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baoqingding · Aug 30, 2019 · cdbdafd · cdbdafd
1 parent 402c488
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Showing 4 changed files with 80 additions and 5 deletions.
diff --git a/README.md b/README.md
@@ -70,7 +70,7 @@ $ mutmap -h
 usage: mutmap -r <FASTA> -c <BAM|FASTQ> -b <BAM|FASTQ>
               -n <INT> -o <OUT_DIR> [-T] [-e <DATABASE>]
 
-MutMap version 2.1.0
+MutMap version 2.1.1
 
 optional arguments:
   -h, --help         show this help message and exit
@@ -89,6 +89,16 @@ optional arguments:
   -t , --threads     Number of threads. If you specify the number
                      below one, then MutMap will use the threads
                      as many as possible. [2]
+  -w , --window      Window size (kb). [2000]
+  -s , --step        Step size (kb). [100]
+  -D , --max-depth   Maximum depth of variants which will be used.
+                     This cutoff will be applied in both of cultivar
+                     and bulk. [250]
+  -d , --min-depth   Minimum depth of variants which will be used.
+                     This cutoff will be applied in both of cultivar
+                     and bulk. [8]
+  -N , --N-rep       Number of replicates for simulation to make 
+                     null distribution. [5000]
   -T, --trim         Trim fastq using trimmomatic.
   -a , --adapter     FASTA of adapter sequences. This will be used
                      when you specify "-T" for trimming.
@@ -204,7 +214,7 @@ 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 2.1.0
+MutPlot version 2.1.1
 
 optional arguments:
   -h, --help            show this help message and exit

diff --git a/mutmap/__init__.py b/mutmap/__init__.py
@@ -1 +1 @@
-__version__ = "2.1.0"
+__version__ = "2.1.1"
diff --git a/mutmap/mutmap.py b/mutmap/mutmap.py
@@ -110,14 +110,34 @@ def mutplot(self):
         if args.snpEff is None:
             cmd = 'mutplot -v {0}/30_vcf/mutmap.vcf.gz \
                            -n {1} \
+                           -w {2} \
+                           -s {3} \
+                           -N {4} \
+                           -D {5} \
+                           -d {6} \
                            -o {0}/40_mutmap'.format(self.out,
-                                                    self.args.N_bulk)
+                                                    self.args.N_bulk,
+                                                    self.args.window,
+                                                    self.args.step,
+                                                    self.args.N_rep,
+                                                    self.args.max_depth,
+                                                    self.args.min_depth)
         else:
             cmd = 'mutplot -v {0}/30_vcf/mutmap.vcf.gz \
                            -n {1} \
+                           -w {2} \
+                           -s {3} \
+                           -N {4} \
+                           -D {5} \
+                           -d {6} \
                            -o {0}/40_mutmap \
-                           -e {2}'.format(self.out,
+                           -e {7}'.format(self.out,
                                           self.args.N_bulk,
+                                          self.args.window,
+                                          self.args.step,
+                                          self.args.N_rep,
+                                          self.args.max_depth,
+                                          self.args.min_depth,
                                           self.args.snpEff)
 
         cmd = clean_cmd(cmd)

diff --git a/mutmap/params.py b/mutmap/params.py
@@ -89,6 +89,51 @@ def mutmap_options(self):
                                   'as many as possible. [2]'),
                             metavar='')
 
+        parser.add_argument('-w',
+                            '--window',
+                            action='store',
+                            default=2000,
+                            type=int,
+                            help='Window size (kb). [2000]',
+                            metavar='')
+
+        parser.add_argument('-s',
+                            '--step',
+                            action='store',
+                            default=100,
+                            type=int,
+                            help='Step size (kb). [100]',
+                            metavar='')
+
+        parser.add_argument('-D',
+                            '--max-depth',
+                            action='store',
+                            default=250,
+                            type=int,
+                            help=('Maximum depth of variants which will be used.\n'
+                                  'This cutoff will be applied in both of cultivar\n'
+                                  'and bulk. [250]'),
+                            metavar='')
+
+        parser.add_argument('-d',
+                            '--min-depth',
+                            action='store',
+                            default=8,
+                            type=int,
+                            help=('Minimum depth of variants which will be used.\n'
+                                  'This cutoff will be applied in both of cultivar\n'
+                                  'and bulk. [8]'),
+                            metavar='')
+
+        parser.add_argument('-N',
+                            '--N-rep',
+                            action='store',
+                            default=5000,
+                            type=int,
+                            help=('Number of replicates for simulation to make \n'
+                                  'null distribution. [5000]'),
+                            metavar='')
+
         parser.add_argument('-T',
                             '--trim',
                             action='store_true',