Finished sequence docstrings. Fixed tests and refactoring consequences.

#268

trifusion/TriSeq.py

@@ -209,13 +209,13 @@ def main_parser(arg, alignment_list):
     if arg.contain_filter:
         print_col("Filtering alignment(s) including a taxa group", GREEN,
                   quiet=arg.quiet)
-        alignments.filter_by_taxa("Contain", arg.contain_filter, pbar=pbar)
+        alignments.filter_by_taxa(arg.contain_filter, "Contain", pbar=pbar)
 
     # Filter by alignments that exclude taxa
     if arg.exclude_filter:
         print_col("Filtering alignments excluding a taxa group", GREEN,
                   quiet=arg.quiet)
-        alignments.filter_by_taxa("Exclude", arg.exclude_filter, pbar=pbar)
+        alignments.filter_by_taxa(arg.exclude_filter, "Exclude", pbar=pbar)
 
     # Filter by codon position
     if arg.codon_filter:
@@ -248,8 +248,7 @@ def main_parser(arg, alignment_list):
     # Concatenation
     if not arg.conversion and not arg.reverse and not arg.consensus:
         print_col("Concatenating", GREEN, quiet=arg.quiet)
-        alignments = alignments.concatenate(alignment_name=os.path.basename(
-            outfile), pbar=pbar)
+        alignments = alignments.concatenate(pbar=pbar)
 
         # Concatenate zorro files
         if arg.zorro:

trifusion/app.py

@@ -4571,8 +4571,6 @@ def popup_info(self, value):
                     self.active_file_inf["aln_format"]
                 content.ids.seq_type.text = "%s" % \
                     self.active_file_inf["seq_type"]
-                content.ids.is_aln.text = "%s" % \
-                    self.active_file_inf["is_aln"]
                 content.ids.seq_size.text = "%s" % \
                     self.active_file_inf["aln_len"]
                 content.ids.n_taxa.text = "%s" % \
@@ -10589,8 +10587,6 @@ def get_file_information(self, file_name=None, mode="alignment"):
                 - seq_type: The sequence type. If DNA, RNA, Protein.
                 - n_taxa: Number of taxa
                 - aln_len: Length of the alignment
-                - is_aln: If the input file is in alignment format of
-                non-aligned sequence set format
                 - model: The model of sequence evolution, if applicable.
                  This is
                 usually only present on Nexus input format
@@ -10619,9 +10615,6 @@ def get_file_information(self, file_name=None, mode="alignment"):
                 file_inf["n_taxa"] = len([x for x in
                     aln.taxa_list if x in self.active_taxa_list])
 
-                # Get if is alignment
-                file_inf["is_aln"] = str(aln.is_alignment)
-
                 # Get length of largest sequence if not aligned, or
                 # alignment length
                 file_inf["aln_len"] = aln.locus_length

trifusion/data/resources/background_tasks.py

@@ -59,7 +59,7 @@ def load_proc(aln_list, file_list, nm, queue):
     try:
         if aln_list:
             aln_list.add_alignment_files(file_list,
-                                         shared_namespace=nm)
+                                         ns=nm)
             aln_obj = aln_list
         else:
             aln_obj = AlignmentList(file_list, shared_namespace=nm)
@@ -410,7 +410,7 @@ def filter_aln(aln, table_out="_filter"):
             # Get taxa list from taxa groups
             ns.main_msg = "Filter (by taxa)"
             taxa_list = taxa_groups[taxa_filter_settings[1]]
-            aln.filter_by_taxa(taxa_filter_settings[0], taxa_list, ns=ns)
+            aln.filter_by_taxa(taxa_list, taxa_filter_settings[0], ns=ns)
 
         # Filter codon positions
         if secondary_options["codon_filter"]:
@@ -470,8 +470,7 @@ def concatenation(aln, table_in=""):
             zorro_data = data.Zorro(aln, zorro_suffix)
             zorro_data.write_to_file(output_file)
 
