Fixed EI-CoreBioinformatics#148; also, now metrics/score files will c…

…orrectly report whether a transcript was "reference" to begin with.

Mikado/loci/superlocus.py

@@ -1146,7 +1146,7 @@ def define_loci(self):
                                            use_transcript_scores=self._use_transcript_scores,
                                            stranded=self.stranded,
                                            verified_introns=self.locus_verified_introns,
-                                           logger = self.logger,
+                                           logger=self.logger,
                                            source=self.source
                                            )
                 else:
@@ -1163,6 +1163,7 @@ def define_loci(self):
                     self.logger.debug("Removing %s (primary: %s) as it has no reference transcripts",
                                       lid, self.loci[lid].primary_transcript_id)
                     del self.loci[lid]
+            self.logger.debug("Remaining loci in %s: %s", self.id, ",".join(list(self.loci.keys())))
 
         return
 
@@ -1428,4 +1429,4 @@ def id(self) -> str:
 
     @property
     def lost_transcripts(self):
-        return self.__lost.copy()
+        return self.__lost.copy()

Mikado/picking/picker.py

@@ -399,9 +399,9 @@ def __print_gff_headers(self, locus_out, score_keys):
             session = sqlalchemy.orm.sessionmaker(bind=engine)()
             dbutils.DBBASE.metadata.create_all(engine)
 
-        metrics = Superlocus.available_metrics[3:]
+        metrics = Superlocus.available_metrics[4:]
         metrics.extend(["external.{}".format(_.source) for _ in session.query(ExternalSource.source).all()])
-        metrics = Superlocus.available_metrics[:3] + sorted(metrics)
+        metrics = Superlocus.available_metrics[:4] + sorted(metrics)
 
         if self.sub_out != '':
             assert isinstance(self.sub_out, str)

Mikado/transcripts/transcript.py

@@ -259,6 +259,7 @@ def __init__(self, *args,
         # Mock setting of base hidden variables
         self.__id = ""
         self.__finalized = False  # Flag. We do not want to repeat the finalising more than once.
+        self.__source = None
         self._first_phase = None
         self.__logger = None
         self.__strand = self.__score = None
@@ -295,7 +296,7 @@ def __init__(self, *args,
 
         # Starting settings for everything else
         self.__chrom = None
-        self.source = source
+        self.source = self._original_source = source
         self.feature = "transcript"
         self.__start, self.__end = None, None
         self.attributes = dict()
@@ -331,12 +332,12 @@ def __init__(self, *args,
         self.__cds_introntree = IntervalTree()
         self._possibly_without_exons = False
         self._accept_undefined_multi = accept_undefined_multi
-        self.__is_reference = False
 
         if len(args) == 0:
             return
         else:
             self.__initialize_with_line(args[0])
+            self._original_source = self.source
 
         self.feature = intern(self.feature)
 
@@ -838,16 +839,18 @@ def get_internal_orf_beds(self):
 
                 yield new_row
 
-    @property
+    @Metric
     def is_reference(self):
         """Checks whether the transcript has been marked as reference by Mikado prepare"""
-        return self.__is_reference
 
-    @is_reference.setter
-    def is_reference(self, value):
-        if value not in (False, True):
-            raise TypeError("The 'is_reference' attribute must be boolean")
-        self.__is_reference = value
+        if self.json_conf is not None:
+            return self.original_source in self.json_conf.get("prepare", {}).get("files", {}).get(
+                "reference", {})
+        else:
+            return False
+
+    is_reference.category = "External"
+    is_reference.rtype = "bool"
 
     @property
     def frames(self):
@@ -1205,6 +1208,7 @@ def load_dict(self, state):
                 state[key] = intern(state[key])
             setattr(self, key, state[key])
 
