New package - REDItools (#17703)

* New package - REDItools

This PR adds the REDItools package, along with a new package dependency,
py-fisher. This contains a patch generated from the python 2to3 script
as well as some other fixes. I am not sure if the project is ready to
support python-3 yet but I submitted the other patches upstream.

* Update var/spack/repos/builtin/packages/reditools/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

6 files changed, 1042 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/py-fisher/package.py b/var/spack/repos/builtin/packages/py-fisher/package.py
new file mode 100644
index 0000000000..45e0fc5110
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-fisher/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyFisher(PythonPackage):
+    """Fisher's Exact Test.
+
+    Simple, fast implementation of Fisher's exact test."""
+
+    homepage = "https://github.com/brentp/fishers_exact_test"
+    url      = "https://pypi.io/packages/source/f/fisher/fisher-0.1.9.tar.gz"
+
+    version('0.1.9', sha256='d378b3f7e488e2a679c6d0e5ea1bce17bc931c2bfe8ec8424ee47a74f251968d')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-numpy',      type=('build', 'run'))
+    depends_on('py-pytest',     type='test')
diff --git a/var/spack/repos/builtin/packages/reditools/REDItoolDenovo.py.patch b/var/spack/repos/builtin/packages/reditools/REDItoolDenovo.py.patch
new file mode 100644
index 0000000000..a88358829c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/reditools/REDItoolDenovo.py.patch
@@ -0,0 +1,11 @@
+--- a/main/REDItoolDenovo.py	2020-07-16 17:35:46.008030346 -0500
++++ b/main/REDItoolDenovo.py	2020-07-16 17:38:39.700035490 -0500
+@@ -768,7 +768,7 @@
+ for j in ridxinfo.split('\n'): #MOD
+ 	l=(j.strip()).split('\t')
+ 	if l[0] in ['*', '']: continue  #MOD
+- 	if int(l[2])+int(l[3]) > 0: rrefs[l[0]]=int(l[1])
++	if int(l[2])+int(l[3]) > 0: rrefs[l[0]]=int(l[1])
+ frefs=[]
+ fidxinfo=open(fastafile+'.fai')
+ for j in fidxinfo:
diff --git a/var/spack/repos/builtin/packages/reditools/interpreter.patch b/var/spack/repos/builtin/packages/reditools/interpreter.patch
new file mode 100644
index 0000000000..2e3f171e73
--- /dev/null
+++ b/var/spack/repos/builtin/packages/reditools/interpreter.patch
@@ -0,0 +1,41 @@
+diff -ru a/accessory/get_DE_events.py b/accessory/get_DE_events.py
+--- a/accessory/get_DE_events.py	2020-07-16 17:18:47.012982992 -0500
++++ b/accessory/get_DE_events.py	2020-07-16 17:19:47.531986703 -0500
+@@ -1,3 +1,4 @@
++#!/usr/bin/env python
+ #################################### REDI OUT TABLE ########################################################
+ #Region		Position	Reference	Strand	Coverage-q30	MeanQ	BaseCount[A,C,G,T]	   #
+ #AllSubs	Frequency	gCoverage-q30	gMeanQ	gBaseCount[A,C,G,T]	gAllSubs	gFrequency #
+diff -ru a/accessory/readPsl.py b/accessory/readPsl.py
+--- a/accessory/readPsl.py	2020-07-16 17:18:47.012982992 -0500
++++ b/accessory/readPsl.py	2020-07-16 17:20:02.829987622 -0500
+@@ -1,4 +1,4 @@
+-
++#!/usr/bin/env python
+ import sys, os
+ import math
+ 
+diff -ru a/accessory/subCount2.py b/accessory/subCount2.py
+--- a/accessory/subCount2.py	2020-07-16 17:18:47.012982992 -0500
++++ b/accessory/subCount2.py	2020-07-16 17:20:22.650988801 -0500
+@@ -1,3 +1,4 @@
++#!/usr/bin/env python
+ import sys
+ 
+ try:
+diff -ru a/accessory/subCount.py b/accessory/subCount.py
+--- a/accessory/subCount.py	2020-07-16 17:18:47.012982992 -0500
++++ b/accessory/subCount.py	2020-07-16 17:20:35.502989558 -0500
+@@ -1,3 +1,4 @@
++#!/usr/bin/env python
+ import sys
+ 
+ try:
+diff -ru a/main/REDItoolDenovo.py b/main/REDItoolDenovo.py
+--- a/main/REDItoolDenovo.py	2020-07-16 17:18:47.012982992 -0500
++++ b/main/REDItoolDenovo.py	2020-07-16 17:21:01.018991045 -0500
+@@ -1,3 +1,4 @@
++#!/usr/bin/env python
+ # coding=utf-8
+ # Copyright (c) 2013-2014 Ernesto Picardi <ernesto.picardi@uniba.it>
+ #
diff --git a/var/spack/repos/builtin/packages/reditools/package.py b/var/spack/repos/builtin/packages/reditools/package.py
new file mode 100644
index 0000000000..7dd0197a51
--- /dev/null
+++ b/var/spack/repos/builtin/packages/reditools/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Reditools(PythonPackage):
+    """REDItools: python scripts for RNA editing detection by RNA-Seq data.
+
+    REDItools are simple python scripts conceived to facilitate the
+    investigation of RNA editing at large-scale and devoted to research groups
+    that would to explore such phenomenon in own data but don't have sufficient
+    bioinformatics skills. They work on main operating systems (although
+    unix/linux-based OS are preferred), can handle reads from whatever platform
+    in the standard BAM format and implement a variety of filters."""
