v2.3.5

YuSugihara · Oct 5, 2024 · a907bd3 · a907bd3
1 parent a568473
commit a907bd3
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Showing 3 changed files with 3 additions and 87 deletions.
diff --git a/mutmap/mutmap.py b/mutmap/mutmap.py
@@ -130,9 +130,6 @@ def mutplot(self):
 
         if self.args.snpEff is not None:
             cmd = cmd + ' -e {}'.format(self.args.snpEff)
-
-        if self.args.species is not None:
-            cmd = cmd + ' --species {}'.format(self.args.species)
 
         cmd = clean_cmd(cmd)
         p = sbp.Popen(cmd,

diff --git a/mutmap/params.py b/mutmap/params.py
@@ -202,24 +202,6 @@ def mutmap_options(self):
                                   'is suited for BWA. [50]'),
                             metavar='')
 
-        parser.add_argument('--species',
-                            action='store',
-                            choices=['Arabidopsis', 
-                                     'Cucumber', 
-                                     'Maize', 
-                                     'Rapeseed', 
-                                     'Rice', 
-                                     'Tobacco', 
-                                     'Tomato', 
-                                     'Wheat', 
-                                     'Yeast'],
-                            help=('Consider multiple test correction derived by\n'
-                                  'Huang et al. (2019). Please spesify a species name.\n'
-                                  'With this option. QTL-seq produces a theoretical threshold.\n'
-                                  'Currently, Arabidopsis, Cucumber, Maize, Rapeseed,\n'
-                                  'Rice, Tobacco, Tomato, Wheat, and Yeast are supported.'),
-                            metavar='')
-
         # set version
         parser.add_argument('-v',
                             '--version',
@@ -339,24 +321,6 @@ def mutplot_options(self):
                             default=False,
                             help='Output IGV format file to check results on IGV.')
 
-        parser.add_argument('--species',
-                            action='store',
-                            choices=['Arabidopsis', 
-                                     'Cucumber', 
-                                     'Maize', 
-                                     'Rapeseed', 
-                                     'Rice', 
-                                     'Tobacco', 
-                                     'Tomato', 
-                                     'Wheat', 
-                                     'Yeast'],
-                            help=('Consider multiple test correction derived by\n'
-                                  'Huang et al. (2019). Please spesify a species name.\n'
-                                  'With this option. MutMap produces a theoretical threshold.\n'
-                                  'Currently, Arabidopsis, Cucumber, Maize, Rapeseed,\n'
-                                  'Rice, Tobacco, Tomato, Wheat, and Yeast are supported.'),
-                            metavar='')
-
         parser.add_argument('--indel',
                             action='store_true',
                             default=False,

diff --git a/mutmap/vcf2index.py b/mutmap/vcf2index.py
@@ -1,3 +1,4 @@
+
 import os
 import re
 import sys
@@ -16,7 +17,6 @@ def __init__(self, args):
         self.out = args.out
         self.vcf = args.vcf
         self.snpEff = args.snpEff
-        self.species = args.species
         self.N_bulk = args.N_bulk
         self.N_replicates = args.N_rep
         self.min_SNPindex = args.min_SNPindex
@@ -25,53 +25,8 @@ def __init__(self, args):
         if self.snpEff is not None:
             self.ANN_re = re.compile(';ANN=(.*);*')
 
-        if self.species is None:
-            self.p99_index = int(0.99*self.N_replicates) - 1
-            self.p95_index = int(0.95*self.N_replicates) - 1
-        else:
-            k = self.correct_threshold()
-            corr_p99 = 0.01/k
-            corr_p95 = 0.05/k
-            self.p99_index = int((1 - corr_p99)*self.N_replicates) - 1
-            self.p95_index = int((1 - corr_p95)*self.N_replicates) - 1
-
-            if int(corr_p99*self.N_replicates) - 1 < 0:
-                print(('!!WARNING!! Number of replicates for simulation is not '
-                       'enough to consider multiple testing correction. '
-                       'Therefore, the highest SNP-index and the second highest '
-                       'SNP-index were selected for p99 and p95, respectively.'), 
-                       file=sys.stderr)
-
-                self.p99_index = self.N_replicates - 1
-                self.p95_index = self.N_replicates - 2
-
-    def correct_threshold(self):
-        l = 8.4
-
-        if self.species == 'Arabidopsis':
-            k = 5 + 600/l
-        elif self.species == 'Cucumber':
-            k = 7 + 1390/l
-        elif self.species == 'Maize':
-            k = 10 + 2060/l
-        elif self.species == 'Rapeseed':
-            k = 18 + 2520/l
-        elif self.species == 'Rice':
-            k = 12 + 1530/l
-        elif self.species == 'Tobacco':
-            k = 12 + 3270/l
-        elif self.species == 'Tomato':
-            k = 12 + 1470/l
-        elif self.species == 'Wheat':
-            k = 21 + 3140/l
-        elif self.species == 'Yeast':
-            k = 16 + 4900/l
-
-        else:
-            print('You specified not supported species.', file=sys.stderr)
-            sys.exit(1)
-
-        return k
+        self.p99_index = int(0.99*self.N_replicates) - 1
+        self.p95_index = int(0.95*self.N_replicates) - 1
 
     def get_field(self):
         root, ext = os.path.splitext(self.vcf)