fixed bug with CLI of plotting methods introduced in 1.0.16

bin/checkm

@@ -324,7 +324,7 @@ Example: checkm qa ./output/lineage.ms ./output
 
     # generic arguments for plots
     plot_need_qa_results_parser = argparse.ArgumentParser(add_help=False)
-    plot_need_qa_results_parser.add_argument('output_dir', help="directory specified during qa command")
+    plot_need_qa_results_parser.add_argument('results_dir', help="directory specified during qa command")
 
     plot_parser = argparse.ArgumentParser(add_help=False)
     plot_parser.add_argument('bin_dir', help="directory containing bins to plot (fasta format)")
@@ -391,9 +391,9 @@ Example: checkm qa ./output/lineage.ms ./output
                                         formatter_class=CustomHelpFormatter,
                                         description='Create image with GC, CD, and TD distribution plots together.',
                                         epilog='Example: checkm dist_plot ./output ./bins ./plots tetra.tsv 95')
-    plot_dist_parser.add_argument('analyze_dir', help="directory specified during analyze command")
+    plot_dist_parser.add_argument('results_dir', help="directory specified during analyze command")
     plot_dist_parser.add_argument('bin_dir', help="directory containing bins to plot (fasta format)")
-    plot_dist_parser.add_argument('plot_dir', help="directory to hold plots")
+    plot_dist_parser.add_argument('output_dir', help="directory to hold plots")
     plot_dist_parser.add_argument('tetra_profile', help='tetranucleotide profiles for each sequence (see tetra command)')
     plot_dist_parser.add_argument('distributions', help='reference distribution(s) to plot; integer between 0 and 100', nargs='+', type=int, choices=xrange(0, 101), default=95, metavar='dist_value')
 

checkm/VERSION

@@ -1,3 +1,6 @@
+1.0.17
+- fixed bug with CLI of plotting methods introduced in 1.0.16
+
 1.0.16
 - made ~/.checkm the default directory for CheckM reference data
 - "checkm data setRoot <directory>" is no longer interactive and the directory must be given on the command line

checkm/coverageWindows.py

@@ -94,7 +94,7 @@ def run(self, binFiles, bamFile, bAllReads, minAlignPer, maxEditDistPer, windowS
 
         # make sure BAM file is sorted
         if not os.path.exists(bamFile + '.bai'):
-            self.logger.error('  [Error] BAM file is not sorted: ' + bamFile + '\n')
+            self.logger.error('BAM file is not sorted: ' + bamFile + '\n')
             sys.exit(1)
 
         # calculate coverage of each BAM file

checkm/main.py

@@ -411,7 +411,7 @@ def gcPlot(self, options):
         self.logger.info('[CheckM - gc_plot] Creating GC histogram and delta-GC plot.')
 
         checkDirExists(options.bin_dir)
-        makeSurePathExists(options.plot_dir)
+        makeSurePathExists(options.output_dir)
 
         binFiles = self.binFiles(options.bin_dir, options.extension)
 
@@ -424,7 +424,7 @@ def gcPlot(self, options):
             plots.plot(f, options.distributions)
 
             binId = binIdFromFilename(f)
-            outputFile = os.path.join(options.plot_dir, binId) + '.gc_plots.' + options.image_type
+            outputFile = os.path.join(options.output_dir, binId) + '.gc_plots.' + options.image_type
             plots.savePlot(outputFile, dpi=options.dpi)
             self.logger.info('Plot written to: ' + outputFile)
 
@@ -435,7 +435,7 @@ def codingDensityPlot(self, options):
         self.logger.info('[CheckM - coding_plot] Creating coding density histogram and delta-CD plot.')
 
         checkDirExists(options.bin_dir)
-        makeSurePathExists(options.plot_dir)
+        makeSurePathExists(options.output_dir)
 
         binFiles = self.binFiles(options.bin_dir, options.extension)
 
@@ -448,7 +448,7 @@ def codingDensityPlot(self, options):
             plots.plot(f, options.distributions)
 
             binId = binIdFromFilename(f)
-            outputFile = os.path.join(options.plot_dir, binId) + '.coding_density_plots.' + options.image_type
+            outputFile = os.path.join(options.output_dir, binId) + '.coding_density_plots.' + options.image_type
             plots.savePlot(outputFile, dpi=options.dpi)
             self.logger.info('Plot written to: ' + outputFile)
 