+
+    homepage = "https://github.com/BioinfoUNIBA/REDItools"
+    git      = "https://github.com/BioinfoUNIBA/REDItools.git"
+
+    version('1.3_2020-03-20', commit='cf47f3d54f324aeb9650bcf8bfacf5a967762a55')
+
+    depends_on('py-pysam', type=('build', 'run'))
+    depends_on('py-fisher', type=('build', 'run'))
+    depends_on('blat', type='run')
+    depends_on('tabix', type='run')
+
+    patch('REDItoolDenovo.py.patch')
+    patch('interpreter.patch')
+    patch('setup.py.patch')
+    patch('python2to3.patch', when='^python@3:')
diff --git a/var/spack/repos/builtin/packages/reditools/python2to3.patch b/var/spack/repos/builtin/packages/reditools/python2to3.patch
new file mode 100644
index 0000000000..94937d175d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/reditools/python2to3.patch
@@ -0,0 +1,926 @@
+diff -ru a/accessory/AnnotateTable.py b/accessory/AnnotateTable.py
+--- a/accessory/AnnotateTable.py	2020-07-16 16:16:59.360014702 -0500
++++ b/accessory/AnnotateTable.py	2020-07-16 16:17:22.159013630 -0500
+@@ -28,7 +28,7 @@
+ sys.stderr.write('Pysam version used: %s\n' %(pysamVersion))
+ 
+ def usage():
+-	print """
++	print("""
+ USAGE: python AnnotateTable.py [options]
+ Options:
+ -a		Sorted Annotation file
+@@ -44,12 +44,12 @@
+ -C		Columns with base distribution [7,12] (in combination with -S)
+ -o		Save lines to a file
+ -h		Print this help
+-"""
++""")
+ 
+ try:
+ 	opts, args = getopt.getopt(sys.argv[1:], 'i:a:o:hs:c:n:SC:uk:r:',["help"])
+-except getopt.GetoptError, err:
+-	print str(err) 
++except getopt.GetoptError as err:
++	print(str(err)) 
+ 	usage()
+ 	sys.exit()
+ 
+@@ -101,7 +101,7 @@
+ 	a={'A':'T','T':'A','C':'G','G':'C'}
+ 	ss=''
+ 	for i in s.upper():
+-		if a.has_key(i): ss+=a[i]
++		if i in a: ss+=a[i]
+ 		elif i==' ': ss+=' '
+ 		elif i=='-': ss+='-'
+ 		else: ss+='N'
+@@ -125,23 +125,23 @@
+ 	anns='+'
+ 	for i in res:
+ 		if i[3]=='+':
+-			if d['+'].has_key(i[1]):
++			if i[1] in d['+']:
+ 				if i[0] not in d['+'][i[1]][0]: d['+'][i[1]][0]=d['+'][i[1]][0]+','+i[0]
+ 				if i[2]+'-'+i[0] not in d['+'][i[1]][1]: d['+'][i[1]][1]=d['+'][i[1]][1]+','+i[2]+'-'+i[0]
+ 			else:
+ 				d['+'][i[1]]=[i[0],i[2]+'-'+i[0]]
+ 		elif i[3]=='-':
+-			if d['-'].has_key(i[1]):
++			if i[1] in d['-']:
+ 				if i[0] not in d['-'][i[1]][0]: d['-'][i[1]][0]=d['-'][i[1]][0]+','+i[0]
+ 				if i[2]+'-'+i[0] not in d['-'][i[1]][1]: d['-'][i[1]][1]=d['-'][i[1]][1]+','+i[2]+'-'+i[0]
+ 			else:
+ 				d['-'][i[1]]=[i[0],i[2]+'-'+i[0]]
+-	gip='$'.join(d['+'].keys())
+-	featp='$'.join([d['+'][x][0] for x in d['+'].keys()])
+-	tip='$'.join([d['+'][x][1] for x in d['+'].keys()])
+-	gim='$'.join(d['-'].keys())
+-	featm='$'.join([d['-'][x][0] for x in d['-'].keys()])
+-	tim='$'.join([d['-'][x][1] for x in d['-'].keys()])
++	gip='$'.join(list(d['+'].keys()))
++	featp='$'.join([d['+'][x][0] for x in list(d['+'].keys())])
++	tip='$'.join([d['+'][x][1] for x in list(d['+'].keys())])
++	gim='$'.join(list(d['-'].keys()))
++	featm='$'.join([d['-'][x][0] for x in list(d['-'].keys())])
++	tim='$'.join([d['-'][x][1] for x in list(d['-'].keys())])
+ 	p=[featp,gip,tip]
+ 	m=[featm,gim,tim]
+ 	pm=[(featp+'&'+featm).strip('&'),(gip+'&'+gim).strip('&'),(tip+'&'+tim).strip('&')]
+@@ -187,7 +187,7 @@
+ 		elif strand=='-': res=ann[1]
+ 		else: res=ann[2]		
+ 		for i in addc:
+-			print prinfo[i]+ res[i]
++			print(prinfo[i]+ res[i])
+ 	except: sys.exit('Error: not correct position.')
+ 	
+ if af:
+@@ -200,7 +200,7 @@
+ 			h=[i.strip()]
+ 			for k in addc: h.append(hinfo[k])
+ 			if save: o.write('\t'.join(h)+'\n')
+-			else: print '\t'.join(h)
++			else: print('\t'.join(h))
+ 			continue
+ 		if i.startswith(skip): continue
+ 		l=(i.strip()).split('\t')
+@@ -230,7 +230,7 @@
+ 		else: res=ann[2]
+ 		for j in addc: l.append(res[j])
+ 		if save: o.write('\t'.join(l)+'\n')
+-		else: print '\t'.join(l)
++		else: print('\t'.join(l))
+ tabix.close()
+ if save:
+ 	o.close()
+diff -ru a/accessory/FilterTable.py b/accessory/FilterTable.py
+--- a/accessory/FilterTable.py	2020-07-16 16:16:59.360014702 -0500
++++ b/accessory/FilterTable.py	2020-07-16 16:17:22.209013627 -0500
+@@ -30,7 +30,7 @@
+ pid=str(os.getpid()+random.randint(0,999999999))
+ 
+ def usage():
+-	print """
++	print("""
+ USAGE: python FilterTable.py [options]
+ Options:
+ -i		Table file
+@@ -43,12 +43,12 @@
+ -p		Print simple statistics
+ -h		Print this help
+ 
+-"""
++""")
+ 
+ try:
+ 	opts, args = getopt.getopt(sys.argv[1:], 'i:o:f:hs:F:S:Ep',["help"])
+-except getopt.GetoptError, err:
+-	print str(err) 
++except getopt.GetoptError as err:
++	print(str(err)) 
+ 	usage()
+ 	sys.exit()
+ 
+diff -ru a/accessory/get_DE_events.py b/accessory/get_DE_events.py
+--- a/accessory/get_DE_events.py	2020-07-16 16:16:59.360014702 -0500
++++ b/accessory/get_DE_events.py	2020-07-16 16:17:22.646013607 -0500
+@@ -104,7 +104,7 @@
+ 	#WARNING those are np arrays.
