervals.values(),[]), key=lambda peak: peak.importorder):
+        for each in sorted(sum(list(self.intervals.values()),[]), key=lambda peak: peak.importorder):
             yield each
 
     def __getitem__(self, i):
         """
         Indexes the intervals in the order that the intervals were generated
         """
-        return sorted(sum(self.intervals.values(),[]), key=lambda peak: peak.importorder)[i]
+        return sorted(sum(list(self.intervals.values()),[]), key=lambda peak: peak.importorder)[i]
 
     def __delitem__(self,i):
         """

pyDNase/_version.py

@@ -1 +1 @@
-__version__ = "0.2.5"
+__version__ = "0.2.6"

pyDNase/footprinting/__init__.py

@@ -1,26 +1,11 @@
-# Copyright (C) 2016 Jason Piper - j.piper@me.com
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
 import warnings, random
 import numpy as np
 import pyDNase
 from . import WellingtonC
 
 class wellington(object):
 
-    def __init__(self,interval,reads,shoulder_sizes=range(35,36), footprint_sizes = range(11,26,2),FDR_cutoff=0.01,FDR_iterations=100,bonferroni=None):
+    def __init__(self,interval,reads,shoulder_sizes=list(range(35,36)), footprint_sizes = list(range(11,26,2)),FDR_cutoff=0.01,FDR_iterations=100,bonferroni=None):
 
         #Set up the model parameters
         self.shoulder_sizes  = shoulder_sizes
@@ -99,7 +84,7 @@ def footprints(self, withCutoff=-30, merge = 1):
         while templogProb.min() < withCutoff:
             minimapos = templogProb.argmin()
             minimafplen = tempMLE[minimapos]
-            minimaphalffplen = int(minimafplen)/2
+            minimaphalffplen = int(minimafplen/2)
             lbound = max(minimapos-(minimaphalffplen),0)
             rbound = min(minimapos+(minimaphalffplen),len(templogProb))
             ranges.append((lbound,rbound,templogProb.min(),minimafplen))

pyDNase/scripts/dnase_average_profile.py

@@ -1,20 +1,3 @@
-#!/usr/bin/env python
-
-# Copyright (C) 2016 Jason Piper - j.piper@me.com
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
 import argparse
 import pyDNase
 import numpy as np
@@ -72,8 +55,8 @@
             rv.append(reads[each]["-"])
 
 if args.n:
-    fw = [map(float,i)for i in fw]
-    rv = [map(float,i) for i in rv]
+    fw = [list(map(float,i))for i in fw]
+    rv = [list(map(float,i)) for i in rv]
     fw = [np.divide(np.subtract(i, min(i)), np.subtract(max(i) , min(i))) for i in fw]
     rv = [np.divide(np.subtract(i, min(i)), np.subtract(max(i) , min(i))) for i in rv]
 

pyDNase/scripts/dnase_bias_estimator.py

@@ -1,20 +1,3 @@
-#!/usr/bin/env python
-
-# Copyright (C) 2016 Jason Piper - j.piper@me.com
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
 import os, argparse, tempfile, operator, pickle
 from collections import defaultdict
 import pybedtools, pysam
@@ -55,7 +38,7 @@ def generate_6mer_bed(bam_file, gdict):
 		# Ignore unmapped reads
 		if not i.is_unmapped:
 			chrom = samfile.getrname(i.reference_id)
-			if chrom in gdict.keys():
+			if chrom in list(gdict.keys()):
 				# Determine which end of the read is the 5' end
 				if i.is_reverse:
 					strand = "-"
@@ -64,7 +47,7 @@ def generate_6mer_bed(bam_file, gdict):
 					strand  = "+"
 					startbp, endbp = i.reference_start - 3, i.reference_start + 3
 				if startbp > 0 and endbp < gdict[chrom]:
-					print >> outfile, "\t".join((str(i) for i in (chrom, startbp, endbp, 0, 0, strand)))
+					print("\t".join((str(i) for i in (chrom, startbp, endbp, 0, 0, strand))), file=outfile)
 	outfile.close()
 	return outfile.name
 
