git: 350d96226d1b - main - biology/checkm: Update 1.0.18 -> 1.1.8
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Tue, 12 Apr 2022 03:22:32 UTC
The branch main has been updated by yuri:
URL: https://cgit.FreeBSD.org/ports/commit/?id=350d96226d1bcf56747c37a3ba7e33564fc42f69
commit 350d96226d1bcf56747c37a3ba7e33564fc42f69
Author: Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2022-04-11 19:53:21 +0000
Commit: Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2022-04-12 03:22:30 +0000
biology/checkm: Update 1.0.18 -> 1.1.8
Reported by: portscout
---
biology/checkm/Makefile | 10 +-
biology/checkm/distinfo | 6 +-
biology/checkm/files/patch-2to3 | 648 ----------------------------------------
3 files changed, 8 insertions(+), 656 deletions(-)
diff --git a/biology/checkm/Makefile b/biology/checkm/Makefile
index 6bb02b8266de..4c93a679cef4 100644
--- a/biology/checkm/Makefile
+++ b/biology/checkm/Makefile
@@ -1,6 +1,6 @@
PORTNAME= CheckM
DISTVERSIONPREFIX= v
-DISTVERSION= 1.0.18
+DISTVERSION= 1.1.8
CATEGORIES= biology python
MAINTAINER= yuri@FreeBSD.org
@@ -10,10 +10,10 @@ LICENSE= GPLv3
LICENSE_FILE= ${WRKSRC}/LICENSE
RUN_DEPENDS= ${PYNUMPY} \
- ${PYTHON_PKGNAMEPREFIX}DendroPy>=4.0.0:science/py-DendroPy@${PY_FLAVOR} \
- ${PYTHON_PKGNAMEPREFIX}matplotlib>=1.3.1:math/py-matplotlib@${PY_FLAVOR} \
- ${PYTHON_PKGNAMEPREFIX}pysam>=0.8.3:biology/py-pysam@${PY_FLAVOR} \
- ${PYTHON_PKGNAMEPREFIX}scipy>=0.9.0:science/py-scipy@${PY_FLAVOR}
+ ${PYTHON_PKGNAMEPREFIX}DendroPy>=4.4.0:science/py-DendroPy@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}matplotlib>=2.1.0:math/py-matplotlib@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}pysam>=0.12.0.1:biology/py-pysam@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}scipy>=0.19.1:science/py-scipy@${PY_FLAVOR}
USES= dos2unix python:3.7+
USE_GITHUB= yes
diff --git a/biology/checkm/distinfo b/biology/checkm/distinfo
index 35db37fcbe81..b707e945959f 100644
--- a/biology/checkm/distinfo
+++ b/biology/checkm/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1566202999
-SHA256 (Ecogenomics-CheckM-v1.0.18_GH0.tar.gz) = 240184bd7c708cd041d0fc14f81b22af5cb69cb96ae75177aee32effa578ca4e
-SIZE (Ecogenomics-CheckM-v1.0.18_GH0.tar.gz) = 212064
+TIMESTAMP = 1649697676
+SHA256 (Ecogenomics-CheckM-v1.1.8_GH0.tar.gz) = c6e9d007622808ae3312de73d54866292a83857837119380a036036e799c1f38
+SIZE (Ecogenomics-CheckM-v1.1.8_GH0.tar.gz) = 1016432
diff --git a/biology/checkm/files/patch-2to3 b/biology/checkm/files/patch-2to3
deleted file mode 100644
index 04b37972c86e..000000000000
--- a/biology/checkm/files/patch-2to3
+++ /dev/null
@@ -1,648 +0,0 @@
---- checkm/binTools.py.orig 2022-03-15 18:25:01 UTC
-+++ checkm/binTools.py
-@@ -26,7 +26,7 @@ import gzip
-
- import numpy as np
-
--from common import binIdFromFilename, checkFileExists, readDistribution, findNearest
-+from .common import binIdFromFilename, checkFileExists, readDistribution, findNearest
- from checkm.util.seqUtils import readFasta, writeFasta, baseCount
- from checkm.genomicSignatures import GenomicSignatures
- from checkm.prodigal import ProdigalGeneFeatureParser
-@@ -123,34 +123,34 @@ class BinTools():
- seqId = line[1:].split(None, 1)[0]
-
- if seqId in seqIds:
-- print ' [Warning] Sequence %s found multiple times in bin %s.' % (seqId, binId)
-+ print(' [Warning] Sequence %s found multiple times in bin %s.' % (seqId, binId))
- seqIds.add(seqId)
-
- binSeqs[binId] = seqIds
-
- # check for sequences assigned to multiple bins
- bDuplicates = False
-- binIds = binSeqs.keys()
-- for i in xrange(0, len(binIds)):
-- for j in xrange(i + 1, len(binIds)):
-+ binIds = list(binSeqs.keys())
-+ for i in range(0, len(binIds)):
-+ for j in range(i + 1, len(binIds)):
- seqInter = set(binSeqs[binIds[i]]).intersection(set(binSeqs[binIds[j]]))
-
- if len(seqInter) > 0:
- bDuplicates = True
-- print ' Sequences shared between %s and %s: ' % (binIds[i], binIds[j])
-+ print(' Sequences shared between %s and %s: ' % (binIds[i], binIds[j]))
- for seqId in seqInter:
-- print ' ' + seqId
-- print ''
-+ print(' ' + seqId)
-+ print('')
-
- if not bDuplicates:
-- print ' No sequences assigned to multiple bins.'