+ 
+ 	for i in range(0,edit_level_table.shape[0]):
+-	  print i  #keep track of progress
++	  print(i)  #keep track of progress
+ 	  disease_edit_row = edit_level_table.loc[i, disease_people]
+ 	  control_edit_row = edit_level_table.loc[i, control_people]
+ 	  disease_cov_row = cov_table.loc[i, disease_people]
+@@ -206,7 +206,7 @@
+ 	#write the full_table to output
+ 	full_table.to_csv(output_file, sep='\t', index=False)
+ 
+-	print "job completed\n"
++	print("job completed\n")
+ 
+ 
+ 
+@@ -225,12 +225,12 @@
+ 
+ def Sample_percentage(row):
+ 	"""Percentage of samples from each type"""
+-	percentage = (len(filter(lambda x: x!= '-', row))/float(len(row)))*100
++	percentage = (len([x for x in row if x!= '-'])/float(len(row)))*100
+ 	return round(percentage)
+ 
+ def Sample_count(row):
+ 	"""Number of samples from each type"""
+-	count = len(filter(lambda x: x!= '-', row))
++	count = len([x for x in row if x!= '-'])
+ 	return count 
+ 
+ def get_bh(pvalue,siglevel):
+@@ -269,7 +269,7 @@
+ 	if(row_a[-1] != '-' and row_a[-1] != 0.0 and row_a[-1] <= 0.05):
+ 		row =  row[0].split('_') + row[2:]
+ 		row.insert(2, 'A.to.G')
+-		print '\t'.join(map(str,row))
++		print('\t'.join(map(str,row)))
+ 
+ def tuple_replace(i):
+ 	if type(i) == tuple:
+@@ -292,11 +292,11 @@
+ with open(samples_informations_file, 'r') as f:
+     for line in f:
+         if line.startswith('SRR'):
+-            line = map(str.strip, line.split(','))
++            line = list(map(str.strip, line.split(',')))
+             sample_informations.setdefault(line[0], line[1])
+ 
+ 
+-cwd = filter(os.path.isdir, os.listdir(os.getcwd()))
++cwd = list(filter(os.path.isdir, os.listdir(os.getcwd())))
+ all_available_sites = []
+ sample_edited_sites = {}
+ for directory in cwd:
+@@ -306,7 +306,7 @@
+         with open(table,'r') as a:
+             for line in a:
+                 if line.startswith('chr'):
+-                    s = map(str.strip, line.split("\t"))
++                    s = list(map(str.strip, line.split("\t")))
+ 		    if s[7] == 'AG':
+ 	                site, freq, coverage = s[0] + "_" + s[1], s[8], s[4]
+ 			freq_gnum_cov = '%s^%s^%s' %(s[8],eval(s[6])[2],s[4]) 
+@@ -314,14 +314,14 @@
+ 			if (int(coverage) >= min_coverage) and (float(freq) >= min_edit_frequency):
+                 		sample_edited_sites.setdefault((directory, site), []).append((freq, freq_gnum_cov))
+ 
+-table_columns = map(lambda x: x + '_' + sample_informations[x], sorted(sample_informations.keys()))
++table_columns = [x + '_' + sample_informations[x] for x in sorted(sample_informations.keys())]
+ 
+ disease = [i for i in table_columns if i.upper().find('DIS') != -1]
+ controls = [i for i in table_columns if i.upper().find('CTRL') != -1]
+ 
+ if enable_linear_model:
+ 	outtable=''
+-        header = ['chromosome', 'position', 'type_editing'] + map(remove_underscore, controls) + map(remove_underscore, disease)
++        header = ['chromosome', 'position', 'type_editing'] + list(map(remove_underscore, controls)) + list(map(remove_underscore, disease))
+         outtable += '\t'.join(header)
+ 	outtable += '\n'
+         #print '\t'.join(header)
+@@ -329,13 +329,13 @@
+                 row = [chrom]
+                 for col in header[2:]:#header.index('[num_controls/num_disease]')]:
+                         row.append(sample_edited_sites.get((col.split('_')[0],chrom), ['-'])[0])
+-                ctrls = zip(*(zip(controls,row[1:])))[1]
+-                dss = zip(*(zip(disease,row[len(ctrls)+1:])))[1]
+-                ctrls_freq = map(tuple_replace, ctrls)
+-                dss_freq = map(tuple_replace, dss)
++                ctrls = list(zip(*(list(zip(controls,row[1:])))))[1]
++                dss = list(zip(*(list(zip(disease,row[len(ctrls)+1:])))))[1]
++                ctrls_freq = list(map(tuple_replace, ctrls))
++                dss_freq = list(map(tuple_replace, dss))
+                 row.append(str([Sample_count(ctrls), Sample_count(dss)]))
+ 
+-                row_b = map(tuple_replace_bis, row)
++                row_b = list(map(tuple_replace_bis, row))
+                 row_b = row_b[0].split('_') + row_b[2:]
+                 row_b.insert(2, 'A.to.G')
+ 		final_list = row_b[:-1]
+@@ -359,20 +359,20 @@
+ 	if pvalue_correction == 2:
+ 		header += ['pvalue BH corrected']
+ 		
+-	print '\t'.join(header)
++	print('\t'.join(header))
+ 	
+ 	for chrom in sorted(all_available_sites, key = lambda x: Set_Chr_Nr(x)):
+ 		row = [chrom]
+ 		for col in header[3:header.index('[num_controls/num_disease]')]:
+ 			row.append(sample_edited_sites.get((col.split('_')[0],chrom), ['-'])[0])
+-		ctrls = zip(*(zip(controls,row[1:])))[1]
