161 lines
9.8 KiB
Python
Executable File
161 lines
9.8 KiB
Python
Executable File
from __future__ import annotations
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from typing import Any
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CONFIG_HEADERS = [
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"Original_File_Name",
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"Species_Code",
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"Species_Name",
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"Gene_Family",
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"File_Type",
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"Ref",
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"Species_Role",
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"File_Scope",
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"Reference_Use",
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]
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CONFIG_TEMPLATE_ROWS = [
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["Os.genome.fasta", "Os", "Oryza sativa", "", "genome", "FALSE", "target", "whole_genome", ""],
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["Os.gff3", "Os", "Oryza sativa", "", "gff", "FALSE", "target", "whole_genome", ""],
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["Os.cds.fasta", "Os", "Oryza sativa", "", "cds", "FALSE", "target", "whole_genome", ""],
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["Os.pep.fasta", "Os", "Oryza sativa", "", "pep", "FALSE", "target", "whole_genome", ""],
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["At.genome.fasta", "At", "Arabidopsis thaliana", "", "genome", "TRUE", "reference", "whole_genome", "downstream_primary"],
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["At.gff3", "At", "Arabidopsis thaliana", "", "gff", "TRUE", "reference", "whole_genome", "downstream_primary"],
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["At.cds.fasta", "At", "Arabidopsis thaliana", "", "cds", "TRUE", "reference", "whole_genome", "downstream_primary"],
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["At.pep.fasta", "At", "Arabidopsis thaliana", "", "pep", "TRUE", "reference", "whole_genome", "downstream_primary"],
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["Zm.gff3", "Zm", "Zea mays", "", "gff", "FALSE", "comparative", "whole_genome", ""],
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["Zm.pep.fasta", "Zm", "Zea mays", "", "pep", "FALSE", "comparative", "whole_genome", ""],
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["Vv.gff3", "Vv", "Vitis vinifera", "", "gff", "FALSE", "outgroup", "whole_genome", ""],
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["Vv.pep.fasta", "Vv", "Vitis vinifera", "", "pep", "FALSE", "outgroup", "whole_genome", ""],
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["At.WRKY.pep.fasta", "At", "Arabidopsis thaliana", "WRKY", "family_pep", "TRUE", "seed_reference", "known_family", "both"],
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["Os.WRKY.pep.fasta", "Os", "Oryza sativa", "WRKY", "family_pep", "TRUE", "seed_reference", "known_family", "identify_blast"],
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]
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CONFIG_README_ROWS = [
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["config.xlsx template"],
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["Download this file, fill the Analysis sheet and config sheet, then upload it together with genome/GFF/CDS/protein files."],
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["Use the Analysis sheet to declare the gene family once for the whole job. The config sheet keeps per-file metadata."],
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["The first sheet named config is read by the pipeline. Do not put notes or merged cells in that sheet."],
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[],
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["Column", "Chinese meaning", "English description", "Required", "Example / Allowed values"],
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["Original_File_Name", "uploaded original file name", "Original uploaded file name; must match the uploaded file", "Yes", "At.WRKY.pep.fa"],
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["Species_Code", "species short code", "Species code; keep consistent for one species", "Yes", "At, Os, Lc"],
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["Species_Name", "species scientific name", "Optional Latin/scientific name used only as an alias; filenames and Analysis species fields still use Species_Code", "Optional", "Arabidopsis thaliana, Oryza sativa"],
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["Gene_Family", "gene family name", "Optional for whole-genome rows; required for known-family seed rows (e.g. At.WRKY.pep.fasta)", "Optional", "WRKY, NAC, MYB; leave blank for whole-genome resources"],
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["File_Type", "file type", "File type", "Yes", "genome, gff, cds, pep, family_pep, family_cds (legacy: all_pep, protein)"],
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["Ref", "legacy reference flag", "Backward compatible flag. Prefer Species_Role for new projects.", "Recommended", "TRUE or FALSE"],
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["Species_Role", "species role", "Biological role in the analysis", "Recommended", "target, reference, comparative, outgroup, seed_reference"],
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["File_Scope", "file scope", "Whether the file is whole-genome resource or known family seed", "Recommended", "whole_genome, known_family"],
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["Reference_Use", "reference usage", "Optional role for reference rows: identify BLAST evidence, downstream primary reference, or both", "Optional", "identify_blast, downstream_primary, both, none"],
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[],
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["File_Type notes"],
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["genome", "Genome FASTA"],
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["gff", "GFF or GFF3 annotation file"],
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["cds", "CDS FASTA"],
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["pep", "Whole proteome; used for identify and MCScanX background"],
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["all_pep or protein", "Legacy whole-proteome value; treated as pep"],
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["family_pep", "Known family proteins; standardized as Species.Family.pep.fasta"],
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["family_cds", "Known family CDS; standardized as Species.Family.cds.fasta"],
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["pep", "Compatible value: whole_genome rows become Species.pep.fasta; known_family rows become Species.Family.pep.fasta"],
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[],
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["Naming rule"],
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["whole_genome files are standardized as Species.pep.fasta, Species.cds.fasta, Species.genome.fasta, Species_final.gff3"],