@@ -126,16 +109,16 @@ def genome_dic(g_file):
 	expected = get_kmers(shuffled_cuts.seqfn)
 
 	print("Calculating...")
-	enriched = {i:observed[i]/float(expected[i]) for i in observed.keys()}
+	enriched = {i:observed[i]/float(expected[i]) for i in list(observed.keys())}
 
 	print("Dumping bias txt file...")
 	with open(outfile + ".txt", 'w') as ofile:
-		for i in sorted(enriched.items(), key=operator.itemgetter(1)):
-			print >> ofile, "\t".join(map(str,i))
+		for i in sorted(list(enriched.items()), key=operator.itemgetter(1)):
+			print("\t".join(map(str,i)), file=ofile)
 
 	print("Writing bias pickle file...")
 	totalsum = float(sum(enriched.values()))
-	whatdic = {key:{'forward':val/totalsum,'reverse':enriched[rev_comp(key)]/totalsum} for key,val in enriched.iteritems()}
+	whatdic = {key:{'forward':val/totalsum,'reverse':enriched[rev_comp(key)]/totalsum} for key,val in enriched.items()}
 	with open(outfile + ".pickle", "w") as bias_file:
 		pickle.dump(whatdic,bias_file)
 

pyDNase/scripts/dnase_cut_counter.py

@@ -1,20 +1,3 @@
-#!/usr/bin/env python
-
-# Copyright (C) 2016 Jason Piper - j.piper@me.com
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
 import argparse
 import pyDNase
 from clint.textui import progress, puts
@@ -32,5 +15,5 @@
 
 puts("Writing output...")
 for i in progress.bar(regions):
-    i.score   = sum([sum(j) for j in reads[i].values()])
-    print >> ofile, i
+    i.score   = sum([sum(j) for j in list(reads[i].values())])
+    print(i, file=ofile)

pyDNase/scripts/dnase_ddhs_scorer.py

@@ -1,20 +1,3 @@
-#!/usr/bin/env python
-
-# Copyright (C) 2016 Jason Piper - j.piper@me.com
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
 import argparse
 import pyDNase
 import math
@@ -44,12 +27,12 @@
 
 puts("Calculating enrichment for Treatment")
 for i in progress.bar(treat_dhs):
-    treat_total_cuts += sum([sum(j) for j in reads_treat[i].values()])
+    treat_total_cuts += sum([sum(j) for j in list(reads_treat[i].values())])
     treat_base_pairs += len(i)
 
 puts("Calculating enrichment for Control")
 for i in progress.bar(control_dhs):
-    control_total_cuts += sum([sum(j) for j in reads_control[i].values()])
+    control_total_cuts += sum([sum(j) for j in list(reads_control[i].values())])
     control_base_pairs += len(i)
 
 treat_base_pairs   = float(treat_base_pairs)
@@ -61,10 +44,10 @@
 
 puts("Calculating dDHS scores...")
 for i in progress.bar(regions):
-    treat_cuts   =  sum([sum(j) for j in reads_treat[i].values()])
-    control_cuts =  sum([sum(j) for j in reads_control[i].values()])
+    treat_cuts   =  sum([sum(j) for j in list(reads_treat[i].values())])
+    control_cuts =  sum([sum(j) for j in list(reads_control[i].values())])
     LHS = math.sqrt(  treat_cuts /(  treat_total_cuts / treat_base_pairs))
     RHS = math.sqrt(control_cuts /(control_total_cuts / control_base_pairs))
     i.score = LHS - RHS
-    print >> ofile, i
+    print(i, file=ofile)
 ofile.close()

pyDNase/scripts/dnase_fos_scorer.py

@@ -1,20 +1,3 @@
-#!/usr/bin/env python
-
-# Copyright (C) 2016 Jason Piper - j.piper@me.com
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
 import argparse
 import pyDNase
 from clint.textui import progress
@@ -32,4 +15,4 @@
 outfile = open(args.output,"w")
 for i in progress.bar(regions):
     i.score = reads.FOS(i)
-    print >> outfile, i
+    print(i, file=outfile)

pyDNase/scripts/dnase_pretty_picture.py

@@ -59,8 +59,8 @@
         rv.append(reads[each]["-"])
 
 
-fw = [map(float,i) for i in fw]
-rv = [map(float,i) for i in rv]
+fw = [list(map(float,i)) for i in fw]
+rv = [list(map(float,i)) for i in rv]
 fw = [np.divide(np.subtract(i, min(i)), np.subtract(max(i) , min(i))) for i in fw]
 rv = [np.divide(np.subtract(i, min(i)), np.subtract(max(i) , min(i))) for i in rv]
 

pyDNase/scripts/dnase_to_JSON.py

@@ -1,20 +1,3 @@
-#!/usr/bin/env python
-
-# Copyright (C) 2016 Jason Piper - j.piper@me.com
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
 import argparse, pyDNase
 from clint.textui import puts, progress
 parser = argparse.ArgumentParser(description='Writes a JSON file of DNase I cuts for regions from a BED file')

pyDNase/scripts/dnase_to_javatreeview.py

@@ -1,20 +1,3 @@
-#!/usr/bin/env python
-
-# Copyright (C) 2016 Jason Piper - j.piper@me.com
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
 import argparse, pyDNase, csv, random
 import numpy as np
 from clint.textui import puts, progress