+-		dss = zip(*(zip(disease,row[len(ctrls)+1:])))[1] 
+-		ctrls_freq = map(tuple_replace, ctrls)
+-		dss_freq = map(tuple_replace, dss)
++		ctrls = list(zip(*(list(zip(controls,row[1:])))))[1]
++		dss = list(zip(*(list(zip(disease,row[len(ctrls)+1:])))))[1] 
++		ctrls_freq = list(map(tuple_replace, ctrls))
++		dss_freq = list(map(tuple_replace, dss))
+ 		row.append(str([Sample_count(ctrls), Sample_count(dss)]))
+ 		if (Sample_percentage(ctrls) >= min_sample_testing) and (Sample_percentage(dss) >= min_sample_testing):
+-			ctrls_mean = sum(map(float, filter(lambda x: x!= '-', ctrls_freq)))/len(filter(lambda x: x!= '-', ctrls_freq))
+-	                dss_mean = sum(map(float, filter(lambda x: x!= '-', dss_freq)))/len(filter(lambda x : x!= '-', dss_freq))
++			ctrls_mean = sum(map(float, [x for x in ctrls_freq if x!= '-']))/len([x for x in ctrls_freq if x!= '-'])
++	                dss_mean = sum(map(float, [x for x in dss_freq if x!= '-']))/len([x for x in dss_freq if x!= '-'])
+ 			delta_diff =  abs(ctrls_mean - dss_mean)
+ 			pvalue=stats.mannwhitneyu(ctrls_freq, dss_freq, alternative='two-sided')
+ 			row.append(round(delta_diff, 3))
+@@ -388,12 +388,12 @@
+ 				row += ['-', '-']
+ 			else:
+ 				row += ['-', '-', '-']
+-		row_a = map(tuple_replace, row)
+-		row_b = map(tuple_replace_bis, row)
++		row_a = list(map(tuple_replace, row))
++		row_b = list(map(tuple_replace_bis, row))
+ 		if pvalue_correction != 0 and only_significants == 'yes':
+ 			only_sig(row_a,row_b)
+ 		else:
+ 			row_b =  row_b[0].split('_') + row_b[2:]
+ 	                row_b.insert(2, 'A.to.G')
+-			print '\t'.join(map(str,row_b))
++			print('\t'.join(map(str,row_b)))
+ 
+diff -ru a/accessory/GFFtoTabix.py b/accessory/GFFtoTabix.py
+--- a/accessory/GFFtoTabix.py	2020-07-16 16:16:59.360014702 -0500
++++ b/accessory/GFFtoTabix.py	2020-07-16 16:17:22.264013625 -0500
+@@ -31,7 +31,7 @@
+ pid=str(os.getpid()+random.randint(0,999999999))
+ 
+ def usage():
+-	print """
++	print("""
+ USAGE: python GFFtoTabix.py [options]
+ Options:
+ -i		GFF file
+@@ -41,7 +41,7 @@
+ -u		Save an uncompressed GFF copy (add _copy suffix)
+ -h		Print this help
+ 
+-"""
++""")
+ 
+ try:
+ 	opts, args = getopt.getopt(sys.argv[1:], "i:Sb:t:hu",["help"])
+@@ -49,7 +49,7 @@
+ 		usage()
+ 		sys.exit(2)
+ except getopt.GetoptError as err:
+-	print str(err) # will print something like "option -a not recognized"
++	print(str(err)) # will print something like "option -a not recognized"
+ 	usage()
+ 	sys.exit(2)
+ 
+diff -ru a/accessory/rediportal2recoding.py b/accessory/rediportal2recoding.py
+--- a/accessory/rediportal2recoding.py	2020-07-16 16:16:59.360014702 -0500
++++ b/accessory/rediportal2recoding.py	2020-07-16 16:17:22.709013604 -0500
+@@ -41,4 +41,4 @@
+ 				gff_row = line[0] + '\t'+ valore + '\t' + 'ed' + '\t' + line[1] + \
+ 				'\t' + line[1] + '\t' + '.' + '\t' + line[4] + '\t' + '.' + '\t' + \
+ 				'gene_id' + ' '  + '"ed_%s";' %(i) + ' ' + 'transcript_id' + ' ' + '"ed_%s";' %(i)
+-				print gff_row
++				print(gff_row)
+diff -ru a/accessory/SearchInTable.py b/accessory/SearchInTable.py
+--- a/accessory/SearchInTable.py	2020-07-16 16:16:59.360014702 -0500
++++ b/accessory/SearchInTable.py	2020-07-16 16:17:22.309013623 -0500
+@@ -25,7 +25,7 @@
+ #pid=str(os.getpid()+random.randint(0,999999999))
+ 
+ def usage():
+-	print """
++	print("""
+ USAGE: python SearchInTable.py [options]
+ Options:
+ -i		Sorted table file (first col=reference; second col=coordinate 1 based)
+@@ -42,7 +42,7 @@
+ -o		Save found/not found positions on file
+ -h		Print this help
+ 
+-"""
++""")
+ #-k		skip first INT lines [0]
+ 
+ try:
+@@ -51,7 +51,7 @@
+ 		usage()
+ 		sys.exit(2)
+ except getopt.GetoptError as err:
+-	print str(err) # will print something like "option -a not recognized"
++	print(str(err)) # will print something like "option -a not recognized"
+ 	usage()
+ 	sys.exit(2)
+ 
+diff -ru a/accessory/selectPositions.py b/accessory/selectPositions.py
+--- a/accessory/selectPositions.py	2020-07-16 16:16:59.360014702 -0500
++++ b/accessory/selectPositions.py	2020-07-16 16:17:22.833013598 -0500
+@@ -25,7 +25,7 @@
+ pid=str(os.getpid()+random.randint(0,999999999))
+ 
+ def usage():
+-	print """
++	print("""
+ USAGE: python selectPositions.py [options]
+ Options:
+ -i		Table file from REDItools
+@@ -44,7 +44,7 @@
+ -o		Save selected positions on outTable_%s
+ -h		Print this help
+ 
+-"""%(pid)
++"""%(pid))
+ 
+ try:
+ 	opts, args = getopt.getopt(sys.argv[1:], "i:c:C:v:s:f:F:euo:hrd:RV:",["help"])
+@@ -52,7 +52,7 @@
+ 		usage()
+ 		sys.exit(2)
+ except getopt.GetoptError as err:
+-	print str(err) # will print something like "option -a not recognized"
