Modified how bin IDs are identified to improve output tables

checkm/VERSION

@@ -1,3 +1,9 @@
+1.2.0
+- modified how bin IDs are identified to improve output tables
+
+1.1.11
+- fixed error with inverse_transformed being deprecated in newer versions of Matplotlib
+
 1.1.10
 - fixed bug with missing bCalledGenes flag that was impacting a number of commands
 

checkm/common.py

@@ -95,9 +95,12 @@ def checkBinInputExists(binInput, bCalledGenes):
                 have_error = True
         if have_error:
             logger = logging.getLogger("timestamp")
-            logger.error('Input table format is not correct: ' + binInput + '\n')
-            logger.error('If input is nucleotide contigs, please supply 2 column at least: [genome_id, genome_contigs_file]')
-            logger.error('If input is gene, please supply 3 column at least: [genome_id, genome_contigs_file, genome_genes_file]')
+            logger.error('Input table format is not correct: ' +
+                         binInput + '\n')
+            logger.error(
+                'If input is nucleotide contigs, please supply 2 column at least: [genome_id, genome_contigs_file]')
+            logger.error(
+                'If input is gene, please supply 3 column at least: [genome_id, genome_contigs_file, genome_genes_file]')
 
 
 def checkFileExists(inputFile):
@@ -132,7 +135,16 @@ def makeSurePathExists(path):
 
 def binIdFromFilename(filename):
     """Extract bin id from bin filename."""
+
     binId = os.path.basename(filename)
+
+    # remove common compression extensions
+    compress_ext = ['.gz', '.bz2', '.rar', '.tgz', '.zip', '.7z']
+    for ext in compress_ext:
+        if binId.endswith(ext):
+            binId = binId[0:len(binId) - len(ext)]
+            break
+
     binId = os.path.splitext(binId)[0]
 
     return binId

checkm/main.py

@@ -294,7 +294,6 @@ def taxonSet(self, options, db=None):
             options.rank, options.taxon, options.marker_file)
 
         if bValidSet:
-
             self.logger.info('Marker set written to: ' + options.marker_file)
 
         self.timeKeeper.printTimeStamp()
@@ -422,7 +421,6 @@ def qa(self, options):
         aai.run(options.aai_strain, options.analyze_dir, options.alignment_file)
 
         # get HMM file for each bin
-
         markerSetParser = MarkerSetParser(options.threads)
 
         hmmModelInfoFile = os.path.join(

checkm/plot/AbstractPlot.py

@@ -34,6 +34,7 @@ class AbstractPlot(FigureCanvas):
     '''
     Abstract base class for plotting.
     '''
+
     def __init__(self, options):
         self.options = options
 
@@ -60,7 +61,8 @@ def __init__(self, options):
     def savePlot(self, filename, dpi=300):
         imgFormat = filename[filename.rfind('.') + 1:len(filename)]
         if imgFormat in ['png', 'pdf', 'ps', 'eps', 'svg']:
-            self.fig.savefig(filename, format=imgFormat, dpi=dpi, facecolor='white', edgecolor='white', bbox_inches='tight')
+            self.fig.savefig(filename, format=imgFormat, dpi=dpi,
+                             facecolor='white', edgecolor='white', bbox_inches='tight')
         else:
             pass
 
@@ -72,20 +74,22 @@ def labelExtents(self, xLabels, xFontSize, xRotation, yLabels, yFontSize, yRotat
         tempAxes.set_xticks(np.arange(len(xLabels)))
         tempAxes.set_yticks(np.arange(len(yLabels)))
 
-        xText = tempAxes.set_xticklabels(xLabels, size=xFontSize, rotation=xRotation)
-        yText = tempAxes.set_yticklabels(yLabels, size=yFontSize, rotation=yRotation)
+        xText = tempAxes.set_xticklabels(
+            xLabels, size=xFontSize, rotation=xRotation)
+        yText = tempAxes.set_yticklabels(
+            yLabels, size=yFontSize, rotation=yRotation)
 
         bboxes = []
         for label in xText:
             bbox = label.get_window_extent(self.get_renderer())
-            bboxi = bbox.inverse_transformed(self.fig.transFigure)
+            bboxi = bbox.transformed(self.fig.transFigure.inverted())
             bboxes.append(bboxi)
         xLabelBounds = mtransforms.Bbox.union(bboxes)
 
         bboxes = []
         for label in yText:
             bbox = label.get_window_extent(self.get_renderer())
-            bboxi = bbox.inverse_transformed(self.fig.transFigure)
+            bboxi = bbox.transformed(self.fig.transFigure.inverted())
             bboxes.append(bboxi)
         yLabelBounds = mtransforms.Bbox.union(bboxes)
 
