New ISA template for StemCellCore

cubi_tk/isa_tpl/__init__.py

@@ -28,6 +28,7 @@
 - ``isatab-bulk_rnaseq``
 - ``isatab-tumor_normal_dna``
 - ``isatab-tumor_normal_triplets``
+- ``isatab-stem_cell_core``
 
 Adding Templates
 ----------------
@@ -143,6 +144,12 @@ def load_variables(template_name, extra=None):
         description="MS Metabolomics Biocrates kit ISA-tab template",
         configuration=load_variables("isatab-ms_meta_biocrates"),
     ),
+    IsaTabTemplate(
+    name="stem_cell_core",
+    path=os.path.join(_BASE_DIR, "isatab-stem_cell_core"),
+    description="RNA sequencing ISA-tab template from hiPSC for stem cell core projects",
+    configuration=load_variables("isatab-stem_cell_core"),
+    ),
 )
 
 #: Known ISA-tab templates.

cubi_tk/isa_tpl/isatab-stem_cell_core/cookiecutter.json

@@ -0,0 +1,20 @@
+{
+  "investigation_title": "Investigation Title",
+  "sample_names": "sample1,sample2",
+  "a_measurement_type": "transcription profiling",
+  "source_type": ["hiPSC", "tissue"],
+  "source_meta": "Genetic modfications,Passage",
+  "model_type": ["3D", "2D"],
+  "sample_meta": "Tissue type,Differentiation duration,Condition,Treatment,Treatment duration",
+  "library_type": ["Single-Cell", "Bulk"],
+  "library_kit": "{{'SC3Pv3' if cookiecutter.library_type == 'Single-Cell' else ''}}",
+  "dissociation_meta": "{{'Cell count,Removal debris,Removal dead cell,Removal ab cell,Cell fixation,Cell viability' if cookiecutter.library_type == 'Single-Cell' else 'Cell count'}}",
+  "library_construction_meta": "{{'Sequencing kit,RNA amount,QC cell load recovery,QC tape fragment size' if cookiecutter.library_type == 'Single-Cell' else 'Sequencing kit,RNA amount,QC tape fragment size'}}",
+  "sequencing_meta": "Platform,Instrument model,No. targeted reads,QC-notes",
+  "study_title": "{{cookiecutter.investigation_title}}",
+  "i_dir_name": "{{cookiecutter.investigation_title|replace(' ', '_')}}",
+  "s_file_name": "{{cookiecutter.i_dir_name}}",
+  "assay_prefix": "{{cookiecutter.i_dir_name|lower}}",
+  "a_technology_type": "nucleotide sequencing",
+  "assay_name": "{{cookiecutter.a_measurement_type|replace(' ', '_')}}_{{cookiecutter.a_technology_type|replace(' ', '_')}}"
+}

cubi_tk/isa_tpl/isatab-stem_cell_core/{{cookiecutter.i_dir_name}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt

@@ -0,0 +1,8 @@
+{% set sample_names = cookiecutter.sample_names.split(",") -%}
+{% set dissociation_meta = cookiecutter.dissociation_meta.split(",") -%}
+{% set library_construction_meta = cookiecutter.library_construction_meta.split(",") -%}
+{% set sequencing_meta = cookiecutter.sequencing_meta.split(",") -%}
+Sample Name	Protocol REF	Parameter Value[Passed]	Protocol REF	Parameter Value[Dissociation method]{%+ for meta in dissociation_meta %}	Parameter Value[{{meta}}]{% endfor %}	Performer	Date	Protocol REF	Parameter Value[Library kit]	Parameter Value[Library type]	Parameter Value[Multiplex genotype]	Parameter Value[Multiplex sample]	Parameter Value[Multiplex oligo]{%+ for meta in library_construction_meta %}	Parameter Value[{{meta}}]{% endfor %}	Performer	Date	Extract Name	Protocol REF	Parameter Value[Sequencing run]	Parameter Value[Library prefix]	Parameter Value[Barcode kit]	Parameter Value[Barcode name]{%+ for meta in sequencing_meta %}	Parameter Value[{{meta}}]{% endfor %}	Performer	Date	Library Name
+{% for sample_name in sample_names -%}
+{{sample_name|replace("-", "_")}}	OverallQC		Dissociation	{%+ for meta in dissociation_meta %}	{% endfor %}			Library construction	{{cookiecutter.library_kit}}	{{cookiecutter.library_type}} Gene Expression				{%+ for meta in library_construction_meta %}	{% endfor %}		{{sample_name}}_GEX	Nucleic acid sequencing		{{sample_name}}_GEX		{%+ for meta in sequencing_meta %}	{% endfor %}			{{sample_name}}
+{% endfor -%}