++	print(str(err)) # will print something like "option -a not recognized"
+ 	usage()
+ 	sys.exit(2)
+ 
+diff -ru a/accessory/SortGFF.py b/accessory/SortGFF.py
+--- a/accessory/SortGFF.py	2020-07-16 16:16:59.360014702 -0500
++++ b/accessory/SortGFF.py	2020-07-16 16:17:22.357013620 -0500
+@@ -35,7 +35,7 @@
+ pid=str(os.getpid()+random.randint(0,999999999))
+ 
+ def usage():
+-	print """
++	print("""
+ USAGE: python SortGFF.py [options]
+ Options:
+ -i		GFF file
+@@ -44,7 +44,7 @@
+ -t		Temporary directory to use (multiple -t may be used)
+ -h		Print this help
+ 
+-"""%(pid)
++"""%(pid))
+ 
+ try:
+ 	opts, args = getopt.getopt(sys.argv[1:], "i:o:b:t:h",["help"])
+@@ -52,7 +52,7 @@
+ 		usage()
+ 		sys.exit(2)
+ except getopt.GetoptError as err:
+-	print str(err) # will print something like "option -a not recognized"
++	print(str(err)) # will print something like "option -a not recognized"
+ 	usage()
+ 	sys.exit(2)
+ 
+diff -ru a/accessory/SortTable.py b/accessory/SortTable.py
+--- a/accessory/SortTable.py	2020-07-16 16:16:59.360014702 -0500
++++ b/accessory/SortTable.py	2020-07-16 16:17:22.411013618 -0500
+@@ -35,7 +35,7 @@
+ pid=str(os.getpid()+random.randint(0,999999999))
+ 
+ def usage():
+-	print """
++	print("""
+ USAGE: python SortTable.py [options]
+ Options:
+ -i		Table file
+@@ -50,7 +50,7 @@
+ -t		Temporary directory to use (multiple -t may be used)
+ -h		Print this help
+ 
+-"""%(pid)
++"""%(pid))
+ 
+ try:
+ 	opts, args = getopt.getopt(sys.argv[1:], "i:o:b:t:hd:s:c:e:m:O",["help"])
+@@ -58,7 +58,7 @@
+ 		usage()
+ 		sys.exit(2)
+ except getopt.GetoptError as err:
+-	print str(err) # will print something like "option -a not recognized"
++	print(str(err)) # will print something like "option -a not recognized"
+ 	usage()
+ 	sys.exit(2)
+ 
+diff -ru a/accessory/subCount2.py b/accessory/subCount2.py
+--- a/accessory/subCount2.py	2020-07-16 16:16:59.360014702 -0500
++++ b/accessory/subCount2.py	2020-07-16 16:17:22.854013597 -0500
+@@ -28,5 +28,5 @@
+ for i in s:
+ 	try: v=(s[i]/float(all))*100
+ 	except: v=0.0
+-	print i,s[i],all,v
++	print(i,s[i],all,v)
+ 
+diff -ru a/accessory/subCount.py b/accessory/subCount.py
+--- a/accessory/subCount.py	2020-07-16 16:16:59.360014702 -0500
++++ b/accessory/subCount.py	2020-07-16 16:17:22.844013597 -0500
+@@ -30,5 +30,5 @@
+ for i in s:
+ 	try: v=(s[i]/float(all))*100
+ 	except: v=0.0
+-	print i,s[i],all,v
++	print(i,s[i],all,v)
+ 
+diff -ru a/accessory/TableToGFF.py b/accessory/TableToGFF.py
+--- a/accessory/TableToGFF.py	2020-07-16 16:16:59.360014702 -0500
++++ b/accessory/TableToGFF.py	2020-07-16 16:17:22.474013615 -0500
+@@ -29,7 +29,7 @@
+ pid=str(os.getpid()+random.randint(0,999999999))
+ 
+ def usage():
+-	print """
++	print("""
+ USAGE: python TableToGFF.py [options]
+ Options:
+ -i		Table file from REDItools
+@@ -40,7 +40,7 @@
+ -o		Outfile [outTable_%s.gff]
+ -h		Print this help
+ 
+-"""%(pid)
++"""%(pid))
+ 
+ try:
+ 	opts, args = getopt.getopt(sys.argv[1:], "i:o:sthT:b:",["help"])
+@@ -48,7 +48,7 @@
+ 		usage()
+ 		sys.exit(2)
+ except getopt.GetoptError as err:
+-	print str(err) # will print something like "option -a not recognized"
++	print(str(err)) # will print something like "option -a not recognized"
+ 	usage()
+ 	sys.exit(2)
+ 
+diff -ru a/accessory/tableToTabix.py b/accessory/tableToTabix.py
+--- a/accessory/tableToTabix.py	2020-07-16 16:16:59.360014702 -0500
++++ b/accessory/tableToTabix.py	2020-07-16 16:17:22.913013594 -0500
+@@ -31,7 +31,7 @@
+ pid=str(os.getpid()+random.randint(0,999999999))
+ 
+ def usage():
+-	print """
++	print("""
+ USAGE: python tableToTabix.py [options]
+ Options:
+ -i		TAB-delimited file
+@@ -46,7 +46,7 @@
+ -u		Save an uncompressed GFF copy (add _copy suffix)
+ -h		Print this help
+ 
+-"""
++""")
+ 
+ try:
+ 	opts, args = getopt.getopt(sys.argv[1:], "i:Sb:t:hus:c:e:m:0",["help"])
+@@ -54,7 +54,7 @@
+ 		usage()
+ 		sys.exit(2)
+ except getopt.GetoptError as err:
+-	print str(err) # will print something like "option -a not recognized"
++	print(str(err)) # will print something like "option -a not recognized"
+ 	usage()
+ 	sys.exit(2)
+ 
+diff -ru a/main/REDItoolDenovo.py b/main/REDItoolDenovo.py
+--- a/main/REDItoolDenovo.py	2020-07-16 16:16:59.360014702 -0500
++++ b/main/REDItoolDenovo.py	2020-07-16 16:17:21.265013672 -0500
+@@ -75,7 +75,7 @@
+         return 1
+     numerator = 1
+     denominator = 1
+-    for i in xrange(s+1, population + 1):
++    for i in range(s+1, population + 1):
+         numerator *= i
+         denominator *= (i - s)
+     return numerator/denominator
+@@ -275,7 +275,7 @@
+ try: import pysam
+ except: sys.exit('Pysam module not found.')