+        self._original_source = self.source
         self.attributes = {}
         for key, val in state["attributes"].items():
             if val in ["True", "False"]:
@@ -1378,7 +1382,7 @@ def get_available_metrics(cls) -> list:
         #     inspect.getmembers(cls)))
         # assert "tid" in metrics and "parent" in metrics and "score" in metrics
         _metrics = sorted([metric for metric in metrics])
-        final_metrics = ["tid", "alias", "parent", "score"] + _metrics
+        final_metrics = ["tid", "alias", "parent", "original_source", "score"] + _metrics
         return final_metrics
 
     # ###################Class properties##################################
@@ -1558,6 +1562,23 @@ def parent(self, parent):
         if self.__parent:
             self.__parent = [intern(_) for _ in self.__parent]
 
+    @property
+    def source(self):
+        """Source of the transcript. Equivalent to the second field in the GFF/GTF files."""
+        return self.__source
+
+    @source.setter
+    def source(self, source):
+        if source is not None and not isinstance(source, str):
+            raise TypeError("Source values must be strings or None!")
+        self.__source = source
+
+    @property
+    def original_source(self):
+        """This property returns the original source assigned to the transcript (before Mikado assigns its own final
+        source value)."""
+        return self._original_source
+
     @property
     def gene(self):
 
@@ -2681,7 +2702,7 @@ def source_score(self):
 
         if self.json_conf is not None:
             return self.json_conf.get("prepare", {}).get("files", {}).get(
-                "source_score", {}).get(self.source, 0)
+                "source_score", {}).get(self.original_source, 0)
         else:
             return 0
 

Mikado/transcripts/transcript_methods/finalizing.py

@@ -731,9 +731,12 @@ def finalize(transcript):
         transcript.logger.debug("No predetermined has_stop_codon attribute for %s. Attributes: %s",
                                 transcript.id, transcript.attributes)
 
-    for prop in transcript.attributes:
+    for prop in list(transcript.attributes.keys()):
         if hasattr(transcript, prop):
-            setattr(transcript, prop, transcript.attributes[prop])
+            try:
+                setattr(transcript, prop, transcript.attributes[prop])
+            except AttributeError:  # Some instance attributes CANNOT be set from the attributes of the GTF
+                transcript.attributes.pop(prop)
 
