Issue 401 daijin class2 (#402)

Coordinate changes to the configuration files with daijin - The parameter for the assembler 'class' has changed in the configuration file to 'class2' but this was not picked up by changes to daijin. - Removes a noisy print command in the BED12 parser. - Update the tutorial and daijin's CLI. - Update daijin.yaml in accord to Daijin's class2 program loading. Closes #401
EI-CoreBioinformatics · Apr 12, 2021 · e641cf9 · e641cf9
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diff --git a/Mikado/daijin/__init__.py b/Mikado/daijin/__init__.py
@@ -189,7 +189,7 @@ def create_config_parser():
                         required=False, default=[], nargs="*",
                         help="Aligner(s) to use for long reads. Choices: %(choices)s")
     parser.add_argument("-as", "--assemblers", dest="asm_methods", required=False,
-                        choices=["class", "cufflinks", "stringtie", "trinity", "scallop"],
+                        choices=["class2", "cufflinks", "stringtie", "trinity", "scallop"],
                         default=[], nargs="*", help="Assembler(s) to use for the analysis. Choices: %(choices)s")
     mikado = parser.add_argument_group("Options related to the Mikado phase of the pipeline.")
     # scoring = parser.add_argument_group("Options related to the scoring system")

diff --git a/Mikado/daijin/assemble.smk b/Mikado/daijin/assemble.smk
@@ -168,7 +168,7 @@ def makeAsmRunArray(assembler):
 CUFFLINKS_RUNS = makeAsmRunArray("cufflinks")
 TRINITY_RUNS = makeAsmRunArray("trinity")
 STRINGTIE_RUNS = makeAsmRunArray("stringtie")
-CLASS_RUNS = makeAsmRunArray("class")
+CLASS_RUNS = makeAsmRunArray("class2")
 SCALLOP_RUNS = makeAsmRunArray("scallop")
 
 SAMPLE_STR = ",".join(SAMPLES)
@@ -181,12 +181,12 @@ for a in ALIGN_RUNS :
     PORTCULLIS_IN[a] = os.path.join(ALIGN_DIR, "output", a + ".sorted.bam")
 
 aln_abrv = {"tophat":"tph", "star":"sta", "gsnap":"gsp", "hisat":"hst", "gmap":"gmp"}
-asm_abrv = {"cufflinks":"cuf", "stringtie":"stn", "class":"cls", "trinity":"trn", "scallop": "scl"}
+asm_abrv = {"cufflinks":"cuf", "stringtie":"stn", "class2":"cls", "trinity":"trn", "scallop": "scl"}
 
 GTF_ASSEMBLY_METHODS = []
 GFF_ASSEMBLY_METHODS = []
 for asm in ASSEMBLY_METHODS:
-    if asm in ("cufflinks", "stringtie", "class", "scallop"):
+    if asm in ("cufflinks", "stringtie", "class2", "scallop"):
         GTF_ASSEMBLY_METHODS.append(asm)
     elif asm == "trinity":
         GFF_ASSEMBLY_METHODS.append(asm)
@@ -447,7 +447,7 @@ def gmap_intron_lengths(command, MAX_INTRON):
 # Rules
 
 localrules: mikado_cfg, tophat_all, gsnap_all, gsnap_index, star_all, hisat_all, cufflinks_all, trinity_all,
-            stringtie_all, class_all, lr_gmap_all, lr_star_all, clean, align_all, lreads_all, asm_all, all
+            stringtie_all, class2_all, lr_gmap_all, lr_star_all, clean, align_all, lreads_all, asm_all, all
 
 rule all:
     input:
@@ -868,28 +868,28 @@ rule stringtie_all:
     output: os.path.join(ASM_DIR, "stringtie.done")
     shell: "touch {output}"
 
-rule asm_class:
+rule asm_class2:
     input:
         bam=os.path.join(ALIGN_DIR, "output", "{alrun}.sorted.bam"),
         align=rules.align_all.output,
         ref=rules.uncompress_genome.output.genome
     output:
-        link=os.path.join(ASM_DIR, "output", r"class-{run2,\d+}-{alrun}.gtf"),
-        gtf=os.path.join(ASM_DIR, "class", r"class-{run2,\d+}-{alrun}", r"class-{run2}-{alrun}.gtf")
+        link=os.path.join(ASM_DIR, "output", r"class2-{run2,\d+}-{alrun}.gtf"),
+        gtf=os.path.join(ASM_DIR, "class2", r"class2-{run2,\d+}-{alrun}", r"class2-{run2}-{alrun}.gtf")
     params:
-        outdir=os.path.join(ASM_DIR, "class", "class-{run2}-{alrun}"),
-        load=loadPre(config, "class"),
-        extra=lambda wildcards: config["asm_methods"]["class"][int(wildcards.run2)],
-        link_src=os.path.join("..", "class", "class-{run2}-{alrun}", "class-{run2}-{alrun}.gtf")
-    log: os.path.join(ASM_DIR, "logs", "class", "class-{run2}-{alrun}.log")
+        outdir=os.path.join(ASM_DIR, "class2", "class2-{run2}-{alrun}"),
+        load=loadPre(config, "class2"),
+        extra=lambda wildcards: config["asm_methods"]["class2"][int(wildcards.run2)],
+        link_src=os.path.join("..", "class2", "class2-{run2}-{alrun}", "class2-{run2}-{alrun}.gtf")
+    log: os.path.join(ASM_DIR, "logs", "class2", "class2-{run2}-{alrun}.log")
     threads: THREADS
-    message: "Using class to assemble (run {wildcards.run2}): {input.bam}"
+    message: "Using class2 to assemble (run {wildcards.run2}): {input.bam}"
     shell: "{params.load} {CLASS} --clean --force -c \"{params.extra}\" -p {threads} {input.bam} > {output.gtf} \
 2> {log} && ln -sf {params.link_src} {output.link} && touch -h {output.link}"
 
