add iqtree

yangfangs · Jan 10, 2019 · 8c946dc · 8c946dc
1 parent c00de11
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diff --git a/README.rst b/README.rst
@@ -3,7 +3,7 @@ PhySpeTree: automatically reconstructing phylogenetic species tree
 
 |PyPI version| |Docs| |License|
 
-**PhySpeTree is implemented in Python 2.7, designed for Linux system.**
+**PhySpeTree is implemented in Python language (supports Python2.7+ and Python3+), designed for Linux systems.**
 
 **Documents**: `PhySpeTree documentation <https://yangfangs.github.io/physpetools>`_.
 
@@ -226,6 +226,13 @@ Here is an example of setting RAxML advanced options by `--raxml_p`:
     Set FastTree advance parameters,
     please see `FastTree <http://www.microbesonline.org/fasttree/>`_.
 
+--iqtree
+    Reconstruct phylogenetic tree by iqtree.
+
+--iqtree_p
+    Set iqtree advance parameters,
+    please see `IQ-TREE <http://www.iqtree.org/doc/>`_.
+
 build
 ^^^^^^^^^^^^^^^^^^^^
 

diff --git a/docs/docs/usage.md b/docs/docs/usage.md
@@ -272,6 +272,15 @@ The default option:
 
 > Set FastTree advanced parameters, please see [FastTree Helps](http://www.microbesonline.org/fasttree/).
 
+
+**--iqtree**
+
+> Reconstruct species tree by iqtree.
+
+**--iqtree_p**
+
+> Set iqtree advanced parameters, please see [IQ-TREE](http://www.microbesonline.org/fasttree/).
+
 ## build
 
 The `build` module is used to reconstruct species trees with manually prepared sequences. Advanced options are the same as `autobuild` module.

diff --git a/physpetool/phylotree/buildtree.py b/physpetool/phylotree/buildtree.py
@@ -30,6 +30,7 @@
 from physpetool.phylotree.doclustalw import doclustalw_file, doclustalw
 from physpetool.phylotree.dofasttree import doFastTree
 from physpetool.phylotree.dogblocks import dogblocks
+from physpetool.phylotree.doiqtree import doiqtree
 from physpetool.phylotree.domafft import domafft_file, domafft
 from physpetool.phylotree.domuscle import domuscle_file, domuscle
 from physpetool.phylotree.doraxml import doraxml
@@ -55,6 +56,7 @@ def build_hcp(in_put, out_put,
               args_trimal, args_trimal_p,
               args_raxml, args_raxml_p,
               args_fasttree, args_fasttree_p,
+              args_iqtree,args_iqtree_p,
               args_thread):
     '''reconstruct phylogenetic tree by hcp method'''
     out_retrieve = in_put
@@ -78,6 +80,8 @@ def build_hcp(in_put, out_put,
     # reconstruct tree
     if args_fasttree:
         doFastTree(out_f2p, out_put, args_fasttree_p, args_thread)
+    elif args_iqtree:
+        doiqtree(out_f2p, out_put, args_iqtree_p, args_thread)
     elif args_raxml:
         doraxml(out_f2p, out_put, args_raxml_p, args_thread)
 
@@ -90,6 +94,7 @@ def build_srna(in_put, out_put,
                args_trimal, args_trimal_p,
                args_raxml, args_raxml_p,
                args_fasttree, args_fasttree_p,
+               args_iqtree,args_iqtree_p,
                args_thread):
     '''reconstruct phylogenetic tree by ssu rna method'''
     out_retrieve = in_put
@@ -113,6 +118,8 @@ def build_srna(in_put, out_put,
     if args_fasttree:
         args_fasttree_p_add = "-nt " + args_fasttree_p.lstrip()
         doFastTree(out_f2p, out_put, args_fasttree_p_add, args_thread)
+    elif args_iqtree:
+        doiqtree(out_f2p, out_put, args_iqtree_p, args_thread)
     elif args_raxml:
         if args_raxml_p == raxmlpara_pro:
             args_raxml_p = raxmlpara_dna