-        aln = aln.concatenate(alignment_name=basename(output_file),
-                              table_in=table_in, ns=ns)
+        aln = aln.concatenate(table_in=table_in, ns=ns)
 
         # Sets the single alignment to True, for other method to be aware of
         # this
@@ -793,8 +792,7 @@ def writer(aln, filename=None, suffix_str="", conv_suffix="",
                                                    table_out=suffix[1:])
                     if main_operations["concatenation"]:
                         ns.main_msg = "Concatenation"
-                        main_aln = aln_object.concatenate(table_in=suffix[1:],
-                                                          ns=ns)
+                        main_aln = aln_object.concatenate(ns=ns)
 
                 ns.main_msg = "Collapse"
                 main_aln.collapse(haplotype_name=hap_prefix,

trifusion/process/base.py

@@ -69,7 +69,7 @@
 
 
 class CleanUp(object):
-    """Decorator class that handles temporary data for TriSeq and TriStats
+    """Decorator class that handles temporary data for TriSeq and TriStats.
     
     This decorator class wraps the main execution functions of TriSeq and
     TriStats programs. The __init__ requires only the function reference,
@@ -108,7 +108,7 @@ def __init__(self, func):
         self.idx = 0 if self.func.__name__ == "main_parser" else 2
 
     def __call__(self, *args):
-        """Wraps the call of `func`
+        """Wraps the call of `func`.
         
         When the main `func` is called, this code is wrapped around its
         execution. This mainly ensures that the temporary data stored in
@@ -165,7 +165,7 @@ def __call__(self, *args):
 
 
 def merger(ranges):
-    """Generator that merges continuous ranges of tuples in a list
+    """Generator that merges continuous ranges of tuples in a list.
     
     Parameters
     ----------
@@ -213,7 +213,7 @@ def has_colours(stream):
 
 
 def print_col(text, color, i=0, quiet=False):
-    """Custom print function for terminal updates of CLI programs
+    """Custom print function for terminal updates of CLI programs.
     
     This print function homogenizes the progress logging of all CLI programs
     while providing some freedom on the formatting of the progress message,
@@ -261,7 +261,7 @@ def print_col(text, color, i=0, quiet=False):
 class Base(object):
 
     def autofinder(self, reference_file):
-        """Autodetects format, missing data symbol and sequence type
+        """Autodetects format, missing data symbol and sequence type.
         
         Attempts to find the file format, missing data symbol and sequence
         type from a reference file. Due to performance reasons, this function
@@ -393,7 +393,7 @@ def autofinder(self, reference_file):
     @staticmethod
     def get_loci_taxa(loci_file):
         """
-        Get the list of taxa from a .loci file
+        Get the list of taxa from a .loci file.
         
         This is required prior to parsing the alignment in order to 
         correctly add missing data when certain taxa are not present in 
@@ -429,7 +429,7 @@ def get_loci_taxa(loci_file):
     @staticmethod
     def guess_code(sequence):
         """
-        Guess the sequence type, i.e. protein
+        Guess the sequence type, i.e. protein.
         
         Guesses the code of the provided `sequence`, that is, if it is a
         DNA or Protein sequence based on the first sequence of 
@@ -498,7 +498,7 @@ def guess_code(sequence):
     @staticmethod
     def rm_illegal(taxon_string):
         """
-        Removes illegal characters from taxon name
+        Removes illegal characters from taxon name.
         
         The illegal characters are defined in the `illegal_chars`
         variable
@@ -526,7 +526,7 @@ def rm_illegal(taxon_string):
     @staticmethod
     def duplicate_taxa(taxa_list):
         """
-        Identified duplicate items in a list
+        Identified duplicate items in a list.
         
         Used to detect, for instance, duplicated taxa in the Alignment object
         
@@ -549,7 +549,7 @@ def duplicate_taxa(taxa_list):
     @staticmethod
     def read_basic_csv(file_handle):
         """
-        Reads a basic CSV into a list
+        Reads a basic CSV into a list.
         
         Parses a simples CSV file with only one column and one
         or more lines while stripping whitespace.