Fix utilities and minor miscellaneous issues

Mikado/configuration/scoring_files/HISTORIC/insects.yaml

@@ -41,10 +41,6 @@ scoring:
     filter: {operator: lt, value: 3}
     rescaling: target
     value: 1
-  three_utr_num:
-    filter: {operator: lt, value: 3}
-    rescaling: target
-    value: 1
   five_utr_num:
     filter: {operator: lt, value: 4}
     rescaling: target

Mikado/subprograms/__init__.py

@@ -2,7 +2,6 @@
 
 """This module contains the subprograms launched by the Mikado suite"""
 
-# from ..parsers import GTF, GFF, to_gff
 # noinspection PyPep8
 from . import configure
 # noinspection PyPep8

util/calculate_distances.py

@@ -12,6 +12,8 @@
 from scipy.stats.mstats import mquantiles
 from numpy import arange
 
+from Mikado.scales.reference_preparation.indexing import load_index
+from Mikado.utilities import log_utils
 from Mikado.utilities.log_utils import LoggingConfiguration
 
 
@@ -109,7 +111,7 @@ def main():
     args = parser.parse_args()
 
     conf = LoggingConfiguration(log=args.log, log_level=args.log_level)
-    logger = Mikado.utilities.log_utils.create_logger_from_conf(conf, "geomancer", mode="w")
+    logger = log_utils.create_logger_from_conf(conf, "geomancer", mode="w")
     logger.info("Starting to load the GFF3 index")
     with open(args.gff3) as gff3:
         namespace = argparse.Namespace
@@ -119,7 +121,7 @@ def main():
         # Use Mikado compare functions to load the index from the GFF3
         # "genes" is a dictionary of Gene objects, having as keys the gene names
         # "positions" is a dictionary of the form: [chrom][(start, end)] = [GID1, GID2, ...]
-        genes, positions = Mikado.scales.compare.load_index(args, logger)
+        genes, positions = load_index(args, logger)
         # Create a dictionary of interval trees, one per chromosome
         indexer = collections.defaultdict(list).fromkeys(positions)
         for chrom in indexer:

util/create_model.py

@@ -4,7 +4,6 @@
 import argparse
 import csv
 import pickle
-from sklearn.ensemble import RandomForestRegressor
 import numpy as np
 from scipy.stats import hmean
 from Mikado.scales.resultstorer import ResultStorer

util/trim_long_introns.py

@@ -3,13 +3,14 @@
 from Mikado.loci import Transcript, Gene
 import argparse
 import sys
+
+from Mikado.parsers import parser_factory
 from Mikado.parsers.GFF import GFF3
-from Mikado.utilities import to_gff
-from intervaltree import Interval
-from Mikado.utilities.log_utils import create_default_logger
 
 __doc__ = """This script truncates transcript with UTR exons separated by long introns."""
 
+from Mikado.utilities import Interval
+
 
 def remove_introns_from_transcr(transcript, args):
     transcript.finalize()
@@ -78,7 +79,7 @@ def main():
     parser = argparse.ArgumentParser(__doc__)
     parser.add_argument("-mi", "--max-intron", default=10000, dest="max_intron",
                         type=int, help="Maximum intron length for UTR introns.")
-    parser.add_argument("gff", type=to_gff)
+    parser.add_argument("gff", type=parser_factory)
     parser.add_argument("out", default=sys.stdout, type=argparse.FileType("wt"), nargs="?")
     args = parser.parse_args()