-+ print(' No sequences assigned to multiple bins.')
-
- def gcDist(self, seqs):
- """GC statistics for bin."""
- GCs = []
- gcTotal = 0
- basesTotal = 0
-- for _, seq in seqs.iteritems():
-+ for _, seq in seqs.items():
- a, c, g, t = baseCount(seq)
- gc = g + c
- bases = a + c + g + t
-@@ -171,7 +171,7 @@ class BinTools():
-
- codingBasesTotal = 0
- basesTotal = 0
-- for seqId, seq in seqs.iteritems():
-+ for seqId, seq in seqs.items():
- codingBases = prodigalParser.codingBases(seqId)
-
- CDs.append(float(codingBases) / len(seq))
-@@ -186,11 +186,11 @@ class BinTools():
- def binTetraSig(self, seqs, tetraSigs):
- """Tetranucleotide signature for bin. """
- binSize = 0
-- for _, seq in seqs.iteritems():
-+ for _, seq in seqs.items():
- binSize += len(seq)
-
- bInit = True
-- for seqId, seq in seqs.iteritems():
-+ for seqId, seq in seqs.items():
- weightedTetraSig = tetraSigs[seqId] * (float(len(seq)) / binSize)
- if bInit:
- binSig = weightedTetraSig
-@@ -247,32 +247,32 @@ class BinTools():
- meanCD, deltaCDs, CDs = self.codingDensityDist(seqs, prodigalParser)
-
- # find keys into GC and CD distributions
-- closestGC = findNearest(np.array(gcBounds.keys()), meanGC)
-- sampleSeqLen = gcBounds[closestGC].keys()[0]
-+ closestGC = findNearest(np.array(list(gcBounds.keys())), meanGC)
-+ sampleSeqLen = list(gcBounds[closestGC].keys())[0]
- d = gcBounds[closestGC][sampleSeqLen]
-- gcLowerBoundKey = findNearest(d.keys(), (100 - distribution) / 2.0)
-- gcUpperBoundKey = findNearest(d.keys(), (100 + distribution) / 2.0)
-+ gcLowerBoundKey = findNearest(list(d.keys()), (100 - distribution) / 2.0)
-+ gcUpperBoundKey = findNearest(list(d.keys()), (100 + distribution) / 2.0)
-
-- closestCD = findNearest(np.array(cdBounds.keys()), meanCD)
-- sampleSeqLen = cdBounds[closestCD].keys()[0]
-+ closestCD = findNearest(np.array(list(cdBounds.keys())), meanCD)
-+ sampleSeqLen = list(cdBounds[closestCD].keys())[0]
- d = cdBounds[closestCD][sampleSeqLen]
-- cdLowerBoundKey = findNearest(d.keys(), (100 - distribution) / 2.0)
-+ cdLowerBoundKey = findNearest(list(d.keys()), (100 - distribution) / 2.0)
-
-- tdBoundKey = findNearest(tdBounds[tdBounds.keys()[0]].keys(), distribution)
-+ tdBoundKey = findNearest(list(tdBounds[list(tdBounds.keys())[0]].keys()), distribution)
-
- index = 0
-- for seqId, seq in seqs.iteritems():
-+ for seqId, seq in seqs.items():
- seqLen = len(seq)
-
- # find GC, CD, and TD bounds
-- closestSeqLen = findNearest(gcBounds[closestGC].keys(), seqLen)
-+ closestSeqLen = findNearest(list(gcBounds[closestGC].keys()), seqLen)
- gcLowerBound = gcBounds[closestGC][closestSeqLen][gcLowerBoundKey]
- gcUpperBound = gcBounds[closestGC][closestSeqLen][gcUpperBoundKey]
-
-- closestSeqLen = findNearest(cdBounds[closestCD].keys(), seqLen)
-+ closestSeqLen = findNearest(list(cdBounds[closestCD].keys()), seqLen)
- cdLowerBound = cdBounds[closestCD][closestSeqLen][cdLowerBoundKey]
-
-- closestSeqLen = findNearest(tdBounds.keys(), seqLen)