+ from multiprocessing import Process, Queue
+-from Queue import Empty
++from queue import Empty
+ try:
+     from fisher import pvalue
+     exfisher=1
+@@ -292,7 +292,7 @@
+ pid=str(os.getpid()+random.randint(0,999999999))
+ 
+ def usage():
+-	print """
++	print("""
+ USAGE: python REDItoolDenovo.py [options]
+ Options:
+ -i		BAM file
+@@ -343,12 +343,12 @@
+ 	- For Tophat2 use 50
+ 	- For GSNAP use 30
+ 
+-"""%(pid)
++"""%(pid))
+ 
+ try:
+ 	opts, args = getopt.getopt(sys.argv[1:], "b:f:k:t:o:c:q:m:O:s:edpuT:B:v:n:EP:r:hHa:i:lIU:V:w:XG:K:F:g:x:W")
+ except getopt.GetoptError as err:
+-	print str(err) # will print something like "option -a not recognized"
++	print(str(err)) # will print something like "option -a not recognized"
+ 	usage()
+ 	sys.exit(2)
+ 
+@@ -474,7 +474,7 @@
+ 		annfile=a
+ 		uann=1
+ 	else:
+-		print o
++		print(o)
+ 		assert False, "Unhandled Option"
+ 
+ #######
+@@ -532,7 +532,7 @@
+ 		return False
+ 	try:
+ 		os.kill(pid, 0)
+-	except OSError, e:
++	except OSError as e:
+ 		return e.errno == errno.EPERM
+ 	else:
+ 		return True
+@@ -637,9 +637,9 @@
+ 	subs=[]
+ 	subv=[]
+ 	for i in seq.upper():
+-		if b.has_key(i): b[i]+=1
++		if i in b: b[i]+=1
+ 	for i in b:
+-		if not b.has_key(ref): continue
++		if ref not in b: continue
+ 		if b[i]!=0 and i!=ref:
+ 			vv=float(b[i])/(b[i]+b[ref])
+ 			subv.append((b[i],vv,ref+i))
+@@ -690,7 +690,7 @@
+ 	a={'A':'T','T':'A','C':'G','G':'C'}
+ 	ss=''
+ 	for i in s.upper():
+-		if a.has_key(i): ss+=a[i]
++		if i in a: ss+=a[i]
+ 		else: ss+='N'
+ 	return ss	
+ 
+@@ -777,7 +777,7 @@
+ 	frefs.append(l[0])
+ fidxinfo.close()
+ rnof=[]
+-for i in rrefs.keys():
++for i in list(rrefs.keys()):
+ 	if i not in frefs: sys.stderr.write('WARNING: Region %s in RNA-Seq not found in reference file.\n' %(i))
+ #####################		
+ 
+@@ -817,8 +817,8 @@
+ #mainbam=pysam.Samfile(bamfile,"rb")
+ #regions=mainbam.references
+ #mainbam.close()
+-dicregions=dict(rrefs.items())
+-chrs=[x for x in dicregions.keys() if x not in nochrs]
++dicregions=dict(list(rrefs.items()))
++chrs=[x for x in list(dicregions.keys()) if x not in nochrs]
+ sys.stderr.write('Analysis on %i regions.\n' %(len(chrs)))
+ 
+ if infolder!='': outfolder=os.path.join(outfolder_,'denovo_%s_%s' %(infolder,pid))
+@@ -906,7 +906,7 @@
+ 			if pileupread.alignment.has_tag('SA'): continue			
+ 			#s,q,t,qq=pileupread.alignment.seq[pileupread.qpos].upper(),ord(pileupread.alignment.qual[pileupread.qpos])-QVAL,'*',pileupread.alignment.qual[pileupread.qpos]
+ 			# escludi posizioni introniche nei pressi di splice sites
+-			if exss and di.has_key(pileupcolumn.reference_pos+1): continue #MOD
++			if exss and pileupcolumn.reference_pos+1 in di: continue #MOD
+ 			# multiple hit
+ 			if exh: #MOD
+ 				if pileupread.alignment.is_secondary: continue #MOD
+@@ -998,7 +998,7 @@
+ 					elif pileupread.alignment.is_read2: rt=2
+ 					else: rt=0
+ 					rname=pileupread.alignment.query_name+'_%i'%(rt) #MOD
+-					if d.has_key(rname): blatc+='0' #continue
++					if rname in d: blatc+='0' #continue
+ 					else: blatc+='1'					
+ 				# se la base e' diversa dal reference
+ 				# se in regione omopolimerica scarta
+@@ -1032,7 +1032,7 @@
+ 			if not custsub:
+ 				ni='ACGT'
+ 				for b in range(4):
+-					if dsubs.has_key(ref.upper()+ni[b]):
++					if ref.upper()+ni[b] in dsubs:
+ 						dsubs[ref.upper()+ni[b]]+=bcomp[b]
+ 			if expos:
+ 				if chr in extabix.contigs:
+diff -ru a/main/REDItoolDnaRna.py b/main/REDItoolDnaRna.py
+--- a/main/REDItoolDnaRna.py	2020-07-16 16:16:59.360014702 -0500
++++ b/main/REDItoolDnaRna.py	2020-07-16 16:17:21.757013649 -0500
+@@ -23,7 +23,7 @@
+ try: import pysam
+ except: sys.exit('Pysam module not found.')
+ from multiprocessing import Process, Queue
+-from Queue import Empty
++from queue import Empty
+ import gzip
+ 
+ pysamVersion=pysam.__version__
+@@ -34,7 +34,7 @@
+ pid=str(os.getpid()+random.randint(0,999999999))
+ 
+ def usage():
+-	print """
++	print("""
+ USAGE: python REDItoolDnaRNA.py [options]
+ Options:
+ -i		RNA-Seq BAM file
+@@ -103,7 +103,7 @@
+ 	- For Tophat2 use 50
+ 	- For GSNAP use 30
+ 
+-"""%(pid)
++"""%(pid))
+ 
+ #option --fastq	Fastq to get reads [requires --reads], separated by comma [if paired] NOT IMPLEMENTED
+ #option --rmOver	Remove overlapping reads NOT IMPLEMENTED
+@@ -111,7 +111,7 @@
+ try:
+ 	opts, args = getopt.getopt(sys.argv[1:], "i:f:k:t:o:c:q:m:O:s:edpuA:a:B:b:lLv:n:EPr:hHIXG:K:j:C:JDUzw:N:ZW:RVMT:F:x:g:SY:",["help","gzip","reads","addP","rmIndels"])
+ except getopt.GetoptError as err:
+-	print str(err) # will print something like "option -a not recognized"
++	print(str(err)) # will print something like "option -a not recognized"
+ 	usage()
+ 	sys.exit(2)
+ 
+@@ -325,7 +325,7 @@
+ params.append('Analysis ID: %s\n' %(pid))
+ params.append('Analysis time: %s\n' %(script_time))
+ params.append('-i --> RNA-Seq BAM file: %s\n' %(bamfile))
+-params.append('-j --> DNA-Seq BAM file(s): %s\n' %(','.join(dgbamfile.keys())))
++params.append('-j --> DNA-Seq BAM file(s): %s\n' %(','.join(list(dgbamfile.keys()))))
+ params.append('-I --> Sort RNA-Seq BAM file: %i\n' %(sortbam))
+ params.append('-J --> Sort DNA-Seq BAM file: %i\n' %(sortgbam))
+ params.append('-f --> Reference file: %s\n' %(fastafile))
+@@ -483,9 +483,9 @@
+ 	subs=[]
+ 	subv=[]
+ 	for i in seq.upper():
+-		if b.has_key(i): b[i]+=1
++		if i in b: b[i]+=1
+ 	for i in b:
+-		if not b.has_key(ref): continue
++		if ref not in b: continue
+ 		if b[i]!=0 and i!=ref:
+ 			vv=float(b[i])/(b[i]+b[ref])
+ 			subv.append((b[i],vv,ref+i))
+@@ -537,7 +537,7 @@
+ 	a={'A':'T','T':'A','C':'G','G':'C'}
+ 	ss=''
+ 	for i in s.upper():
+-		if a.has_key(i): ss+=a[i]
++		if i in a: ss+=a[i]
+ 		elif i==' ': ss+=' '
+ 		elif i=='-': ss+='-'
+ 		else: ss+='N'
+@@ -682,7 +682,7 @@
+ 		if l.count(i[0])==2:
+ 			s='='
+ 			if i[1]!=i[2]: s='!'
