remove reading_frames_single_stranded function

intact/intact.py

@@ -474,78 +474,6 @@ def has_rev_response_element(alignment, rre_locus, rre_tolerance):
     return None
 #/end def has_rev_response_element
 
-def reading_frames_single_stranded(alignment, sequence, length):
-    """
-    Find all reading frames longer than length in the forward strand
-    of the given sequence.
-
-    Args:
-        sequence: the sequence to check.
-        length: the minimum nucleotide length of a reading frame
-
-    Returns:
-        A list of tuples of (frame_start, frame_end, frame_deletions, frame_insertions)
-    """
-
-    # figure out where the query starts w.r.t HXB2 in case full
-    # genome consensus is not being used
-    # offset = re.search(r'[^-]', str(alignment[1].seq)).start()
-
-    # for each position in the query, figure out how many inserts and
-    # deletes we've seen with respect to the reference
-    delete_offset = []
-    insert_offset = []
-    delete_count = 0
-    insert_count = 0
-
-    for i in range(len(alignment[0])):
-        if alignment[1][i] == "-":
-            delete_count += 1
-            continue
-        if alignment[0][i] == "-":
-            insert_count += 1
-        delete_offset.append(delete_count)
-        insert_offset.append(insert_count)
-
-    long_frames = []
-
-    for frame in range(0, 3):
-
-        for_translation = sequence.seq[frame:]
-        current_length = len(for_translation)
-        for _ in range(3 - current_length % 3):
-            for_translation += 'N'
-
-        protein = Seq.translate(for_translation)
-
-        current_start = 0
-        current_len = 0
-
-
-        for i, elem in enumerate(protein):
-            if elem == "*":
-                fs = current_start * 3 + 0 + frame
-                frame_start = fs + delete_offset[fs] - insert_offset[fs]
-                fe = i * 3 + 1 + frame
-                frame_end = fe + delete_offset[fe] - insert_offset[fe]
-
-                if current_len * 3 >= length:
-                    long_frames.append(
-                        ReceivedORF(frame_start,
-                                    frame_end + 1,
-                                    delete_offset[fe] - delete_offset[fs],
-                                    insert_offset[fe] - insert_offset[fs])
-                    )
-                current_len = 0
-                continue
-            elif current_len == 0:
-                current_start = i
-
-            current_len += 1
-
-    long_frames.sort(key=lambda x: x.start)
-
-    return long_frames
 
 def alignment_score(alignment):
     """