-+ closestSeqLen = findNearest(list(tdBounds.keys()), seqLen)
- tdBound = tdBounds[closestSeqLen][tdBoundKey]
-
- outlyingDists = []
---- checkm/checkmData.py.orig 2022-03-15 18:25:01 UTC
-+++ checkm/checkmData.py
-@@ -85,11 +85,11 @@ class DBConfig(object):
- """Work out if we have permission to write to the CheckM config before attempting to make changes"""
- try:
- open(self.configFile, 'a')
-- except IOError, e:
-- print "You do not seem to have permission to edit the checkm config file"
-- print "located at %s" % self.configFile
-- print "Please try again with updated privileges. Error was:\n"
-- print e
-+ except IOError as e:
-+ print("You do not seem to have permission to edit the checkm config file")
-+ print("located at %s" % self.configFile)
-+ print("Please try again with updated privileges. Error was:\n")
-+ print(e)
- return False
- return True
-
-@@ -167,28 +167,28 @@ class DBManager(mm.ManifestManager):
- else:
- path = os.path.abspath(os.path.expanduser(path))
-
-- print ""
-+ print("")
- if os.path.exists(path):
- # path exists
- if os.access(path, os.W_OK):
- # path is writable
- path_set = True
-- print "Path [%s] exists and you have permission to write to this folder." % path
-+ print("Path [%s] exists and you have permission to write to this folder." % path)
- else:
-- print "Path [%s] exists but you do not have permission to write to this folder." % path
-+ print("Path [%s] exists but you do not have permission to write to this folder." % path)
- else:
- # path does not exist, try to make it
- "Path [%s] does not exist so I will attempt to create it" % path
- try:
- self.makeSurePathExists(path)
-- print "Path [%s] has been created and you have permission to write to this folder." % path
-+ print("Path [%s] has been created and you have permission to write to this folder." % path)
- path_set = True
- except Exception:
-- print "Unable to make the folder, Error was: %s" % sys.exc_info()[0]
-+ print("Unable to make the folder, Error was: %s" % sys.exc_info()[0])
- minimal = True
-
- # (re)make the manifest file
-- print "(re) creating manifest file (please be patient)."
-+ print("(re) creating manifest file (please be patient).")
- self.createManifest(path, self.config.values["localManifestName"])
-
- return path
-@@ -196,8 +196,8 @@ class DBManager(mm.ManifestManager):
- def checkPermissions(self):
- """See if the user has permission to write to the data directory"""
- if not os.access(self.config.values["dataRoot"], os.W_OK):
-- print "You do not seem to have permission to edit the CheckM data folder"
-- print "located at %s" % self.config.values["dataRoot"]
-+ print("You do not seem to have permission to edit the CheckM data folder")
-+ print("located at %s" % self.config.values["dataRoot"])
- return False
-
- return True
---- checkm/coverage.py.orig 2022-03-15 18:25:01 UTC
-+++ checkm/coverage.py
-@@ -62,7 +62,7 @@ class Coverage():
- binId = binIdFromFilename(binFile)
-