@@ -459,7 +459,7 @@ def tetraDistPlot(self, options):
         self.logger.info('[CheckM - tetra_plot] Creating tetra-distance histogram and delta-TD plot.')
 
         checkDirExists(options.bin_dir)
-        makeSurePathExists(options.plot_dir)
+        makeSurePathExists(options.output_dir)
 
         binFiles = self.binFiles(options.bin_dir, options.extension)
 
@@ -475,7 +475,7 @@ def tetraDistPlot(self, options):
             binId = binIdFromFilename(f)
             plots.plot(f, tetraSigs, options.distributions)
 
-            outputFile = os.path.join(options.plot_dir, binId) + '.tetra_dist_plots.' + options.image_type
+            outputFile = os.path.join(options.output_dir, binId) + '.tetra_dist_plots.' + options.image_type
             plots.savePlot(outputFile, dpi=options.dpi)
             self.logger.info('Plot written to: ' + outputFile)
 
@@ -486,7 +486,7 @@ def distributionPlots(self, options):
         self.logger.info('[CheckM - dist_plot] Creating GC, CD, and TD distribution plots.')
 
         checkDirExists(options.bin_dir)
-        makeSurePathExists(options.plot_dir)
+        makeSurePathExists(options.output_dir)
 
         binFiles = self.binFiles(options.bin_dir, options.extension)
 
@@ -502,7 +502,7 @@ def distributionPlots(self, options):
             binId = binIdFromFilename(f)
             plots.plot(f, tetraSigs, options.distributions)
 
-            outputFile = os.path.join(options.plot_dir, binId) + '.ref_dist_plots.' + options.image_type
+            outputFile = os.path.join(options.output_dir, binId) + '.ref_dist_plots.' + options.image_type
             plots.savePlot(outputFile, dpi=options.dpi)
             self.logger.info('Plot written to: ' + outputFile)
 
@@ -513,7 +513,7 @@ def tetraPcaPlot(self, options):
         self.logger.info('[CheckM - tetra_pca] Creating PCA plot of tetranucleotide signatures.')
 
         checkDirExists(options.bin_dir)
-        makeSurePathExists(options.plot_dir)
+        makeSurePathExists(options.output_dir)
 
         binFiles = self.binFiles(options.bin_dir, options.extension)
 
@@ -530,7 +530,7 @@ def tetraPcaPlot(self, options):
             plots.plot(f, seqIds, pc, variance)
 
             binId = binIdFromFilename(f)
-            outputFile = os.path.join(options.plot_dir, binId) + '.tetra_pca_plots.' + options.image_type
+            outputFile = os.path.join(options.output_dir, binId) + '.tetra_pca_plots.' + options.image_type
             plots.savePlot(outputFile, dpi=options.dpi)
             self.logger.info('Plot written to: ' + outputFile)
 
@@ -542,7 +542,7 @@ def coveragePcaPlot(self, options):
 
         checkDirExists(options.bin_dir)
         checkFileExists(options.coverage_file)
-        makeSurePathExists(options.plot_dir)
+        makeSurePathExists(options.output_dir)
 
         binFiles = self.binFiles(options.bin_dir, options.extension)
 
@@ -579,7 +579,7 @@ def coveragePcaPlot(self, options):
             plots.plot(f, seqIds, pc, variance)
 
             binId = binIdFromFilename(f)
-            outputFile = os.path.join(options.plot_dir, binId) + '.cov_pca_plots.' + options.image_type
+            outputFile = os.path.join(options.output_dir, binId) + '.cov_pca_plots.' + options.image_type
             plots.savePlot(outputFile, dpi=options.dpi)
             self.logger.info('Plot written to: ' + outputFile)
 
@@ -591,7 +591,7 @@ def gcBiasPlot(self, options):
         self.logger.info('[CheckM - gc_bias_plot] Plotting bin coverage as a function of GC.')
 
