update to v2.3.3

README.md

@@ -1,5 +1,5 @@
 # MutMap User Guide
-#### version 2.3.2
+#### version 2.3.3
 
 ## Table of contents
 - [What is MutMap?](#What-is-MutMap)
@@ -71,16 +71,15 @@ trimmomatic --help
 
 ## Usage
 
-Current version can not plot too contiguous reference genome.
-**We highly recommend you to run MutMap without spcifying '--species' for multiple testing correction, initially.**
+If your reference genome has more than 50 contigs (or chromosomes), only significant contigs will be plotted.
 
 ```
 mutmap -h
 
 usage: mutmap -r <FASTA> -c <BAM|FASTQ> -b <BAM|FASTQ>
               -n <INT> -o <OUT_DIR> [-T] [-e <DATABASE>]
 
-MutMap version 2.3.2
+MutMap version 2.3.3
 
 optional arguments:
   -h, --help         show this help message and exit
@@ -229,7 +228,7 @@ usage: mutplot -v <VCF> -o <OUT_DIR> -n <INT> [-w <INT>] [-s <INT>]
                [-D <INT>] [-d <INT>] [-N <INT>] [-m <FLOAT>]
                [-S <INT>] [-e <DATABASE>] [--igv] [--indel]
 
-MutPlot version 2.3.2
+MutPlot version 2.3.3
 
 optional arguments:
   -h, --help            show this help message and exit

mutmap/__init__.py

@@ -1 +1 @@
-__version__ = "2.3.2"
+__version__ = "2.3.3"

mutmap/plot.py

@@ -1,11 +1,10 @@
-import os
+import sys
 import warnings
 warnings.filterwarnings("ignore")
 import pandas as pd
 import matplotlib
 matplotlib.use('Agg')
 import matplotlib.pyplot as plt
-from mutmap.utils import time_stamp
 
 
 class Plot(object):
@@ -63,6 +62,22 @@ def read_files(self):
 
         return snp_index, sliding_window
 
+    def get_significant_contigs(self, N_chr, snp_index, sliding_window):
+
+        print(('!!WARNING!! Your reference genome has too many contigs (>50). '
+               'Therefore, only significant contigs will be plotted.'), file=sys.stderr)
+
+        significant_windows = sliding_window[abs(sliding_window['mean_p95']) <= \
+                                             abs(sliding_window['mean_SNPindex'])]
+
+        significant_contigs = list(significant_windows['CHROM'].drop_duplicates())
+
+        N_chr = len(significant_contigs)
+        snp_index = snp_index[snp_index['CHROM'].isin(significant_contigs)]
+        sliding_window = sliding_window[sliding_window['CHROM'].isin(significant_contigs)]
+
+        return N_chr, snp_index, sliding_window
+
     def set_plot_style(self, N_chr):
         if N_chr == 1:
             style = (1, 1)
@@ -79,6 +94,12 @@ def run(self):
         snp_index, sliding_window = self.read_files()
 
         N_chr = len(sliding_window['CHROM'].unique())
+
+        if N_chr > 50:
+            N_chr, self.snp_index, self.sliding_window = self.get_significant_contigs(N_chr, 
+                                                                                      snp_index, 
+                                                                                      sliding_window)
+
         N_col, N_raw = self.set_plot_style(N_chr)
 
         fig = plt.figure(figsize=(self.fig_width*N_col, self.fig_height*N_raw))