- seqs = readFasta(binFile)
-- for seqId, seq in seqs.iteritems():
-+ for seqId, seq in seqs.items():
- seqIdToBinId[seqId] = binId
- seqIdToSeqLen[seqId] = len(seq)
-
-@@ -97,12 +97,12 @@ class Coverage():
- print(header)
-
- # get length of all seqs
-- for bamFile, seqIds in coverageInfo.iteritems():
-- for seqId in seqIds.keys():
-+ for bamFile, seqIds in coverageInfo.items():
-+ for seqId in list(seqIds.keys()):
- seqIdToSeqLen[seqId] = seqIds[seqId].seqLen
-
- # write coverage stats for all scaffolds to file
-- for seqId, seqLen in seqIdToSeqLen.iteritems():
-+ for seqId, seqLen in seqIdToSeqLen.items():
- rowStr = seqId + '\t' + seqIdToBinId.get(seqId, DefaultValues.UNBINNED) + '\t' + str(seqLen)
- for bamFile in bamFiles:
- bamId = binIdFromFilename(bamFile)
-@@ -171,7 +171,7 @@ class Coverage():
- writeProc.join()
- except:
- # make sure all processes are terminated
-- print traceback.format_exc()
-+ print(traceback.format_exc())
- for p in workerProc:
- p.terminate()
-
-@@ -271,16 +271,16 @@ class Coverage():
- if self.logger.getEffectiveLevel() <= logging.INFO:
- sys.stderr.write('\n')
-
-- print ''
-- print ' # total reads: %d' % totalReads
-- print ' # properly mapped reads: %d (%.1f%%)' % (totalMappedReads, float(totalMappedReads) * 100 / totalReads)
-- print ' # duplicate reads: %d (%.1f%%)' % (totalDuplicates, float(totalDuplicates) * 100 / totalReads)
-- print ' # secondary reads: %d (%.1f%%)' % (totalSecondary, float(totalSecondary) * 100 / totalReads)
-- print ' # reads failing QC: %d (%.1f%%)' % (totalFailedQC, float(totalFailedQC) * 100 / totalReads)
-- print ' # reads failing alignment length: %d (%.1f%%)' % (totalFailedAlignLen, float(totalFailedAlignLen) * 100 / totalReads)
-- print ' # reads failing edit distance: %d (%.1f%%)' % (totalFailedEditDist, float(totalFailedEditDist) * 100 / totalReads)
-- print ' # reads not properly paired: %d (%.1f%%)' % (totalFailedProperPair, float(totalFailedProperPair) * 100 / totalReads)
-- print ''
-+ print('')
-+ print(' # total reads: %d' % totalReads)
-+ print(' # properly mapped reads: %d (%.1f%%)' % (totalMappedReads, float(totalMappedReads) * 100 / totalReads))
-+ print(' # duplicate reads: %d (%.1f%%)' % (totalDuplicates, float(totalDuplicates) * 100 / totalReads))
-+ print(' # secondary reads: %d (%.1f%%)' % (totalSecondary, float(totalSecondary) * 100 / totalReads))
-+ print(' # reads failing QC: %d (%.1f%%)' % (totalFailedQC, float(totalFailedQC) * 100 / totalReads))
-+ print(' # reads failing alignment length: %d (%.1f%%)' % (totalFailedAlignLen, float(totalFailedAlignLen) * 100 / totalReads))
-+ print(' # reads failing edit distance: %d (%.1f%%)' % (totalFailedEditDist, float(totalFailedEditDist) * 100 / totalReads))
-+ print(' # reads not properly paired: %d (%.1f%%)' % (totalFailedProperPair, float(totalFailedProperPair) * 100 / totalReads))
-+ print('')
-
- def parseCoverage(self, coverageFile):
- """Read coverage information from file."""