@@ -98,12 +102,14 @@ def xLabelExtents(self, labels, fontSize, rotation=0):
 
         tempAxes = self.fig.add_axes([0, 0, 1.0, 1.0])
         tempAxes.set_xticks(np.arange(len(labels)))
-        xLabels = tempAxes.set_xticklabels(labels, size=fontSize, rotation=rotation)
+        xLabels = tempAxes.set_xticklabels(
+            labels, size=fontSize, rotation=rotation)
 
         bboxes = []
         for label in xLabels:
             bbox = label.get_window_extent(self.get_renderer())
-            bboxi = bbox.inverse_transformed(self.fig.transFigure)
+
+            bboxi = bbox.transformed(self.fig.transFigure.inverted())
             bboxes.append(bboxi)
         xLabelBounds = mtransforms.Bbox.union(bboxes)
 
@@ -116,12 +122,13 @@ def yLabelExtents(self, labels, fontSize, rotation=0):
 
         tempAxes = self.fig.add_axes([0, 0, 1.0, 1.0])
         tempAxes.set_yticks(np.arange(len(labels)))
-        yLabels = tempAxes.set_yticklabels(labels, size=fontSize, rotation=rotation)
+        yLabels = tempAxes.set_yticklabels(
+            labels, size=fontSize, rotation=rotation)
 
         bboxes = []
         for label in yLabels:
             bbox = label.get_window_extent(self.get_renderer())
-            bboxi = bbox.inverse_transformed(self.fig.transFigure)
+            bboxi = bbox.transformed(self.fig.transFigure.inverted())
             bboxes.append(bboxi)
         yLabelBounds = mtransforms.Bbox.union(bboxes)
 
@@ -172,5 +179,5 @@ def boundingBox(self, data, ax, label, bBoundingBoxes, bLabels):
 
         if bLabels:
             ax.annotate(label, xy=(min(data[:, 0]), max(data[:, 1])), xytext=(0, 0),
-                            textcoords='offset points', ha='right', va='bottom',
-                            bbox=dict(boxstyle='round,pad=0.5', fc=(0.5, 0.5, 0.5), alpha=0.1))
+                        textcoords='offset points', ha='right', va='bottom',
+                        bbox=dict(boxstyle='round,pad=0.5', fc=(0.5, 0.5, 0.5), alpha=0.1))

checkm/plot/codingDensityPlots.py

@@ -37,7 +37,7 @@
 class CodingDensityPlots(AbstractPlot):
     def __init__(self, options):
         AbstractPlot.__init__(self, options)
-        
+
         self.logger = logging.getLogger('timestamp')
 
     def plot(self, fastaFile, distributionsToPlot):
@@ -55,9 +55,11 @@ def plot(self, fastaFile, distributionsToPlot):
 
     def plotOnAxes(self, fastaFile, distributionsToPlot, axesHist, axesDeltaCD):
         # parse Prodigal output
-        gffFile = os.path.join(self.options.results_dir, 'bins', binIdFromFilename(fastaFile), DefaultValues.PRODIGAL_GFF)
+        gffFile = os.path.join(self.options.results_dir, 'bins', binIdFromFilename(
+            fastaFile), DefaultValues.PRODIGAL_GFF)
         if not os.path.exists(gffFile):
-            self.logger.error('Missing gene feature file (%s). This plot if not compatible with the --genes option.' % DefaultValues.PRODIGAL_GFF)
+            self.logger.error(
+                'Missing gene feature file (%s). This plot if not compatible with the --genes option.' % DefaultValues.PRODIGAL_GFF)
             sys.exit(1)
 
         prodigalParser = ProdigalGeneFeatureParser(gffFile)
@@ -87,7 +89,8 @@ def plotOnAxes(self, fastaFile, distributionsToPlot, axesHist, axesDeltaCD):
                 end += self.options.cd_window_size
 
         if len(data) == 0:
-            axesHist.set_xlabel('[Error] No seqs >= %d, the specified window size' % self.options.cd_window_size)
+            axesHist.set_xlabel(
+                '[Error] No seqs >= %d, the specified window size' % self.options.cd_window_size)
             return
 