cubi_tk/isa_tpl/isatab-stem_cell_core/{{cookiecutter.i_dir_name}}/i_Investigation.txt

@@ -0,0 +1,100 @@
+ONTOLOGY SOURCE REFERENCE
+Term Source Name	UO	OBI	NCBITAXON	OMIM	HP	ORPHA
+Term Source File	http://data.bioontology.org/ontologies/UO	http://data.bioontology.org/ontologies/OBI	http://data.bioontology.org/ontologies/NCBITAXON	http://data.bioontology.org/ontologies/OMIM	http://data.bioontology.org/ontologies/HP	http://data.bioontology.org/ontologies/ORDO
+Term Source Version	48	35	10	12	570	2.8
+Term Source Description	Units of Measurement Ontology	Ontology for Biomedical Investigations	National Center for Biotechnology Information (NCBI) Organismal Classification	Online Mendelian Inheritance in Man	Human Phenotype Ontology	Orphanet Rare Disease Ontology
+INVESTIGATION
+Investigation Identifier	""
+Investigation Title	{{cookiecutter.investigation_title}}
+Investigation Description	""
+Investigation Submission Date	""
+Investigation Public Release Date	""
+Comment[Created With Configuration]	/path/to/isa-configurations/bih_studies/bih_stem_cell_core
+Comment[Last Opened With Configuration]	bih_stem_cell_core
+INVESTIGATION PUBLICATIONS
+Investigation PubMed ID
+Investigation Publication DOI
+Investigation Publication Author List
+Investigation Publication Title
+Investigation Publication Status
+Investigation Publication Status Term Accession Number
+Investigation Publication Status Term Source REF
+INVESTIGATION CONTACTS
+Investigation Person Last Name
+Investigation Person First Name
+Investigation Person Mid Initials
+Investigation Person Email
+Investigation Person Phone
+Investigation Person Fax
+Investigation Person Address
+Investigation Person Affiliation
+Investigation Person Roles
+Investigation Person Roles Term Accession Number
+Investigation Person Roles Term Source REF
+STUDY
+Study Identifier	{{cookiecutter.i_dir_name}}
+Study Title	{{cookiecutter.investigation_title}}
+Study Description	""
+Comment[Study Grant Number]	""
+Comment[Study Funding Agency]	""
+Study Submission Date	""
+Study Public Release Date	""
+Study File Name	s_{{cookiecutter.s_file_name}}.txt
+STUDY DESIGN DESCRIPTORS
+Study Design Type
+Study Design Type Term Accession Number
+Study Design Type Term Source REF
+STUDY PUBLICATIONS
+Study PubMed ID
+Study Publication DOI
+Study Publication Author List
+Study Publication Title
+Study Publication Status
+Study Publication Status Term Accession Number
+Study Publication Status Term Source REF
+STUDY FACTORS
+Study Factor Name
+Study Factor Type
+Study Factor Type Term Accession Number
+Study Factor Type Term Source REF
+STUDY ASSAYS
+Study Assay File Name	a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt
+Study Assay Measurement Type	{{cookiecutter.a_measurement_type}}
+Study Assay Measurement Type Term Accession Number	http://purl.obolibrary.org/obo/OBI_0000424
+Study Assay Measurement Type Term Source REF	OBI
+Study Assay Technology Type	{{cookiecutter.a_technology_type}}
+Study Assay Technology Type Term Accession Number	http://purl.obolibrary.org/obo/OBI_0000626
+Study Assay Technology Type Term Source REF	OBI
+Study Assay Technology Platform	Illumina
+STUDY PROTOCOLS
+{% set source_meta = cookiecutter.source_meta.split(",") -%}
+{% set sample_meta = cookiecutter.sample_meta.split(",") -%}
+{% set dissociation_meta = cookiecutter.dissociation_meta.split(",") -%}
+{% set library_construction_meta = cookiecutter.library_construction_meta.split(",") -%}
+{% set sequencing_meta = cookiecutter.sequencing_meta.split(",") -%}
+Study Protocol Name	OverallQC	Differentiation	Sample collection	Dissociation	Library construction	Nucleic acid sequencing
+Study Protocol Type	OverallQC	Differentiation	Sample collection	Dissociation	Library construction	Nucleic acid sequencing
+Study Protocol Type Term Accession Number	""	""	""	""	""	""
+Study Protocol Type Term Source REF	""	""	""	""	""	""
+Study Protocol Description	""	""	""	""	""	""
+Study Protocol URI	""	""	""	""	""	""
+Study Protocol Version	""	""	""	""	""	""
+Study Protocol Parameters Name	Passed	Protocol numbers;Culture type;Differentiation dates;No. of passages;Well format	SampleType;Collection reagent	Dissociation method{% for meta in dissociation_meta -%};{{meta}}{% endfor %}	Library kit;Library type;Multiplex genotype;Multiplex sample;Multiplex oligo{% for meta in library_construction_meta -%};{{meta}}{% endfor %}	Sequencing run;Library prefix;Barcode kit;Barcode name{% for meta in sequencing_meta -%};{{meta}}{% endfor %}
+Study Protocol Parameters Name Term Accession Number	""	";;;;"	";"	"{% for meta in dissociation_meta -%};{% endfor %}"	";;;;{% for meta in library_construction_meta -%};{% endfor %}"	";;;{% for meta in sequencing_meta -%};{% endfor %}"
+Study Protocol Parameters Name Term Source REF	""	";;;;"	";"	"{% for meta in dissociation_meta -%};{% endfor %}"	";;;;{% for meta in library_construction_meta -%};{% endfor %}"	";;;{% for meta in sequencing_meta -%};{% endfor %}"
+Study Protocol Components Name	""	""	""	""	""	""
+Study Protocol Components Type	""	""	""	""	""	""
+Study Protocol Components Type Term Accession Number	""	""	""	""	""	""
+Study Protocol Components Type Term Source REF	""	""	""	""	""	""
+STUDY CONTACTS
+Study Person Last Name
+Study Person First Name
+Study Person Mid Initials
+Study Person Email
+Study Person Phone
+Study Person Fax
+Study Person Address
+Study Person Affiliation
+Study Person Roles
+Study Person Roles Term Accession Number
+Study Person Roles Term Source REF