-@@ -301,7 +301,7 @@ class Coverage():
- if seqId not in coverageStats[binId]:
- coverageStats[binId][seqId] = {}
-
-- for i in xrange(3, len(lineSplit), 3):
-+ for i in range(3, len(lineSplit), 3):
- bamId = lineSplit[i]
- coverage = float(lineSplit[i + 1])
- coverageStats[binId][seqId][bamId] = coverage
-@@ -325,7 +325,7 @@ class Coverage():
-
- # calculate mean coverage (weighted by scaffold length)
- # for each bin under each BAM file
-- for i in xrange(3, len(lineSplit), 3):
-+ for i in range(3, len(lineSplit), 3):
- bamId = lineSplit[i]
- coverage = float(lineSplit[i + 1])
- binCoverages[binId][bamId].append(coverage)
-@@ -341,13 +341,13 @@ class Coverage():
-
- profiles = defaultdict(dict)
- for binId in binStats:
-- for bamId, stats in binStats[binId].iteritems():
-+ for bamId, stats in binStats[binId].items():
- binLength, meanBinCoverage = stats
- coverages = binCoverages[binId][bamId]
-
- varCoverage = 0
- if len(coverages) > 1:
-- varCoverage = mean(map(lambda x: (x - meanBinCoverage) ** 2, coverages))
-+ varCoverage = mean([(x - meanBinCoverage) ** 2 for x in coverages])
-
- profiles[binId][bamId] = [meanBinCoverage, sqrt(varCoverage)]
-
---- checkm/coverageWindows.py.orig 2022-03-15 18:25:01 UTC
-+++ checkm/coverageWindows.py
-@@ -188,10 +188,10 @@ class CoverageWindows():
- try:
- end += windowSize
- except:
-- print '*****************'
-- print end
-- print windowSize
-- print '******************'
-+ print('*****************')
-+ print(end)
-+ print(windowSize)
-+ print('******************')
-
- coverage = float(sum(readLoader.coverage)) / seqLen
-
-@@ -239,13 +239,13 @@ class CoverageWindows():
- if self.logger.getEffectiveLevel() <= logging.INFO:
- sys.stderr.write('\n')
-
-- print ''
-- print ' # total reads: %d' % totalReads
-- print ' # properly mapped reads: %d (%.1f%%)' % (totalMappedReads, float(totalMappedReads) * 100 / totalReads)
-- print ' # duplicate reads: %d (%.1f%%)' % (totalDuplicates, float(totalDuplicates) * 100 / totalReads)
-- print ' # secondary reads: %d (%.1f%%)' % (totalSecondary, float(totalSecondary) * 100 / totalReads)
-- print ' # reads failing QC: %d (%.1f%%)' % (totalFailedQC, float(totalFailedQC) * 100 / totalReads)
-- print ' # reads failing alignment length: %d (%.1f%%)' % (totalFailedAlignLen, float(totalFailedAlignLen) * 100 / totalReads)
-- print ' # reads failing edit distance: %d (%.1f%%)' % (totalFailedEditDist, float(totalFailedEditDist) * 100 / totalReads)
-- print ' # reads not properly paired: %d (%.1f%%)' % (totalFailedProperPair, float(totalFailedProperPair) * 100 / totalReads)
-- print ''
-+ print('')
-+ print(' # total reads: %d' % totalReads)
-+ print(' # properly mapped reads: %d (%.1f%%)' % (totalMappedReads, float(totalMappedReads) * 100 / totalReads))
-+ print(' # duplicate reads: %d (%.1f%%)' % (totalDuplicates, float(totalDuplicates) * 100 / totalReads))
-+ print(' # secondary reads: %d (%.1f%%)' % (totalSecondary, float(totalSecondary) * 100 / totalReads))
-+ print(' # reads failing QC: %d (%.1f%%)' % (totalFailedQC, float(totalFailedQC) * 100 / totalReads))
-+ print(' # reads failing alignment length: %d (%.1f%%)' % (totalFailedAlignLen, float(totalFailedAlignLen) * 100 / totalReads))
-+ print(' # reads failing edit distance: %d (%.1f%%)' % (totalFailedEditDist, float(totalFailedEditDist) * 100 / totalReads))
-+ print(' # reads not properly paired: %d (%.1f%%)' % (totalFailedProperPair, float(totalFailedProperPair) * 100 / totalReads))
-+ print('')
---- checkm/manifestManager.py.orig 2022-03-15 18:25:01 UTC
-+++ checkm/manifestManager.py
-@@ -47,8 +47,8 @@ __MANIFEST__ = ".dmanifest"
- # system includes
- import os
- import hashlib
--import urllib2
--import urllib
-+import urllib.request, urllib.error, urllib.parse
-+import urllib.request, urllib.parse, urllib.error
- import shutil
- import errno
-
-@@ -121,15 +121,15 @@ class ManifestManager(object):
- source = ""
- # first we assume it is remote
- try:
-- s_man = urllib2.urlopen(sourceManifestLocation + "/" + sourceManifestName, None, self.timeout)
-+ s_man = urllib.request.urlopen(sourceManifestLocation + "/" + sourceManifestName, None, self.timeout)
- source = sourceManifestLocation + "/"
- except ValueError:
- # then it is probably a file
- s_man = open(os.path.join(sourceManifestLocation, sourceManifestName))
- source = os.path.join(sourceManifestLocation) + os.path.sep
-- except urllib2.URLError:
-+ except urllib.error.URLError:
- # problems connecting to server, perhaps user is behind a proxy or firewall
-- print "Error: failed to connect to server."