         # Histogram plot
@@ -100,7 +103,8 @@ def plotOnAxes(self, fastaFile, distributionsToPlot, axesHist, axesDeltaCD):
 
         axesHist.hist(data, bins=bins, density=True, color=(0.5, 0.5, 0.5))
         axesHist.set_xlabel('% coding density')
-        axesHist.set_ylabel('% windows (' + str(self.options.cd_window_size) + ' bp)')
+        axesHist.set_ylabel(
+            '% windows (' + str(self.options.cd_window_size) + ' bp)')
 
         # Prettify plot
         for a in axesHist.yaxis.majorTicks:
@@ -128,8 +132,10 @@ def plotOnAxes(self, fastaFile, distributionsToPlot, axesHist, axesDeltaCD):
         meanCD, deltaCDs, _ = binTools.codingDensityDist(seqs, prodigalParser)
 
         # Delta-CD vs sequence length plot
-        axesDeltaCD.scatter(deltaCDs, seqLens, c=abs(deltaCDs), s=10, lw=0.5, cmap='gray_r')
-        axesDeltaCD.set_xlabel(r'$\Delta$ CD (mean coding density = %.1f%%)' % (meanCD * 100))
+        axesDeltaCD.scatter(deltaCDs, seqLens, c=abs(
+            deltaCDs), s=10, lw=0.5, ec='black', cmap='gray_r')
+        axesDeltaCD.set_xlabel(
+            r'$\Delta$ CD (mean coding density = %.1f%%)' % (meanCD * 100))
         axesDeltaCD.set_ylabel('Sequence length (kbp)')
 
         _, yMaxSeqs = axesDeltaCD.get_ylim()
@@ -142,8 +148,10 @@ def plotOnAxes(self, fastaFile, distributionsToPlot, axesHist, axesDeltaCD):
             # find closest distribution values
             sampleSeqLen = list(dist[closestCD].keys())[0]
             d = dist[closestCD][sampleSeqLen]
-            cdLowerBoundKey = findNearest(list(d.keys()), (100 - distToPlot) / 2.0)
-            cdUpperBoundKey = findNearest(list(d.keys()), (100 + distToPlot) / 2.0)
+            cdLowerBoundKey = findNearest(
+                list(d.keys()), (100 - distToPlot) / 2.0)
+            cdUpperBoundKey = findNearest(
+                list(d.keys()), (100 + distToPlot) / 2.0)
 
             xL = []
             xU = []
@@ -168,15 +176,17 @@ def plotOnAxes(self, fastaFile, distributionsToPlot, axesHist, axesDeltaCD):
         axesDeltaCD.set_xlim([xMinSeqs, xMaxSeqs])
 
         # draw vertical line at x=0
-        axesDeltaCD.vlines(0, 0, yMaxSeqs, linestyle='dashed', color=self.axesColour, zorder=0)
+        yticks = axesDeltaCD.get_yticks()
+        axesDeltaCD.vlines(0, 0, yticks[-1], linestyle='dashed',
+                           color=self.axesColour, zorder=0)
 
         # Change sequence lengths from bp to kbp
-        yticks = axesDeltaCD.get_yticks()
         kbpLabels = []
         for seqLen in yticks:
             label = '%.1f' % (float(seqLen) / 1000)
             label = label.replace('.0', '')  # remove trailing zero
             kbpLabels.append(label)
+        axesDeltaCD.set_yticks(yticks)
         axesDeltaCD.set_yticklabels(kbpLabels)
 
         # Prettify plot

checkm/plot/gcPlots.py

@@ -75,7 +75,8 @@ def plotOnAxes(self, fastaFile, distributionsToPlot, axesHist, axesDeltaGC):
                 end += self.options.gc_window_size
 
         if len(data) == 0:
-            axesHist.set_xlabel('[Error] No seqs >= %d, the specified window size' % self.options.gc_window_size)
+            axesHist.set_xlabel(
+                '[Error] No seqs >= %d, the specified window size' % self.options.gc_window_size)
             return
 