cubi_tk/isa_tpl/isatab-stem_cell_core/{{cookiecutter.i_dir_name}}/s_{{cookiecutter.s_file_name}}.txt

@@ -0,0 +1,7 @@
+{% set sample_names = cookiecutter.sample_names.split(",") -%}
+{% set source_meta = cookiecutter.source_meta.split(",") -%}
+{% set sample_meta = cookiecutter.sample_meta.split(",") -%}
+Source Name	Characteristics[Organism]	Term Source REF	Term Accession Number	Characteristics[ExperimentName]	Characteristics[Source Type]	Characteristics[Cellline]{%+ for meta in source_meta %}	Characteristics[{{meta}}]{% endfor %}	Protocol REF	Parameter Value[Protocol numbers]	Parameter Value[Culture type]	Parameter Value[Differentiation dates]	Parameter Value[No. of passages]	Parameter Value[Well format]	Performer	Protocol REF	Parameter Value[SampleType]	Parameter Value[Collection reagent]	Performer	Date	Sample Name{%+ for meta in sample_meta %}	Characteristics[{{meta}}]{% endfor %}
+{% for sample_name in sample_names -%}
+{{sample_name|replace("-", "_")}}	Homo sapiens	NCBITAXON	http://purl.bioontology.org/ontology/NCBITAXON/9606		{{cookiecutter.source_type}}	BIHi00XYZ{%+ for meta in source_meta %}	{% endfor %}	Differentiation		{{cookiecutter.model_type}}					Sample collection					{{sample_name|replace("-", "_")}}{%+ for meta in sample_meta %}	{% endfor %}
+{% endfor -%}