     # transcript = __calc_cds_introns(transcript)
 

Singularity.def

@@ -0,0 +1,206 @@
+Bootstrap: docker
+From: centos:7
+OSversion: 7
+Include: yum wget
+# If you want the updates (available at the bootstrap date) to be installed
+# inside the container during the bootstrap instead of the General Availability
+# point release (7.x) then uncomment the following line
+
+# UpdateURL: http://yum-repos.hpccluster/centos/7/updates/$basearch/
+
+%test
+    python3.6 --version
+    pip3.6 --version
+    gcc --version
+    make --version
+
+    python3.6 -c "import numpy"
+
+
+%environment
+    export PATH="/usr/local/bin:$PATH:/usr/local/conda/bin/"
+    source /usr/local/conda/bin/activate
+    export AUGUSTUS_CONFIG_PATH=/opt/augustus-3.3/config/
+    export TRINITY_HOME=/usr/local/bin/trinityrnaseq/
+    export  PATH=$PATH:${TRINITY_HOME}
+    alias python=python3.6
+
+
+%post
+    mkdir /jic
+    mkdir /nbi
+    mkdir /tgac
+    mkdir /ei
+    mkdir /tsl
+    mkdir /opt/software
+
+    ### Install your packages ###
+    cd /opt/software/
+
+    yum -y install centos-release-scl
+    yum -y install scl-utils
+    yum -y install devtoolset-7-gcc*
+    scl enable devtoolset-7 bash
+    which gcc
+    gcc --version
+    mkdir -p /etc/profile.d/
+    echo -e '#!/bin/bash\nsource scl_source enable devtoolset-7' > /etc/profile.d/enablegcc7.sh
+
+    gcc --version
+    make --version
+
+    # Clean up yum
+    yum clean all
+
+    version=2.5.1
+    cd /usr/local/src
+    wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+    bash Miniconda3-latest-Linux-x86_64.sh -b -p /usr/local/conda
+    export PATH="/usr/local/conda/bin:$PATH"
+    source activate
+    conda install -y -c conda-forge pip
+
+    python3 --version
+    cd $(dirname $(which python3))
+    cd /opt/software/
+
+    # Install python requirements
+    wget https://github.com/lucventurini/mikado/blob/1.2.4/requirements.txt
+    cat requirements.txt
+    pip3 install -r requirements.txt
+
+    # Now install mikado
+    pip3.6 install --prefix=/usr/local/ mikado==1.2.4
+    # pip3.6 install --prefix=/usr/local/ networkit==4.6  # High-performance networks in Python
+    mikado --help
+
+    # Finally install EiAnnot
+    git clone --recursive https://github.com/lucventurini/ei-annotation.git
+    cd ei-annotation;
+    git checkout 0.0.2;
+    cd eicore;
+    python3 setup.py bdist_wheel;
+    pip3.6 install --prefix=/usr/local/ -U dist/*whl;
+    cd ../;
+    python3 setup.py bdist_wheel;
+    pip install --prefix=/usr/local/ -U dist/*whl;
+    cd /opt/software/
+
+
+%apprun snakemake
+	snakemake "@"
+
+%apprun hisat2-build
+	hisat2-build "@"
+
+%apprun jupyter
+	jupyter "@"
+
+%apprun gmap-build
+	gmap-build "@"
+
+%apprun gmap
+	gmap "@"
+
+%apprun gsnap
+	gsnap "@"
+
+%apprun mikado
+	mikado "@"
+
+%apprun samtools
+	samtools "@"
+
+%apprun portcullis
+	portcullis "@"
+
+%apprun junctools
+	junctools "@"
+
+%apprun stringtie
+	stringtie "@"
+
+%apprun class
+	class "@"
+
+%apprun hisat2
+	hisat2 "@"
+
+%apprun augustus
+        /opt/augustus-3.3/bin/augustus "@"
+
+%apprun filterBam
+	/opt/augustus-3.3/bin/filterBam "@"
+
+%apprun aln2wig
+	/opt/augustus-3.3/bin/aln2wig "@"
+
+%apprun joingenes
+	/opt/augustus-3.3/bin/joingenes "@"
+
+%apprun etraining
+	/opt/augustus-3.3/bin/etraining "@"
+
+%apprun bam2hints
+	/opt/augustus-3.3/bin/bam2hints "@"
+
+%apprun fastBlockSearch
+	/opt/augustus-3.3/bin/fastBlockSearch "@"
+
+%apprun homGeneMapping
+	/opt/augustus-3.3/bin/homGeneMapping "@"
+
+%apprun prepareAlign
+	prepareAlign "@"
+
+%apprun utrrnaseq
+	utrrnaseq "@"
+
+%apprun paftools
+	k8 $(which paftools.js) "@"
+
+%apprun k8
+	k8 "@"
+
+%apprun eiannot
+	eiannot "@"
+
+%apprun strawberry
+	strawberry "@"
+
+%apprun class
+	class "@"
+
+%apprun scallop
+	scallop "@"
+
+%apprun ruby
+	ruby "@"
+
+%apprun STAR
+	STAR "@"
+
+%apprun STARlong
+	STARlong "@"
+
+%apprun diamond
+    diamond "@"
+
+%apprun prinseq
+    /usr/local/bin/prinseq-lite-0.20.4/prinseq-lite.pl "@"
+
+%apprun "prinseq-lite.pl"
+    /usr/local/bin/prinseq-lite-0.20.4/prinseq-lite.pl "@"
+
+%apprun gt
+    gt "@"
+
+%apprun gffread
+    gffread "@"
+
+%apprun cufflinks
+    cufflinks "@"
+
+%apprun cuffcompare
+    cuffcompare "@"
+