         checkDirExists(options.bin_dir)
-        makeSurePathExists(options.plot_dir)
+        makeSurePathExists(options.output_dir)
 
         binFiles = self.binFiles(options.bin_dir, options.extension)
 
@@ -607,7 +607,7 @@ def gcBiasPlot(self, options):
             plots.plot(f, coverageProfile)
 
             binId = binIdFromFilename(f)
-            outputFile = os.path.join(options.plot_dir, binId) + '.gc_bias_plot.' + options.image_type
+            outputFile = os.path.join(options.output_dir, binId) + '.gc_bias_plot.' + options.image_type
             plots.savePlot(outputFile, dpi=options.dpi)
             self.logger.info('Plot written to: ' + outputFile)
 
@@ -619,7 +619,7 @@ def nxPlot(self, options):
         self.logger.info('[CheckM - nx_plot] Creating Nx-plots.')
 
         checkDirExists(options.bin_dir)
-        makeSurePathExists(options.plot_dir)
+        makeSurePathExists(options.output_dir)
 
         binFiles = self.binFiles(options.bin_dir, options.extension)
 
@@ -631,7 +631,7 @@ def nxPlot(self, options):
             filesProcessed += 1
             nx.plot(f)
 
-            outputFile = os.path.join(options.plot_dir, binId) + '.nx_plot.' + options.image_type
+            outputFile = os.path.join(options.output_dir, binId) + '.nx_plot.' + options.image_type
             nx.savePlot(outputFile, dpi=options.dpi)
             self.logger.info('Plot written to: ' + outputFile)
 
@@ -643,7 +643,7 @@ def cumulativeLengthPlot(self, options):
         self.logger.info('[CheckM - len_plot] Creating cumulative sequence length plot.')
 
         checkDirExists(options.bin_dir)
-        makeSurePathExists(options.plot_dir)
+        makeSurePathExists(options.output_dir)
 
         binFiles = self.binFiles(options.bin_dir, options.extension)
 
@@ -655,7 +655,7 @@ def cumulativeLengthPlot(self, options):
             filesProcessed += 1
             plot.plot(f)
 
-            outputFile = os.path.join(options.plot_dir, binId) + '.seq_len_plot.' + options.image_type
+            outputFile = os.path.join(options.output_dir, binId) + '.seq_len_plot.' + options.image_type
             plot.savePlot(outputFile, dpi=options.dpi)
             self.logger.info('Plot written to: ' + outputFile)
 
@@ -667,7 +667,7 @@ def lengthHistogram(self, options):
         self.logger.info('[CheckM - len_hist] Creating sequence length histogram.')
 
         checkDirExists(options.bin_dir)
-        makeSurePathExists(options.plot_dir)
+        makeSurePathExists(options.output_dir)
 
         binFiles = self.binFiles(options.bin_dir, options.extension)
 
@@ -679,7 +679,7 @@ def lengthHistogram(self, options):
             filesProcessed += 1
             plot.plot(f)
 
-            outputFile = os.path.join(options.plot_dir, binId) + '.len_hist.' + options.image_type
+            outputFile = os.path.join(options.output_dir, binId) + '.len_hist.' + options.image_type
             plot.savePlot(outputFile, dpi=options.dpi)
             self.logger.info('Plot written to: ' + outputFile)
 
@@ -691,14 +691,14 @@ def markerPlot(self, options):
         self.logger.info('[CheckM - marker_plot] Creating marker gene position plot.')
 
         checkDirExists(options.bin_dir)
-        makeSurePathExists(options.plot_dir)
+        makeSurePathExists(options.output_dir)
 