-+ print("Error: failed to connect to server.")
- return (None, None, None, None, None)
-
- first_line = True
-@@ -140,11 +140,11 @@ class ManifestManager(object):
- # get the type of the manifest
- s_type = self.getManType(line)
- if s_type != l_type:
-- print "Error: type of source manifest (%s) does not match type of local manifest (%s)" % (s_type, l_type)
-+ print("Error: type of source manifest (%s) does not match type of local manifest (%s)" % (s_type, l_type))
- return (None, None, None, None, None)
- else:
- # no type specified
-- print "Error: type of source manifest is not specified. Is this a valid manifest file?"
-+ print("Error: type of source manifest is not specified. Is this a valid manifest file?")
- return (None, None, None, None, None)
-
- self.type = l_type
-@@ -174,7 +174,7 @@ class ManifestManager(object):
- deleted.append(fields[0])
-
- # check for new files
-- for f in source_man.keys():
-+ for f in list(source_man.keys()):
- if source_man[f][2] == False:
- if source_man[f][0] == '-':
- addedDirs.append(f)
-@@ -190,28 +190,28 @@ class ManifestManager(object):
- modified_size += int(source_man[f][1])
-
- if len(addedFiles) > 0:
-- print "#------------------------------------------------------"
-- print "# Source contains %d new file(s) (%s)" % (len(addedFiles), self.formatData(new_size))
-+ print("#------------------------------------------------------")
-+ print("# Source contains %d new file(s) (%s)" % (len(addedFiles), self.formatData(new_size)))
- for f in addedFiles:
-- print "\t".join([self.formatData(int(source_man[f][1])), f])
-+ print("\t".join([self.formatData(int(source_man[f][1])), f]))
-
- if len(addedDirs) > 0:
-- print "#------------------------------------------------------"
-- print "# Source contains %d new folders(s)" % (len(addedDirs))
-+ print("#------------------------------------------------------")
-+ print("# Source contains %d new folders(s)" % (len(addedDirs)))
- for f in addedDirs:
-- print f
-+ print(f)
-
- if len(modified) > 0:
-- print "#------------------------------------------------------"
-- print "# Source contains %d modified file(s) (%s)" % (len(modified), self.formatData(modified_size))
-+ print("#------------------------------------------------------")
-+ print("# Source contains %d modified file(s) (%s)" % (len(modified), self.formatData(modified_size)))
- for f in modified:
-- print f
-+ print(f)
-
- if len(deleted) > 0:
-- print "#------------------------------------------------------"
-- print "# %d files have been deleted in the source:" % len(deleted)
-+ print("#------------------------------------------------------")
-+ print("# %d files have been deleted in the source:" % len(deleted))
- for f in deleted:
-- print f
-+ print(f)
- else:
- return (source,
- [(a, source_man[a]) for a in addedFiles],
-@@ -245,13 +245,13 @@ class ManifestManager(object):
- for f in modified:
- total_size += int(f[1][1])
- if total_size != 0:
-- print "****************************************************************"
-- print "%d new file(s) to be downloaded from source" % len(added_files)
-- print "%d existing file(s) to be updated" % len(modified)
-- print "%s will need to be downloaded" % self.formatData(total_size)
-+ print("****************************************************************")
-+ print("%d new file(s) to be downloaded from source" % len(added_files))
-+ print("%d existing file(s) to be updated" % len(modified))
-+ print("%s will need to be downloaded" % self.formatData(total_size))
- do_down = self.promptUserDownload()
- if not do_down:
-- print "Download aborted"
-+ print("Download aborted")
-
- update_manifest = False
- if do_down:
-@@ -262,13 +262,13 @@ class ManifestManager(object):