diff --git a/physpetool/phylotree/doiqtree.py b/physpetool/phylotree/doiqtree.py
@@ -0,0 +1,57 @@
+# ########################## Copyrights and License #############################
+#                                                                               #
+# Copyright 2016 Yang Fang <[email protected]>                              #
+#                                                                               #
+# This file is part of PhySpeTree.                                              #
+# https://xiaofeiyangyang.github.io/physpetools/                                #
+#                                                                               #
+# PhySpeTree is free software: you can redistribute it and/or modify it under   #
+# the terms of the GNU Lesser General Public License as published by the Free   #
+# Software Foundation, either version 3 of the License, or (at your option)     #
+# any later version.                                                            #
+#                                                                               #
+# PhySpeTree is distributed in the hope that it will be useful, but WITHOUT ANY #
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS     #
+# FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more  #
+# details.                                                                      #
+#                                                                               #
+# You should have received a copy of the GNU Lesser General Public License      #
+# along with PhySpeTree. If not, see <http://www.gnu.org/licenses/>.            #
+#                                                                               #
+# ###############################################################################
+"""
+function to call iqtree and iqtree reconstruct tree.
+"""
+import os
+
+import subprocess
+
+from physpetool.phylotree.log import getLogging
+from physpetool.softwares.path import getlocalpath
+
+logdoiqtree = getLogging('iqtree')
+
+
+def doiqtree(inputfile, outputfile, iqtreepara, thread):
+    # Use FASTA format build tree
+    # input_fasta = inputfile.replace('.phy', '')
+    iqtreePath = getlocalpath()
+    thread_to_str = str(thread)
+    out_tree_name = os.path.join(outputfile, "iqtree.tree")
+    if not os.path.exists(outputfile):
+        os.mkdir(outputfile)
+    if thread_to_str is '1':
+        cmd = iqtreePath + "/iqtree " + "-s " + inputfile + " -pre " + out_tree_name + iqtreepara
+        subprocess.call(cmd, shell=True)
+    else:
+        # set the threads
+        cmd = iqtreePath + "/iqtree " + "-s " + inputfile + " -pre " + out_tree_name + " -nt " + thread_to_str + iqtreepara
+        subprocess.call(cmd, shell=True)
+    logdoiqtree.info("Phylogenetic species tree reconstructed by iqtree was completed")
+
+
+if __name__ == '__main__':
+    doiqtree("/home/yangfang/PhySpeTree/iqtree-1.6.9-Linux/example.phy",
+               "/home/yangfang/PhySpeTree/iqtree-1.6.9-Linux/test/",
+               " -m MF", "1"
+               )
diff --git a/physpetool/physpe/autobuild.py b/physpetool/physpe/autobuild.py
@@ -26,6 +26,7 @@
 """
 from physpetool.phylotree.doclustalw import doclustalw_file, doclustalw
 from physpetool.phylotree.dofasttree import doFastTree
+from physpetool.phylotree.doiqtree import doiqtree
 from physpetool.phylotree.domafft import domafft, domafft_file
 from physpetool.phylotree.domuscle import domuscle_file, domuscle
 from physpetool.phylotree.dogblocks import dogblocks
@@ -120,6 +121,10 @@ def start_args(input):
                               default=False, help='Reconstruct phylogenetic tree by FastTree.')
     advance_args.add_argument('--fasttree_p', action='store', dest='fasttree_parameter',
                               default='', help='Set FastTree advance parameters. ')
+    advance_args.add_argument('--iqtree', action='store_true', dest='iqtree',
+                              default=False, help='Reconstruct phylogenetic tree by iqtree.')
+    advance_args.add_argument('--iqtree_p', action='store', dest='iqtree_parameter',
+                              default='', help='Set iqtree advance parameters. ')
 
 
 def starting(args):
@@ -156,6 +161,7 @@ def starting(args):
                       args.trimal, args.trimal_parameter,
                       args.raxml, args.raxml_parameter,
                       args.fasttree, args.fasttree_parameter,
+                      args.iqtree, args.iqtree_parameter,
                       args.thread)
 
     # Reconstruct phylogenetic tree by extend highly conserved proteins.
@@ -169,6 +175,7 @@ def starting(args):
                       args.trimal, args.trimal_parameter,
                       args.raxml, args.raxml_parameter,
                       args.fasttree, args.fasttree_parameter,
+                      args.iqtree, args.iqtree_parameter,
                       args.thread, args.extenddata)
 
     # Reconstruct phylogenetic tree by extend ssu rna method.
@@ -182,6 +189,7 @@ def starting(args):
                        args.trimal, args.trimal_parameter,
                        args.raxml, args.raxml_parameter,
                        args.fasttree, args.fasttree_parameter,
+                       args.iqtree, args.iqtree_parameter,
                        args.thread, args.extenddata)
     # Reconstruct phylogenetic tree by highly conserved proteins.
     elif args.HCP:
@@ -194,6 +202,7 @@ def starting(args):
                  args.trimal, args.trimal_parameter,
                  args.raxml, args.raxml_parameter,
                  args.fasttree, args.fasttree_parameter,
+                 args.iqtree, args.iqtree_parameter,
                  args.thread)
 
 def starting_hcp(in_put, out_put,
@@ -204,6 +213,7 @@ def starting_hcp(in_put, out_put,
                  args_trimal, args_trimal_p,
                  args_raxml, args_raxml_p,
                  args_fasttree, args_fasttree_p,
+                 args_iqtree,args_iqtree_p,
                  args_thread):
     '''reconstruct phylogenetic tree by hcp method'''
     hcp_input, recovery_dic = checkKeggOrganism(in_put)
@@ -230,6 +240,8 @@ def starting_hcp(in_put, out_put,
     # reconstruct tree
     if args_fasttree:
         doFastTree(out_f2p, out_put, args_fasttree_p, args_thread)
+    elif args_iqtree:
+        doiqtree(out_f2p, out_put, args_iqtree_p, args_thread)
     elif args_raxml:
         doraxml(out_f2p, out_put, args_raxml_p, args_thread)
 