-rule class_all:
-    input: expand(os.path.join(ASM_DIR, "output", "class-{run2}-{alrun}.gtf"), run2=CLASS_RUNS, alrun=ALIGN_RUNS)
-    output: os.path.join(ASM_DIR, "class.done")
+rule class2_all:
+    input: expand(os.path.join(ASM_DIR, "output", "class2-{run2}-{alrun}.gtf"), run2=CLASS_RUNS, alrun=ALIGN_RUNS)
+    output: os.path.join(ASM_DIR, "class2.done")
     shell: "touch {output}"
 
 rule lr_gmap:

diff --git a/Mikado/parsers/bed12.py b/Mikado/parsers/bed12.py
@@ -503,7 +503,6 @@ def _parse_attributes(self, attributes):
         """
 
         self.attribute_order = []
-        print("Parsing", attributes)
 
         infolist = self._attribute_pattern.findall(attributes.rstrip().rstrip(";"))
 

diff --git a/docs/Tutorial/Daijin_tutorial.rst b/docs/Tutorial/Daijin_tutorial.rst
@@ -199,7 +199,7 @@ Now we will configure Daijin for the run::
        -m permissive --sample-sheet sample_sheet.tsv \
        --flank 500 -i 50 26000 --threads 2 \
        --genome Reference/Drosophila_melanogaster.BDGP6.dna.toplevel.fa \
-       -al hisat -as class stringtie -od Dmelanogaster --name Dmelanogaster \
+       -al hisat -as class2 stringtie -od Dmelanogaster --name Dmelanogaster \
        -o daijin.toml --prot-db Reference/Aedes_aegypti.fasta;
 
 This will create three files in the working directory:
@@ -211,7 +211,7 @@ This will create three files in the working directory:
 .. code-block:: yaml
 
     blast: 'source blast-2.3.0'
-    class: 'source class-2.12'
+    class2: 'source class-2.12'
     cufflinks: ''
     gmap: ''
     hisat: 'source HISAT-2.0.4'
@@ -256,15 +256,15 @@ You can also ask Daijin to display the steps to be executed, inclusive of their
 
 When Daijin is finished, have a look inside the folder Dmelanogaster/3-assemblies/output/; you will find the following GTF files:
 
-* Dmelanogaster/3-assemblies/output/class-0-hisat-ERR1662533-0.gtf
-* Dmelanogaster/3-assemblies/output/class-0-hisat-ERR1662534-0.gtf
+* Dmelanogaster/3-assemblies/output/class2-0-hisat-ERR1662533-0.gtf
+* Dmelanogaster/3-assemblies/output/class2-0-hisat-ERR1662534-0.gtf
 * Dmelanogaster/3-assemblies/output/stringtie-0-hisat-ERR1662533-0.gtf
 * Dmelanogaster/3-assemblies/output/stringtie-0-hisat-ERR1662534-0.gtf
 
 These are standard `GTF files <http://www.ensembl.org/info/website/upload/gff.html>`_ reporting the assembled transcripts for each method. We can have a feel for how they compare with our reference annotation by, again, using ``mikado util stats``. Conveniently, Daijin has already performed this analysis for us, and the files will be present in the same folder:
 
-* Dmelanogaster/3-assemblies/output/class-0-hisat-ERR1662533-0.gtf.stats
-* Dmelanogaster/3-assemblies/output/class-0-hisat-ERR1662534-0.gtf.stats
+* Dmelanogaster/3-assemblies/output/class2-0-hisat-ERR1662533-0.gtf.stats
+* Dmelanogaster/3-assemblies/output/class2-0-hisat-ERR1662534-0.gtf.stats
 * Dmelanogaster/3-assemblies/output/stringtie-0-hisat-ERR1662533-0.gtf.stats
 * Dmelanogaster/3-assemblies/output/stringtie-0-hisat-ERR1662534-0.gtf.stats
 