- self.makeSurePathExists(full_path)
- for add in added_files:
- full_path = os.path.abspath(os.path.join(localManifestLocation, add[0]))
-- urllib.urlretrieve(source+add[0], full_path)
-+ urllib.request.urlretrieve(source+add[0], full_path)
- for modify in modified:
- full_path = os.path.abspath(os.path.join(localManifestLocation, modify[0]))
-- urllib.urlretrieve(source+modify[0], full_path)
-+ urllib.request.urlretrieve(source+modify[0], full_path)
-
- if update_manifest:
-- print "(re) creating manifest file (please be patient)"
-+ print("(re) creating manifest file (please be patient)")
- self.createManifest(localManifestLocation, manifestName=localManifestName)
-
- return True
-@@ -303,19 +303,19 @@ class ManifestManager(object):
- input_not_ok = True
- minimal=False
- valid_responses = {'Y':True,'N':False}
-- vrs = ",".join([x.lower() for x in valid_responses.keys()])
-+ vrs = ",".join([x.lower() for x in list(valid_responses.keys())])
- while(input_not_ok):
- if(minimal):
-- option = raw_input("Download? ("+vrs+") : ").upper()
-+ option = input("Download? ("+vrs+") : ").upper()
- else:
-- option = raw_input("Confirm you want to download this data\n" \
-+ option = input("Confirm you want to download this data\n" \
- "Changes *WILL* be permanent\n" \
- "Continue? ("+vrs+") : ").upper()
- if(option in valid_responses):
-- print "****************************************************************"
-+ print("****************************************************************")
- return valid_responses[option]
- else:
-- print "ERROR: unrecognised choice '"+option+"'"
-+ print("ERROR: unrecognised choice '"+option+"'")
- minimal = True
-
- def walk(self, parents, full_path, rel_path, dirs, files, skipFile=__MANIFEST__):
---- checkm/taxonParser.py.orig 2022-03-15 18:25:01 UTC
-+++ checkm/taxonParser.py
-@@ -73,8 +73,8 @@ class TaxonParser():
- numMarkers, numMarkerSets = markerSet.size()
- pTable.add_row([rank, taxon, markerSet.numGenomes, numMarkers, numMarkerSets])
-
-- print ''
-- print pTable.get_string()
-+ print('')
-+ print(pTable.get_string())
-
- def markerSet(self, rank, taxon, markerFile):
- """Obtain specified taxonomic-specific marker set."""
---- checkm/uniqueMarkers.py.orig 2022-03-15 18:25:01 UTC
-+++ checkm/uniqueMarkers.py
-@@ -51,7 +51,7 @@ def getOppositeRankSpecificTaxonId(cursor, *args):
- query.append(' %s != \'%s\' ' % (ranks[len(args) - 1], args[-1]))
- query.append(' %s IS NULL' % ranks[len(args)])
- query_string = 'AND'.join(query)
-- print query_string
-+ print(query_string)
- result = cursor.execute('SELECT Id, "Count" FROM taxons WHERE %s' % query_string)
- return result.fetchall()
-
-@@ -121,7 +121,7 @@ def doWork(args):
- markers_from_others[Id] += count
-
- descriptive_markers = []
-- for marker_id, _ in marker_in_taxon_mapping.items():
-+ for marker_id, _ in list(marker_in_taxon_mapping.items()):
- if marker_id in markers_from_others:
- fraction_in_others = float(markers_from_others[marker_id]) / float(others_total_count)
- if fraction_in_others <= args.exclude:
-@@ -135,7 +135,7 @@ def doWork(args):
- des_markers.append(getDescriptiveMarkers(cur, i))
-
- for des_acc, des_name in des_markers:
-- print des_acc, des_name
-+ print(des_acc, des_name)
-
- if __name__ == '__main__':
-
---- checkm/util/img.py.orig 2022-03-15 18:25:01 UTC
-+++ checkm/util/img.py
-@@ -195,7 +195,7 @@ class IMG(object):
- genomeIdsOfInterest = set()
- for genomeId in metadata:
- bKeep = True
-- for r in xrange(0, len(searchTaxa)):
-+ for r in range(0, len(searchTaxa)):
- if taxonStr == 'universal':
- bKeep = True
- elif taxonStr == 'prokaryotes' and (metadata[genomeId]['taxonomy'][0] == 'Bacteria' or metadata[genomeId]['taxonomy'][0] == 'Archaea'):