+-			if us.has_key(i[0]): us[i[0]].append((x,s))
++			if i[0] in us: us[i[0]].append((x,s))
+ 			else: us[i[0]]=[(x,s)]
+ 		x+=1
+ 	for i in us:
+@@ -753,7 +753,7 @@
+ 	pysam.faidx(fastafile)
+ ###########################################################
+ # Check reference for name consistency
+-grefs=dgdic.keys()
++grefs=list(dgdic.keys())
+ rrefs={}
+ ridxinfo=pysam.idxstats(bamfile)
+ for j in ridxinfo.split('\n'): #MOD
+@@ -769,7 +769,7 @@
+ fidxinfo.close()
+ # in rna-seq
+ rnof=[]
+-for i in rrefs.keys():
++for i in list(rrefs.keys()):
+ 	if i not in frefs: sys.stderr.write('WARNING: Region %s in RNA-Seq not found in reference file.\n' %(i))
+ if len(gbamfile)!=0:
+ 	for i in grefs:
+@@ -833,9 +833,9 @@
+ #regions=mainbam.references
+ #regionslens=mainbam.lengths
+ #mainbam.close()
+-dicregions=dict(rrefs.items())
++dicregions=dict(list(rrefs.items()))
+ #dicregions=dict([(regions[x],regionslens[x]) for x in range(len(regions))])
+-chrs=[x for x in dicregions.keys() if x not in nochrs]
++chrs=[x for x in list(dicregions.keys()) if x not in nochrs]
+ if fworkR: sys.stderr.write('Analysis on region %s:%i-%i.\n' %(workR[0],workR[1][0],workR[1][1]))
+ else: sys.stderr.write('Analysis on %i regions.\n' %(len(chrs)))
+ ###########################################################
+@@ -883,7 +883,7 @@
+ 	isgbam=1
+ 	inputs=myinput.split('$')
+ 	chr,bamfile,start_region,lenregion,suff_=inputs[0],inputs[1],int(inputs[2]),int(inputs[3]),inputs[4]
+-	if not dgdic.has_key(chr): isgbam=0
++	if chr not in dgdic: isgbam=0
+ 	outfile=os.path.join(outfolder,'table_%s'%(suff_))
+ 	if slist:
+ 		if gziptab: outrna=gzip.open(os.path.join(outfolder,'pileupRNA_%s.gz'%(suff)),'wb')
+@@ -1024,7 +1024,7 @@
+ 							if pileupread.alignment.is_read1: rt=1
+ 							elif pileupread.alignment.is_read2: rt=2
+ 							rname=pileupread.alignment.query_name+'_%i'%(rt)
+-							if gd.has_key(rname): gblatc+='0' #continue
++							if rname in gd: gblatc+='0' #continue
+ 							else: gblatc+='1'
+ 						# se la base e' diversa dal reference
+ 						# se in regione omopolimerica scarta
+@@ -1079,7 +1079,7 @@
+ 				#s,q,t,qq=pileupread.alignment.query_sequence[pileupread.query_position].upper(),pileupread.alignment.query_qualities[pileupread.query_position],'*',pileupread.alignment.qual[pileupread.query_position]
+ 				#s,q,t,qq=pileupread.alignment.seq[pileupread.qpos].upper(),ord(pileupread.alignment.qual[pileupread.qpos])-QVAL,'*',pileupread.alignment.qual[pileupread.qpos]
+ 				# escludi posizioni introniche nei pressi di splice sites
+-				if exss and di.has_key(pileupcolumn.reference_pos+1): continue
++				if exss and pileupcolumn.reference_pos+1 in di: continue
+ 				# multiple hit
+ 				if exh:
+ 					if pileupread.alignment.is_secondary: continue
+@@ -1179,7 +1179,7 @@
+ 						elif pileupread.alignment.is_read2: rt=2
+ 						else: rt=0
+ 						rname=pileupread.alignment.query_name+'_%i'%(rt)
+-						if d.has_key(rname): blatc+='0' #continue
++						if rname in d: blatc+='0' #continue
+ 						else: blatc+='1'
+ 					# se la base e' diversa dal reference
+ 					# se in regione omopolimerica scarta
+@@ -1213,7 +1213,7 @@
+ 							else: addpos=(pileupread.alignment.query_name,'-',pileupread.alignment.reference_name,'-',pileupread.alignment.reference_start,pileupread.alignment.reference_end,0 , 0)
+ 							rqname_comp=rqname+'$'+pileupread.alignment.reference_name+'$'+str(pileupcolumn.reference_pos+1)
+ 							#addpos=(chr+'_'+str(pileupcolumn.reference_pos+1),pileupcolumn.reference_pos+1)
+-							if not grdb.has_key(rqname):
++							if rqname not in grdb:
+ 								#print rqname reference_start
+ 								outreads.write('>'+rqname_comp+'\n'+rseqname+'\n')
+ 								#grdb[rqname]=[addpos]
+@@ -1221,7 +1221,7 @@
+ 							#	if addpos not in grdb[rqname]:
+ 							#		grdb[rqname].append(addpos)
+ 							if addP:
+-								if not grdb2.has_key(rname): grdb2[rname]=addpos
++								if rname not in grdb2: grdb2[rname]=addpos
+ 			if seq.strip()!='':
+ 				#print seq,qual,squal
+ 				if rmIndel:
+@@ -1268,7 +1268,7 @@
+ 				if exinv and subs=='-': continue
+ 				if not checkSubs(subs): continue
+ 				#print out rna-seq info + dna-seq
+-				if gdic.has_key(pileupcolumn.reference_pos): # abbiamo l'informazione genomica
++				if pileupcolumn.reference_pos in gdic: # abbiamo l'informazione genomica
+ 					if exnonh and not gdic[pileupcolumn.reference_pos][1]: continue
+ 					if mystrand=='0':
+ 						gdic[pileupcolumn.reference_pos][0][2]=comp2(eval(gdic[pileupcolumn.reference_pos][0][2]))
+diff -ru a/main/REDItoolKnown.py b/main/REDItoolKnown.py
+--- a/main/REDItoolKnown.py	2020-07-16 16:16:59.360014702 -0500
++++ b/main/REDItoolKnown.py	2020-07-16 16:17:22.063013634 -0500
+@@ -23,7 +23,7 @@
+ try: import pysam
+ except: sys.exit('Pysam module not found.')