@@ -273,9 +273,9 @@ Daijin has also created a summary of these statistics in Dmelanogaster/3-assembl
 +------------------------------------------+---------+--------------------+---------------+------------------------+-----------------------+--------------------------+---------+------------------------+-----------------+
 | File                                     |   genes |   monoexonic_genes |   transcripts |   transcripts_per_gene |   transcript_len_mean |   monoexonic_transcripts |   exons |   exons_per_transcript |   exon_len_mean |
 +==========================================+=========+====================+===============+========================+=======================+==========================+=========+========================+=================+
-| class-0-hisat-ERR1662533-0.gtf.stats     |   11535 |                852 |         13958 |                   1.2  |               1429.86 |                      852 |   57554 |                   4.12 |          346.77 |
+| class2-0-hisat-ERR1662533-0.gtf.stats     |   11535 |                852 |         13958 |                   1.2  |               1429.86 |                      852 |   57554 |                   4.12 |          346.77 |
 +------------------------------------------+---------+--------------------+---------------+------------------------+-----------------------+--------------------------+---------+------------------------+-----------------+
-| class-0-hisat-ERR1662534-0.gtf.stats     |   11113 |                884 |         13341 |                   1.19 |               1448.07 |                      884 |   55123 |                   4.13 |          350.47 |
+| class2-0-hisat-ERR1662534-0.gtf.stats     |   11113 |                884 |         13341 |                   1.19 |               1448.07 |                      884 |   55123 |                   4.13 |          350.47 |
 +------------------------------------------+---------+--------------------+---------------+------------------------+-----------------------+--------------------------+---------+------------------------+-----------------+
 | stringtie-0-hisat-ERR1662533-0.gtf.stats |   15490 |               6252 |         18995 |                   1.22 |               1668.17 |                     6446 |   63798 |                   3.36 |          496.67 |
 +------------------------------------------+---------+--------------------+---------------+------------------------+-----------------------+--------------------------+---------+------------------------+-----------------+
@@ -292,8 +292,8 @@ We can assess the similarity of these assemblies to the reference annotation by
   mkdir -p Comparisons;
   mikado compare -r Reference/Drosophila_melanogaster.BDGP6.89.gtf --index -l Reference/index.log;
   # Compare the CLASS2 assemblies against the reference
-  mikado compare -r Reference/Drosophila_melanogaster.BDGP6.89.gtf -l Comparisons/class_ERR1662533.log -o Comparisons/class_ERR1662533 -p Dmelanogaster/3-assemblies/output/class-0-hisat-ERR1662533-0.gtf;
-  mikado compare -r Reference/Drosophila_melanogaster.BDGP6.89.gtf -l Comparisons/class_ERR1662534.log -o Comparisons/class_ERR1662534 -p Dmelanogaster/3-assemblies/output/class-0-hisat-ERR1662534-0.gtf;
+  mikado compare -r Reference/Drosophila_melanogaster.BDGP6.89.gtf -l Comparisons/class2_ERR1662533.log -o Comparisons/class2_ERR1662533 -p Dmelanogaster/3-assemblies/output/class2-0-hisat-ERR1662533-0.gtf;
+  mikado compare -r Reference/Drosophila_melanogaster.BDGP6.89.gtf -l Comparisons/class2_ERR1662534.log -o Comparisons/class2_ERR1662534 -p Dmelanogaster/3-assemblies/output/class2-0-hisat-ERR1662534-0.gtf;
   # Compare the StringTie assemblies against the reference:
   mikado compare -r Reference/Drosophila_melanogaster.BDGP6.89.gtf -l Comparisons/stringtie_ERR1662534.log -o Comparisons/stringtie_ERR1662534 -p Dmelanogaster/3-assemblies/output/stringtie-0-hisat-ERR1662534-0.gtf;
   mikado compare -r Reference/Drosophila_melanogaster.BDGP6.89.gtf -l Comparisons/stringtie_ERR1662533.log -o Comparisons/stringtie_ERR1662533 -p Dmelanogaster/3-assemblies/output/stringtie-0-hisat-ERR1662533-0.gtf;

diff --git a/docs/Tutorial/daijin.yaml b/docs/Tutorial/daijin.yaml
@@ -6,7 +6,7 @@ align_methods:
   hisat:
   - ''
 asm_methods:
-  class:
+  class2:
   - ''
   stringtie:
   - ''
@@ -23,7 +23,7 @@ load:
   #  Commands to use to load/select the versions of the programs to use. Leave an empty
   #  string if no loading is necessary.
   blast: 'source blast+-2.3.0'
-  class: 'source class-2.12'
+  class2: 'source class-2.12'
   cufflinks: ''
   gmap: ''
   hisat: 'source HISAT-2.0.4'

diff --git a/docs/Usage/Daijin.rst b/docs/Usage/Daijin.rst
@@ -159,7 +159,7 @@ Daijin can be configured so to run each assembler and/or aligner multiple times,
       - ''
       - "-k 10"
     asm_methods:
-      class:
+      class2:
       - ''
       - "--set-cover"
       stringtie:
-Original file line number
+Diff line change
@@ Expand Up / @@ -503,7 +503,6 @@ def _parse_attributes(self, attributes): @@
             """
             self.attribute_order = []
-            print("Parsing", attributes)
             infolist = self._attribute_pattern.findall(attributes.rstrip().rstrip(";"))
@@ Expand Down @@