-@@ -222,8 +222,8 @@ class IMG(object):
-
- def lineageStats(self, metadata, mostSpecificRank):
- stats = {}
-- for r in xrange(0, mostSpecificRank + 1):
-- for _, data in metadata.iteritems():
-+ for r in range(0, mostSpecificRank + 1):
-+ for _, data in metadata.items():
- taxaStr = ';'.join(data['taxonomy'][0:r + 1])
- stats[taxaStr] = stats.get(taxaStr, 0) + 1
-
-@@ -231,9 +231,9 @@ class IMG(object):
-
- def lineagesSorted(self, metadata, mostSpecificRank=6):
- lineages = []
-- for r in xrange(0, mostSpecificRank + 1):
-+ for r in range(0, mostSpecificRank + 1):
- taxa = set()
-- for _, data in metadata.iteritems():
-+ for _, data in metadata.items():
- if 'unclassified' not in data['taxonomy'][0:r + 1]:
- taxa.add(';'.join(data['taxonomy'][0:r + 1]))
-
-@@ -274,7 +274,7 @@ class IMG(object):
- geneIdToFamilyIds[geneId].add(clusterId)
- count[clusterId] = count.get(clusterId, 0) + 1
-
-- for clusterId, c in count.iteritems():
-+ for clusterId, c in count.items():
- if clusterId not in table:
- table[clusterId] = {}
- table[clusterId][genomeId] = c
-@@ -288,7 +288,7 @@ class IMG(object):
-
- def filterGeneCountTable(self, genomeIds, table, ubiquityThreshold=0.9, singleCopyThreshold=0.9):
- idsToFilter = []
-- for pfamId, genomeCounts in table.iteritems():
-+ for pfamId, genomeCounts in table.items():
- ubiquity = 0
- singleCopy = 0
- for genomeId in genomeIds:
-@@ -342,7 +342,7 @@ class IMG(object):
- # are a few cases where this isn't tree (?) so only PFAMs/TIGRFAMs
- # with GFF entries are considered.
- familyIdToScaffoldIds = {}
-- for pfamId, geneIds in pfamIdToGeneIds.iteritems():
-+ for pfamId, geneIds in pfamIdToGeneIds.items():
- scaffolds = []
- for geneId in geneIds:
- scaffold = genePosition.get(geneId, None)
-@@ -352,7 +352,7 @@ class IMG(object):
- if scaffolds:
- familyIdToScaffoldIds[pfamId] = scaffolds
-
-- for tigrId, geneIds in tigrIdToGeneIds.iteritems():
-+ for tigrId, geneIds in tigrIdToGeneIds.items():
- scaffolds = []
- for geneId in geneIds:
- scaffold = genePosition.get(geneId, None)
-@@ -362,9 +362,9 @@ class IMG(object):
- if scaffold:
- familyIdToScaffoldIds[tigrId] = scaffolds
- except:
-- print '[BUG]: __genomeIdToClusterScaffold'
-- print sys.exc_info()[0]
-- print genomeId, geneId, tigrId, pfamId
-+ print('[BUG]: __genomeIdToClusterScaffold')
-+ print(sys.exc_info()[0])
-+ print(genomeId, geneId, tigrId, pfamId)
- sys.exit()
-
- return familyIdToScaffoldIds
-@@ -400,7 +400,7 @@ class IMG(object):
- seqs = readFasta(genomeFile)
-
- seqLens = {}
-- for seqId, seq in seqs.iteritems():
-+ for seqId, seq in seqs.items():
- seqLens[seqId] = len(seq)
-
- return seqLens
-@@ -462,7 +462,7 @@ class IMG(object):
- # are a few cases where this isn't tree (?) so only PFAMs/TIGRFAMs
- # with GFF entries are considered.
- familyIdToGenomePositions = {}
-- for pfamId, geneIds in pfamIdToGeneIds.iteritems():
-+ for pfamId, geneIds in pfamIdToGeneIds.items():
- positions = []
- for geneId in geneIds:
- position = genePosition.get(geneId, None)
-@@ -472,7 +472,7 @@ class IMG(object):
- if positions:
- familyIdToGenomePositions[pfamId] = positions
-
-- for tigrId, geneIds in tigrIdToGeneIds.iteritems():
-+ for tigrId, geneIds in tigrIdToGeneIds.items():
- positions = []
- for geneId in geneIds:
- position = genePosition.get(geneId, None)
-@@ -482,9 +482,9 @@ class IMG(object):
- if positions:
- familyIdToGenomePositions[tigrId] = positions
- except:
-- print '[BUG]: __genomeFamilyPositions'
-- print sys.exc_info()[0]
-- print genomeId, geneId, tigrId, pfamId
-+ print('[BUG]: __genomeFamilyPositions')
-+ print(sys.exc_info()[0])
-+ print(genomeId, geneId, tigrId, pfamId)
- sys.exit()
-
- return familyIdToGenomePositions