@@ -242,6 +254,7 @@ def starting_srna(in_put, out_put,
                   args_trimal, args_trimal_p,
                   args_raxml, args_raxml_p,
                   args_fasttree, args_fasttree_p,
+                  args_iqtree,args_iqtree_p,
                   args_thread):
     '''reconstruct phylogenetic tree by ssu rna method'''
     ssu_input,recovery_dic = checkSilvaOrganism(in_put)
@@ -270,6 +283,8 @@ def starting_srna(in_put, out_put,
     if args_fasttree:
         args_fasttree_p_add = "-nt " + args_fasttree_p.lstrip()
         doFastTree(out_f2p, out_put, args_fasttree_p_add, args_thread)
+    elif args_iqtree:
+        doiqtree(out_f2p, out_put, args_iqtree_p, args_thread)
     elif args_raxml:
         if args_raxml_p is raxmlpara_pro:
             args_raxml_p = raxmlpara_dna
@@ -284,6 +299,7 @@ def starting_ehcp(in_put, out_put,
                   args_trimal, args_trimal_p,
                   args_raxml, args_raxml_p,
                   args_fasttree, args_fasttree_p,
+                  args_iqtree,args_iqtree_p,
                   args_thread, args_extenddata):
     '''reconstruct phylogenetic tree by ehcp method'''
     hcp_input, recovery_dic = checkKeggOrganism(in_put)
@@ -319,6 +335,8 @@ def starting_ehcp(in_put, out_put,
     # reconstruct tree
     if args_fasttree:
         doFastTree(out_f2p, out_put, args_fasttree_p, args_thread)
+    elif args_iqtree:
+        doiqtree(out_f2p, out_put, args_iqtree_p, args_thread)
     elif args_raxml:
         doraxml(out_f2p, out_put, args_raxml_p, args_thread)
 
@@ -331,6 +349,7 @@ def starting_esrna(in_put, out_put,
                    args_trimal, args_trimal_p,
                    args_raxml, args_raxml_p,
                    args_fasttree, args_fasttree_p,
+                   args_iqtree,args_iqtree_p,
                    args_thread, args_extenddata):
     '''reconstruct phylogenetic tree by ssu rna extend method'''
     extend_check = checkFile(args_extenddata)
@@ -366,6 +385,8 @@ def starting_esrna(in_put, out_put,
     if args_fasttree:
         args_fasttree_p_add = "-nt " + args_fasttree_p.lstrip()
         doFastTree(out_f2p, out_put, args_fasttree_p_add, args_thread)
+    elif args_iqtree:
+        doiqtree(out_f2p, out_put, args_iqtree_p, args_thread)
     elif args_raxml:
         if args_raxml_p is raxmlpara_pro:
             args_raxml_p = raxmlpara_dna

diff --git a/physpetool/physpe/build.py b/physpetool/physpe/build.py
@@ -98,6 +98,10 @@ def start_args(input):
                               default=False, help='Reconstruct phylogenetic tree by FastTree.')
     advance_args.add_argument('--fasttree_p', action='store', dest='fasttree_parameter',
                               default='', help='Set FastTree advance parameters. ')
+    advance_args.add_argument('--iqtree', action='store_true', dest='iqtree',
+                              default=False, help='Reconstruct phylogenetic tree by iqtree.')
+    advance_args.add_argument('--iqtree_p', action='store', dest='iqtree_parameter',
+                              default='', help='Set iqtree advance parameters. ')
 
 
 def starting(args):
@@ -127,6 +131,7 @@ def starting(args):
                    args.trimal, args.trimal_parameter,
                    args.raxml, args.raxml_parameter,
                    args.fasttree, args.fasttree_parameter,
+                   args.iqtree, args.iqtree_parameter,
                    args.thread)
     elif args.HCP:
         setlogdir(out_put)
@@ -138,4 +143,5 @@ def starting(args):
                   args.trimal, args.trimal_parameter,
                   args.raxml, args.raxml_parameter,
                   args.fasttree, args.fasttree_parameter,
+                  args.iqtree, args.iqtree_parameter,
                   args.thread)
diff --git a/physpetool/softwares/iqtree b/physpetool/softwares/iqtree