Circos: added gene density, mismatches, coverage tracks, cosmetic cha…

…nges
ablab · Aug 14, 2017 · e0e6212 · e0e6212
1 parent 23490ee
commit e0e6212
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Showing 6 changed files with 188 additions and 62 deletions.
diff --git a/quast.py b/quast.py
@@ -238,7 +238,7 @@ def main(args):
                 report_for_icarus_fpath_pattern = None
                 stdout_pattern = None
             draw_alignment_plots = qconfig.draw_svg or qconfig.create_icarus_html
-            draw_circos_plot = qconfig.draw_plots and ref_fpath
+            draw_circos_plot = qconfig.draw_plots and ref_fpath and len(aligned_contigs_fpaths)
             number_of_steps = sum([int(bool(value)) for value in [draw_alignment_plots, draw_circos_plot, all_pdf_fpath]])
             if draw_alignment_plots:
                 ########################################################################
@@ -255,7 +255,7 @@ def main(args):
             if draw_circos_plot:
                 logger.main_info('  %d of %d: Creating Circos plots...' % (2 if draw_alignment_plots else 1, number_of_steps))
                 circos_png_fpath = circos.do(ref_fpath, contigs_fpaths, report_for_icarus_fpath_pattern, circos_gc_fpath,
-                                             features_containers, os.path.join(output_dirpath, 'circos'), logger)
+                                             features_containers, cov_fpath, os.path.join(output_dirpath, 'circos'), logger)
 
             if all_pdf_fpath:
                 # full report in PDF format: all tables and plots

diff --git a/quast_libs/basic_stats.py b/quast_libs/basic_stats.py
@@ -11,6 +11,7 @@
 from os.path import join
 
 from quast_libs import fastaparser, qconfig, qutils, reporting, plotter
+from quast_libs.circos import set_window_size
 from quast_libs.log import get_logger
 logger = get_logger(qconfig.LOGGER_DEFAULT_NAME)
 
@@ -81,14 +82,13 @@ def save_icarus_GC(ref_fpath, gc_fpath):
 
 
 def save_circos_GC(ref_fpath, reference_length, gc_fpath):
-    max_points = 25000
-    n = min(20000, max(100, reference_length // max_points))
+    window_size = set_window_size(reference_length)
     with open(gc_fpath, 'w') as out_f:
         for name, seq_full in fastaparser.read_fasta(ref_fpath):
-            for i in range(0, len(seq_full), n):
-                seq = seq_full[i:i + n]
-                GC_percent = get_GC_percent(seq, n)
-                out_f.write('\t'.join([name, str(i), str(i + n), str(GC_percent) + '\n']))
+            for i in range(0, len(seq_full), window_size):
+                seq = seq_full[i:i + window_size]
+                GC_percent = get_GC_percent(seq, window_size)
+                out_f.write('\t'.join([name, str(i), str(i + window_size), str(GC_percent) + '\n']))
 
 
 def binning_coverage(cov_values, nums_contigs):