remove dead code

util/get_query_aminoacids_table.py

@@ -3,9 +3,6 @@
 
 def get_query_aminoacids_table(sequence):
     if not hasattr(sequence.seq, "query_aminoacids_table"):
-        try:
-            sequence.seq.query_aminoacids_table = [translate_to_aminoacids(sequence.seq, i) for i in range(3)]
-        except Bio.Data.CodonTable.TranslationError as e:
-            sequence.seq.query_aminoacids_table = e
+        sequence.seq.query_aminoacids_table = [translate_to_aminoacids(sequence.seq, i) for i in range(3)]
 
     return sequence.seq.query_aminoacids_table

util/log.py

@@ -1,8 +1,4 @@
-import inspect
 import logging
-import os
-import select
-import subprocess
 
 FORMAT = '%(asctime)s - %(name)s - %(levelname)s - %(message)s'
 
@@ -12,46 +8,5 @@
 def error(error):
     logger.error(error)
 
-def warning(warning):
-    logger.warning(warning)
-
 def info(info):
     logger.info(info)
-
-def debug(debug):
-    logger.debug(debug)
-
-def logging_call(popenargs, output_stream, error_function):
-
-    """
-    Call a subprocess and log the output to stderr to a logfile.
-
-    Args:
-        popenargs: The arguments to run in the subprocess
-        output_stream: The stream to pipe stdout to
-
-    Returns:
-        A path to the SAM output file created.
-    """
-    process = subprocess.Popen(" ".join(popenargs), 
-                               stdout=output_stream, 
-                               stderr=subprocess.PIPE,
-                               shell=True,
-                               env=os.environ)
-
-    # Get the caller of this function, 
-    # so we can report where we're logging from.
-    current_frame = inspect.currentframe()
-    calling_frame = inspect.getouterframes(current_frame, 2)
-
-    def check_io():
-           while True:
-                err = process.stderr.readline().decode()
-                if err:
-                    error_function("From " + calling_frame[1][3] + " - " + err.rstrip())
-                else:
-                    break
-
-    # keep checking stdout/stderr until the child exits
-    while process.poll() is None:
-        check_io()

util/subtypes.py

@@ -61,31 +61,3 @@ def convert_from_aligned_to_reference(position, alignment):
             subtype_pos += 1
         if alignment[1][i] != "-":
             hxb2_pos += 1
-
-def map_hxb2_positions_to_subtype(subtype):
-    """
-    Convert position numbers in HXB2 to the equivalent in another subtype.
-
-    Args:
-        subtype: subtype position to convert to
-    """
-
-    sequences = [HXB2(), subtype_sequence(subtype)]
-    alignment = wrappers.mafft(sequences)
-    return coords.map_positions(alignment[0], alignment[1])
-
-def map_subtype_positions_to_hxb2(orientation, subtype):
-    """
-    Convert position numbers in HXB2 to the equivalent in another subtype.
-
-    Args:
-        subtype: subtype position to convert to
-    """
-
-    sequences = [subtype_sequence(subtype), HXB2()]
-    if orientation == "reverse":
-        sequences = [SeqRecord.SeqRecord(Seq.reverse_complement(s.seq),
-                                         id = s.id, name = s.name) for s in sequences]
-
-    alignment = wrappers.mafft(sequences)
-    return coords.map_positions(alignment[0], alignment[1])