         # Histogram plot
@@ -88,7 +89,8 @@ def plotOnAxes(self, fastaFile, distributionsToPlot, axesHist, axesDeltaGC):
 
         axesHist.hist(data, bins=bins, density=True, color=(0.5, 0.5, 0.5))
         axesHist.set_xlabel('% GC')
-        axesHist.set_ylabel('% windows (' + str(self.options.gc_window_size) + ' bp)')
+        axesHist.set_ylabel(
+            '% windows (' + str(self.options.gc_window_size) + ' bp)')
 
         # Prettify plot
         for a in axesHist.yaxis.majorTicks:
@@ -116,8 +118,10 @@ def plotOnAxes(self, fastaFile, distributionsToPlot, axesHist, axesDeltaGC):
         meanGC, deltaGCs, _ = binTools.gcDist(seqs)
 
         # Delta-GC vs Sequence length plot
-        axesDeltaGC.scatter(deltaGCs, seqLens, c=abs(deltaGCs), s=10, lw=0.5, cmap='gray_r')
-        axesDeltaGC.set_xlabel(r'$\Delta$ GC (mean GC = %.1f%%)' % (meanGC * 100))
+        axesDeltaGC.scatter(deltaGCs, seqLens, c=abs(
+            deltaGCs), s=10, lw=0.5, ec='black', cmap='gray_r')
+        axesDeltaGC.set_xlabel(
+            r'$\Delta$ GC (mean GC = %.1f%%)' % (meanGC * 100))
         axesDeltaGC.set_ylabel('Sequence length (kbp)')
 
         _, yMaxSeqs = axesDeltaGC.get_ylim()
@@ -130,8 +134,10 @@ def plotOnAxes(self, fastaFile, distributionsToPlot, axesHist, axesDeltaGC):
             # find closest distribution values
             sampleSeqLen = list(dist[closestGC].keys())[0]
             d = dist[closestGC][sampleSeqLen]
-            gcLowerBoundKey = findNearest(list(d.keys()), (100 - distToPlot) / 2.0)
-            gcUpperBoundKey = findNearest(list(d.keys()), (100 + distToPlot) / 2.0)
+            gcLowerBoundKey = findNearest(
+                list(d.keys()), (100 - distToPlot) / 2.0)
+            gcUpperBoundKey = findNearest(
+                list(d.keys()), (100 + distToPlot) / 2.0)
 
             xL = []
             xU = []
@@ -156,15 +162,17 @@ def plotOnAxes(self, fastaFile, distributionsToPlot, axesHist, axesDeltaGC):
         axesDeltaGC.set_xlim([xMinSeqs, xMaxSeqs])
 
         # draw vertical line at x=0
-        axesDeltaGC.vlines(0, 0, yMaxSeqs, linestyle='dashed', color=self.axesColour, zorder=0)
+        yticks = axesDeltaGC.get_yticks()
+        axesDeltaGC.vlines(0, 0, yticks[-1], linestyle='dashed',
+                           color=self.axesColour, zorder=0)
 
         # Change sequence lengths from bp to kbp
-        yticks = axesDeltaGC.get_yticks()
         kbpLabels = []
         for seqLen in yticks:
             label = '%.1f' % (float(seqLen) / 1000)
             label = label.replace('.0', '')  # remove trailing zero
             kbpLabels.append(label)
+        axesDeltaGC.set_yticks(yticks)
         axesDeltaGC.set_yticklabels(kbpLabels)
 
         # Prettify plot

checkm/plot/tetraDistPlots.py

@@ -41,7 +41,8 @@ def plot(self, fastaFile, tetraSigs, distributionsToPlot):
         axesHist = self.fig.add_subplot(121)
         axesDeltaTD = self.fig.add_subplot(122)
 
