Starts to implement a plotting function for ALStructure

Author: StuntsPT

structure_threader/plotter/structplot.py

@@ -1,6 +1,6 @@
 #!/usr/bin/python3
 
-# Copyright 2015-2018 Francisco Pina Martins <[email protected]>
+# Copyright 2015-2019 Francisco Pina Martins <[email protected]>
 # and Diogo N. Silva <[email protected]>
 # This file is part of structure_threader.
 # structure_threader is free software: you can redistribute it and/or modify
@@ -100,7 +100,8 @@ def __init__(self, kfile, fmt, get_indv=False):
 
         parse_methods = {"structure": self._parse_structure,
                          "faststructure": self._parse_faststructure,
-                         "maverick": self._parse_maverick}
+                         "maverick": self._parse_maverick,
+                         "alstructure": self._parse_alstructure}
 
         # Let the parsing begin
         parse_methods[self.fmt]()
@@ -302,6 +303,22 @@ def _parse_maverick(self):
                                            dtype="|U20",
                                            skip_header=1).T[1].T)
 
+        def _parse_alstructure(self):
+            """
+            Parses the meanQ array of a single ALStructure output file
+            Sets the qvals array, the number of individual taxa (nind)
+            and number of clusters (k)
+            """
+
+            self.qvals = np.genfromtxt(self.file_path)
+            self.qvals = np.delete(self.qvals, 0, 0)
+            self.qvals = np.delete(self.qvals, 0, 1)
+
+            try:
+                self.nind, self.k = self.qvals.shape
+            except ValueError:
+                self.k = 1
+
 
 class PlotList(AuxSanity):
     """

structure_threader/structure_threader.py

@@ -218,6 +218,9 @@ def create_plts(wrapped_prog, bestk, arg):
         plt_files = [os.path.join(os.path.join(arg.outpath, "mav_K" + str(i)),
                                   "outputQmatrix_ind_K" + str(i) + ".csv")
                      for i in arg.k_list]
+    elif wrapped_prog == "alstructure":
+        plt_files = [os.path.join(os.path.join(arg.outpath, "alstr_K" + str(i)))
+                     for i in arg.k_list]
 
     else:
         plt_files = [os.path.join(arg.outpath, "fS_run_K.") + str(i) + ".meanQ"
@@ -288,9 +291,9 @@ def full_run(arg):
         wrapped_prog = "structure"
     elif "-als" in sys.argv:
         wrapped_prog = "alstructure"
-        arg.threads = 1
-        arg.notests = True
-        arg.k_list = [x for x in arg.k_list if x != 1]
+        arg.threads = 1  # Depencency handling forces this
+        arg.notests = True  # No way to perform K tests with ALS
+        arg.k_list = [x for x in arg.k_list if x != 1]  # ALS can't have K=1
 
     structure_threader(wrapped_prog, arg)