         # generate plot for each bin
         binFiles = self.binFiles(options.bin_dir, options.extension)
 
         resultsParser = ResultsParser(None)
-        markerGeneStats = resultsParser.parseMarkerGeneStats(options.output_dir)
-        binStats = resultsParser.parseBinStatsExt(options.output_dir)
+        markerGeneStats = resultsParser.parseMarkerGeneStats(options.results_dir)
+        binStats = resultsParser.parseBinStatsExt(options.results_dir)
 
         plot = MarkerGenePosPlot(options)
         filesProcessed = 1
@@ -713,7 +713,7 @@ def markerPlot(self, options):
             bPlotted = plot.plot(f, markerGeneStats[binId], binStats[binId])
 
             if bPlotted:
-                outputFile = os.path.join(options.plot_dir, binId) + '.marker_pos_plot.' + options.image_type
+                outputFile = os.path.join(options.output_dir, binId) + '.marker_pos_plot.' + options.image_type
                 plot.savePlot(outputFile, dpi=options.dpi)
                 self.logger.info('Plot written to: ' + outputFile)
             else:
@@ -727,7 +727,7 @@ def parallelCoordPlot(self, options):
         self.logger.info('[CheckM - par_plot] Creating parallel coordinate plot of GC and coverage.')
 
         checkDirExists(options.bin_dir)
-        makeSurePathExists(options.plot_dir)
+        makeSurePathExists(options.output_dir)
         checkFileExists(options.coverage_file)
 
         binFiles = self.binFiles(options.bin_dir, options.extension)
@@ -742,7 +742,7 @@ def parallelCoordPlot(self, options):
         seqStats = {}
         for f in binFiles:
             binId = binIdFromFilename(f)
-            seqStats[binId] = binStats.sequenceStats(options.output_dir, f)
+            seqStats[binId] = binStats.sequenceStats(options.results_dir, f)
 
         # create plot for each bin
 
@@ -755,7 +755,7 @@ def parallelCoordPlot(self, options):
 
             plot.plot(binId, seqStats, coverageStats)
 
-            outputFile = os.path.join(options.plot_dir, binId) + '.paralel_coord_plot.' + options.image_type
+            outputFile = os.path.join(options.output_dir, binId) + '.paralel_coord_plot.' + options.image_type
             plot.savePlot(outputFile, dpi=options.dpi)
             self.logger.info('Plot written to: ' + outputFile)
 
@@ -767,7 +767,7 @@ def binQAPlot(self, options):
         self.logger.info('[CheckM - bin_qa_plot] Creating bar plot of bin quality.')
 
         checkDirExists(options.bin_dir)
-        makeSurePathExists(options.plot_dir)
+        makeSurePathExists(options.output_dir)
 
         binFiles = self.binFiles(options.bin_dir, options.extension)
 
@@ -790,7 +790,7 @@ def binQAPlot(self, options):
             bMakePlot = plot.plot(binFiles, binStatsExt, options.bIgnoreHetero, None)
 
         if bMakePlot:
-            outputFile = os.path.join(options.plot_dir, 'bin_qa_plot.' + options.image_type)
+            outputFile = os.path.join(options.output_dir, 'bin_qa_plot.' + options.image_type)
             plot.savePlot(outputFile, dpi=options.dpi)
 
             self.logger.info('Plot written to: ' + outputFile)

checkm/plot/codingDensityPlots.py

@@ -21,6 +21,7 @@
 
 import os
 import sys
+import logging
 
 import numpy as np
 
@@ -36,6 +37,8 @@
 class CodingDensityPlots(AbstractPlot):
     def __init__(self, options):
         AbstractPlot.__init__(self, options)
+
+        self.logger = logging.getLogger('timestamp')
 
     def plot(self, fastaFile, distributionsToPlot):
         # Set size of figure
@@ -52,9 +55,9 @@ def plot(self, fastaFile, distributionsToPlot):
 
     def plotOnAxes(self, fastaFile, distributionsToPlot, axesHist, axesDeltaCD):
         # parse Prodigal output
-        gffFile = os.path.join(self.options.out_folder, '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):
-            print '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()
 
         prodigalParser = ProdigalGeneFeatureParser(gffFile)

checkm/plot/markerGenePosPlot.py

@@ -92,7 +92,7 @@ def plot(self, binFile, markerGeneStats, binStats):
 
         # get position of genes in bin
         prodigalFastaParser = ProdigalFastaParser()
-        geneFile = os.path.join(self.options.out_folder, 'bins', binId, DefaultValues.PRODIGAL_AA)
+        geneFile = os.path.join(self.options.results_dir, 'bins', binId, DefaultValues.PRODIGAL_AA)
         genePos = prodigalFastaParser.genePositions(geneFile)
 
         # Set size of figure