-        self.plotOnAxes(fastaFile, tetraSigs, distributionsToPlot, axesHist, axesDeltaTD)
+        self.plotOnAxes(fastaFile, tetraSigs,
+                        distributionsToPlot, axesHist, axesDeltaTD)
 
         self.fig.tight_layout(pad=1, w_pad=1)
         self.draw()
@@ -78,7 +79,8 @@ def plotOnAxes(self, fastaFile, tetraSigs, distributionsToPlot, axesHist, axesDe
                 end += self.options.td_window_size
 
         if len(data) == 0:
-            axesHist.set_xlabel('[Error] No seqs >= %d, the specified window size' % self.options.td_window_size)
+            axesHist.set_xlabel(
+                '[Error] No seqs >= %d, the specified window size' % self.options.td_window_size)
             return
 
         deltaTDs = np.array(deltaTDs)
@@ -93,7 +95,8 @@ def plotOnAxes(self, fastaFile, tetraSigs, distributionsToPlot, axesHist, axesDe
 
         axesHist.hist(data, bins=bins, density=True, color=(0.5, 0.5, 0.5))
         axesHist.set_xlabel(r'$\Delta$ TD')
-        axesHist.set_ylabel('% windows (' + str(self.options.td_window_size) + ' bp)')
+        axesHist.set_ylabel(
+            '% windows (' + str(self.options.td_window_size) + ' bp)')
 
         # Prettify plot
         for a in axesHist.yaxis.majorTicks:
@@ -117,10 +120,12 @@ def plotOnAxes(self, fastaFile, tetraSigs, distributionsToPlot, axesHist, axesDe
                 spine.set_color(self.axesColour)
 
         # get CD bin statistics
-        meanTD, deltaTDs = binTools.tetraDiffDist(seqs, genomicSig, tetraSigs, binSig)
+        meanTD, deltaTDs = binTools.tetraDiffDist(
+            seqs, genomicSig, tetraSigs, binSig)
 
         # Delta-TD vs Sequence length plot
-        axesDeltaTD.scatter(deltaTDs, seqLens, c=abs(deltaTDs), s=10, lw=0.5, cmap='gray_r')
+        axesDeltaTD.scatter(deltaTDs, seqLens, c=abs(
+            deltaTDs), s=10, lw=0.5, ec='black', cmap='gray_r')
         axesDeltaTD.set_xlabel(r'$\Delta$ TD (mean TD = %.2f)' % meanTD)
         axesDeltaTD.set_ylabel('Sequence length (kbp)')
 
@@ -129,7 +134,8 @@ def plotOnAxes(self, fastaFile, tetraSigs, distributionsToPlot, axesHist, axesDe
 
         # plot reference distributions
         for distToPlot in distributionsToPlot:
-            boundKey = findNearest(list(dist[list(dist.keys())[0]].keys()), distToPlot)
+            boundKey = findNearest(
+                list(dist[list(dist.keys())[0]].keys()), distToPlot)
 
             x = []
             y = []
@@ -150,7 +156,8 @@ def plotOnAxes(self, fastaFile, tetraSigs, distributionsToPlot, axesHist, axesDe
                         if j == len(x) - 1:
                             x[j] = x[i]
                         else:
-                            x[j] = (x[j - 1] + x[j + 1]) / 2  # interpolate values from neighbours
+                            # interpolate values from neighbours
+                            x[j] = (x[j - 1] + x[j + 1]) / 2
 
                         if x[j] > x[i]:
                             x[j] = x[i]
@@ -164,15 +171,17 @@ def plotOnAxes(self, fastaFile, tetraSigs, distributionsToPlot, axesHist, axesDe
         axesDeltaTD.set_xlim([xMinSeqs, xMaxSeqs])
 
         # draw vertical line at x=0
-        axesDeltaTD.vlines(0, 0, yMaxSeqs, linestyle='dashed', color=self.axesColour, zorder=0)
+        yticks = axesDeltaTD.get_yticks()
+        axesDeltaTD.vlines(0, 0, yticks[-1], linestyle='dashed',
+                           color=self.axesColour, zorder=0)
 
         # Change sequence lengths from bp to kbp
-        yticks = axesDeltaTD.get_yticks()
         kbpLabels = []
         for seqLen in yticks:
             label = '%.1f' % (float(seqLen) / 1000)
             label = label.replace('.0', '')  # remove trailing zero
             kbpLabels.append(label)
+        axesDeltaTD.set_yticks(yticks)
         axesDeltaTD.set_yticklabels(kbpLabels)
 
         # Prettify plot