default aligner: mafft

Author: zhangrengang

evolution_example

@@ -1929,7 +1929,6 @@ def bootstrap_species_tree(OFdir, outdir, bootstrap=1000, iqtree_options='-mset
     new_treefile = '{}.treefile'.format(prefix)
     new_treefile_rooted = '{}.rooted.tre'.format(prefix)
     print('re-root with {}'.format([root]), file=sys.stderr)
-    # result.re_root(new_treefile, root, new_treefile_rooted)
     cmd = 'nw_reroot {} {} > {}'.format(
         new_treefile, root, new_treefile_rooted)
     os.system(cmd)

soi/OrthoFinder.py

@@ -1,6 +1,3 @@
-from .colors import Colors
-from .mcscan import Collinearity, Gff, XCollinearity
-from lazy_property import LazyWritableProperty as lazyproperty
 import sys
 import numpy as np
 import collections
@@ -9,6 +6,9 @@
 from matplotlib.gridspec import GridSpec
 mpl.use("Agg")
 mpl.rcParams['pdf.fonttype'] = 42
+from lazy_property import LazyWritableProperty as lazyproperty
+from .colors import Colors
+from .mcscan import Collinearity, Gff, XCollinearity
 
 
 def eval(collinearities, orthologs, gff, ref=None, pre=None):
@@ -86,26 +86,18 @@ def plot_eval(d_rcs, outfig, legend_fontsize=9):
         bm = sum(rcs.refcounts[:, 1])  # gene number of all blocks
         kargs = dict(color=colors[i], alpha=1, label=_sp)
         ax0.plot(-2, -2, linestyle='-', marker='o',  **kargs)
-# ax0.barh(0, 0, height=0, left=0, align='center', label=_sp)
 
         ax1.plot(range(1, nb+1), np.cumsum(ns),
                  drawstyle="steps-post",  **kargs)
         ax2.plot(range(1, nb+1), ns, drawstyle="steps-post", **kargs)
-# ax2.scatter(i50, sn50, label=_sp)
         ax3.scatter(len(rcs.ns), bm, **kargs)
-# ax4.hist(rcs.extended_frs, bins=40, histtype='step', **kargs)
         hist_plot(rcs.extended_frs, ax4, bins=40, **kargs)
-# ax4.scatter(rcs.frs, rcs.ns,  alpha=0.6, label=_sp)
-# ax5.scatter(fn50, sn50, alpha=0.8, label=_sp)
         ax5.scatter(fm, sm, **kargs)
 
-# ax5.hist(rcs.extended_ns, bins=30, histtype='step', label=_sp)
-# ax5.scatter(np.mean(rcs.extended_frs), np.mean(rcs.extended_ns), label=_sp)
         ax6.scatter(fm, om, **kargs)
-# ax7.hist(rcs.extended_ois, bins=40, histtype='step', **kargs)
         hist_plot(rcs.extended_ois, ax7, bins=40, **kargs)
         ax8.plot(rcs.refcounts[:, 0], rcs.refcounts[:, 1], **kargs)
-# print(sn50, sm)
+
         line = [sp1, sp2, nb, bm, int(min(ns)), int(max(ns)), int(np.median(ns)),
                 round(np.mean(ns), 1), sm, round(fm, 2), round(om, 2)]
         print('\t'.join(map(str, line)))

soi/evaluator.py

@@ -42,7 +42,6 @@ def __init__(self, info):
         try:
             self.species, self.raw_gene = id.split('|', 1)
         except ValueError:
-            # logger.warn('Species id not found in `{}`, ignoring'.format(id))
             self.species, self.raw_gene = None, id
 
     def __str__(self):
@@ -132,14 +131,10 @@ def parse_ks(self):
          GC, ML_Score, AICc, Akaike_Weight, Model) = self.info
         self.sequence = Sequence
         self.method = Method
-# try: self.ka = float(Ka)
-# except ValueError: self.ka =None
         try:
             self.ks = float(Ks)
         except ValueError:
             self.ks = 0  # too few substitution, NA
-# try: self.kaks = float(Ka_Ks)
-# except ValueError: self.kaks = None
 
     def parse_pair(self):
         if not hasattr(self, 'pair'):
@@ -2300,7 +2295,7 @@ def d_gff(self):
         return Gff(self.gff).get_genes()
 
     def get_trees(self):  # gene trees
-        '''完全符合倍性比的基因树'''
+        '''Gene trees that perfectly matches the ploidy ratio.'''
         from creat_ctl import sort_version
         if not os.path.exists(self.tmpdir):
             os.mkdir(self.tmpdir)
@@ -2916,7 +2911,7 @@ class ToAstral(ColinearGroups):
     def __init__(self, input=None, pep=None, spsd=None, cds=None, tmpdir='tmp', root=None, both=True, suffix=None,
                  ncpu=50, max_taxa_missing=0.5, max_mean_copies=10, max_copies=5, singlecopy=False, onlyaln=False,
                  source=None, orthtype='orthologues', fast=True, concat=False, clean=False, overwrite=False,
-                 aligner='muscle', trimal_opts='-automated1', iqtree_opts=''):
+                 aligner='mafft', trimal_opts='-automated1', iqtree_opts=''):
         self.input = input
         self.pep = pep
         self.cds = cds