+ from multiprocessing import Process, Queue
+-from Queue import Empty
++from queue import Empty
+ 
+ pysamVersion=pysam.__version__
+ 
+@@ -34,7 +34,7 @@
+ pid=str(os.getpid()+random.randint(0,999999999))
+ 
+ def usage():
+-	print """
++	print("""
+ USAGE: python REDItoolKnown.py [options]
+ Options:
+ -i		BAM file
+@@ -82,12 +82,12 @@
+ 	- For Tophat2 use 50
+ 	- For GSNAP use 30
+ 
+-"""%(pid)
++"""%(pid))
+ 
+ try:
+ 	opts, args = getopt.getopt(sys.argv[1:], "i:f:k:t:o:c:q:m:O:s:edpuT:B:Sv:n:EP:r:hHIXG:K:l:C:F:x:g:U")
+ except getopt.GetoptError as err:
+-	print str(err) # will print something like "option -a not recognized"
++	print(str(err)) # will print something like "option -a not recognized"
+ 	usage()
+ 	sys.exit(2)
+ 
+@@ -257,7 +257,7 @@
+         return False
+     try:
+         os.kill(pid, 0)
+-    except OSError, e:
++    except OSError as e:
+         return e.errno == errno.EPERM
+     else:
+         return True
+@@ -361,9 +361,9 @@
+ 	subs=[]
+ 	subv=[]
+ 	for i in seq.upper():
+-		if b.has_key(i): b[i]+=1
++		if i in b: b[i]+=1
+ 	for i in b:
+-		if not b.has_key(ref): continue
++		if ref not in b: continue
+ 		if b[i]!=0 and i!=ref:
+ 			vv=float(b[i])/(b[i]+b[ref])
+ 			subv.append((b[i],vv,ref+i))
+@@ -414,7 +414,7 @@
+ 	a={'A':'T','T':'A','C':'G','G':'C'}
+ 	ss=''
+ 	for i in s.upper():
+-		if a.has_key(i): ss+=a[i]
++		if i in a: ss+=a[i]
+ 		else: ss+='N'
+ 	return ss	
+ 
+@@ -524,7 +524,7 @@
+ fidxinfo.close()
+ # in rna-seq
+ rnof=[]
+-for i in rrefs.keys():
++for i in list(rrefs.keys()):
+ 	if i not in frefs: sys.stderr.write('WARNING: Region %s in RNA-Seq not found in reference file.\n' %(i))
+ ##################################
+ 
+@@ -568,8 +568,8 @@
+ #mainbam.close()
+ #dicregions=dict([(regions[x],regionslens[x]) for x in range(len(regions))])
+ #chrs=[x for x in regions if x not in nochrs]
+-dicregions=dict(rrefs.items())
+-chrs=[x for x in dicregions.keys() if x not in nochrs]
++dicregions=dict(list(rrefs.items()))
++chrs=[x for x in list(dicregions.keys()) if x not in nochrs]
+ sys.stderr.write('Analysis on %i regions.\n' %(len(chrs)))
+ 
+ if infolder!='': outfolder=os.path.join(outfolder_,'known_%s_%s' %(infolder,pid))
+@@ -654,7 +654,7 @@
+ 			# else explore bam to find exact positions
+ 			for pileupcolumn in bam.pileup(chr,startk,endk,stepper='nofilter', max_depth=MAX_DEPTH):
+ 				if not startk<=pileupcolumn.reference_pos<=endk: continue
+-				if not kdic.has_key(pileupcolumn.reference_pos+1): continue
++				if pileupcolumn.reference_pos+1 not in kdic: continue
+ 				ref=fasta.fetch(chr,pileupcolumn.reference_pos,pileupcolumn.reference_pos+1).upper()
+ 				seq,qual,strand,squal,blatc='',0,'',[],''
+ 				if rmsh:
+@@ -668,7 +668,7 @@
+ 					if pileupread.alignment.is_supplementary: continue
+ 					if pileupread.alignment.has_tag('SA'): continue
+ 					# escludi posizioni introniche nei pressi di splice sites
+-					if exss and di.has_key(pileupcolumn.reference_pos+1): continue
++					if exss and pileupcolumn.reference_pos+1 in di: continue
+ 					# multiple hit
+ 					if exh:
+ 						if pileupread.alignment.is_secondary: continue
+@@ -754,7 +754,7 @@
+ 							elif pileupread.alignment.is_read2: rt=2
+ 							else: rt=0
+ 							rname=pileupread.alignment.query_name+'_%i'%(rt)
+-							if d.has_key(rname): blatc+='0' #continue
++							if rname in d: blatc+='0' #continue
+ 							else: blatc+='1'
+ 						# se la base e' diversa dal reference
+ 						# se in regione omopolimerica scarta
diff --git a/var/spack/repos/builtin/packages/reditools/setup.py.patch b/var/spack/repos/builtin/packages/reditools/setup.py.patch
new file mode 100644
index 0000000000..f65345ad92
--- /dev/null
+++ b/var/spack/repos/builtin/packages/reditools/setup.py.patch
@@ -0,0 +1,11 @@
+--- a/setup.py	2020-07-16 14:01:48.601449013 -0500
++++ b/setup.py	2020-07-16 14:02:31.547441668 -0500
+@@ -33,7 +33,7 @@
+           'Operating System :: POSIX',
+           'Programming Language :: Python',
+           ],
+-	long_description=open('README').read(),
++	long_description=open('README_1.md').read(),
+ 	platforms=['Linux','Unix','MacOS']
+ )
+