Version 0.12.0: new definition for _, small BF

EI-CoreBioinformatics · Feb 15, 2016 · b71ba96 · b71ba96
1 parent 63840af
commit b71ba96
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Showing 4 changed files with 5 additions and 5 deletions.
diff --git a/mikado_lib/scales/assigner.py b/mikado_lib/scales/assigner.py
@@ -512,7 +512,7 @@ def compare(cls, prediction: Transcript, reference: Transcript) -> (ResultStorer
         - f    gene fusion - in this case, this ccode will be followed by the
         ccodes of the matches for each gene, separated by comma
         - _    Complete match, for monoexonic transcripts
-        (nucleotide F1>=95% - i.e. min(precision,recall)>=90.4%
+        (nucleotide F1>=80% - i.e. min(precision,recall)>=66.7%
         - m    Exon overlap between two monoexonic transcripts
         - n    Potential extension of the reference - we have added new splice junctions
         *outside* the boundaries of the transcript itself
@@ -583,7 +583,7 @@ def compare(cls, prediction: Transcript, reference: Transcript) -> (ResultStorer
             else:
                 ccode = "c"  # We will set this to x at the end of the function
 
-        elif junction_f1 == 1 and nucl_f1 >= 0.95:
+        elif junction_f1 == 1 and nucl_f1 >= 0.80:
             reference_exon = reference.exons[0]
             ccode = "_"  # We have recovered all the junctions
             # if prediction.strand == reference.strand or prediction.strand is None:

diff --git a/mikado_lib/serializers/blast_serializer/xml_serialiser.py b/mikado_lib/serializers/blast_serializer/xml_serialiser.py
@@ -6,7 +6,7 @@
 import functools
 
 import sqlalchemy
-from Bio import SeqIO
+# from Bio import SeqIO
 import sqlalchemy.exc
 from Bio.Blast.NCBIXML import parse as xparser
 from sqlalchemy.orm.session import sessionmaker

diff --git a/mikado_lib/subprograms/serialise.py b/mikado_lib/subprograms/serialise.py
@@ -309,7 +309,7 @@ def serialise_parser():
                       """)
 
     blast = parser.add_argument_group()
-    blast.add_argument("--max_target_seqs", type=int, default=sys.maxsize,
+    blast.add_argument("--max_target_seqs", type=int, default=None,
                        help="Maximum number of target sequences.")
     blast.add_argument("--blast_targets", default=None, type=to_seqio, help="Target sequences")
     blast.add_argument("--discard-definition", action="store_true", default=False,

diff --git a/setup.py b/setup.py
@@ -15,7 +15,7 @@
 setup(
 
     name="Mikado",
-    version="0.11.1",
+    version="0.12.0",
 
     description="A Python3 annotation program to select the best gene model in each locus",
     long_description=long_description,