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["known_family seed files are standardized as Species.Family.pep.fasta or Species.Family.cds.fasta"],
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[],
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["Upload rule"],
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["You may upload any .xlsx file name. The latest uploaded Excel file will be normalized to config.xlsx."],
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["If you upload another Excel file later, it replaces the current config.xlsx for this job."],
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[],
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["Filling guide (how to think about this table)"],
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["1) Genome Prepare = species-level normalization (no family binding)"],
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["- For target/reference/comparative/outgroup species, upload whole-genome resources and set File_Scope=whole_genome."],
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["- Use Species_Role=reference for whole-genome resources of the reference species (for example Arabidopsis At)."],
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["- Use Species_Role=seed_reference only for curated known family member FASTA/subfamily labels (File_Scope=known_family, Gene_Family required)."],
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["2) Two analysis paths are both supported"],
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["- Path A (known family): you already know the family (e.g. WRKY). Fill Analysis!Family=WRKY, use seed_reference (At.WRKY.pep.fa) + whole-genome pep of target species; then run identify with prefix like Multi.WRKY."],
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["- Path B (unknown family): leave Gene_Family empty for whole-genome rows, run RNA-seq -> enrichment -> choose candidate family; then run identify using Species.pep.fasta."],
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["3) Roles and what they mean"],
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["- target: main species you study in the paper."],
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["- reference: whole-genome resources for the reference species (background/reference proteome, GFF, CDS, genome)."],
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["- comparative: additional species for cross-species comparison/synteny."],
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["- outgroup: distant species for tree rooting or evolution context."],
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["- seed_reference: curated known family members used as identify BLAST evidence and/or downstream reference context, depending on Reference_Use."],
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["- Reference_Use=identify_blast: use this known-family FASTA only for identify reference-protein search."],
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["- Reference_Use=downstream_primary: use this species as the default downstream reference, not as extra identify BLAST evidence unless separately listed."],
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["- Reference_Use=both: use for both identify BLAST and downstream reference context."],
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["4) Minimal rules to avoid mistakes"],
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["- Do not put random notes/merged cells in the config sheet."],
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["- Species_Code is the machine identity and filename prefix; do not put Latin names in Species_Code."],
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["- Species_Name is optional and only maps Latin names back to Species_Code during literature/methodology extraction."],
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["- Whole-genome rows: Gene_Family can be empty; file naming will be Species.*."],
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["- Known-family rows: Gene_Family must be filled; naming will be Species.Family.*."],
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["- Identify BLAST runs only when config declares a known-family/seed reference protein row; otherwise identify is HMM-only."],
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["- Ref is legacy; Species_Role is recommended for new jobs."],
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]
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def config_template_examples() -> list[dict[str, Any]]:
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return [dict(zip(CONFIG_HEADERS, row)) for row in CONFIG_TEMPLATE_ROWS]
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def build_config_template_workbook():
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try:
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from openpyxl import Workbook
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from openpyxl.styles import Alignment, Font, PatternFill
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from openpyxl.utils import get_column_letter
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except Exception as exc:
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raise RuntimeError(f"openpyxl is required to generate config.xlsx template: {exc}")
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wb = Workbook()
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ws = wb.active
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ws.title = "config"
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ws.append(CONFIG_HEADERS)
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for row in CONFIG_TEMPLATE_ROWS:
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ws.append(row)
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header_fill = PatternFill("solid", fgColor="D9EAF7")
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for cell in ws[1]:
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cell.font = Font(bold=True)
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cell.fill = header_fill
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cell.alignment = Alignment(horizontal="center")
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widths = [28, 16, 28, 16, 18, 10, 18, 18, 22]
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for idx, width in enumerate(widths, start=1):
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ws.column_dimensions[get_column_letter(idx)].width = width
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ws.freeze_panes = "A2"
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analysis = wb.create_sheet("Analysis", 0)
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analysis_rows = [
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["Key", "Value", "Description"],
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["Family", "WRKY", "Gene family for this job. This is the preferred source when the user does not name a family."],
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["Target_Species", "Os", "Optional comma-separated target species codes."],
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["Reference_Species", "At", "Optional reference species code."],
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["Comparative_Species", "Zm,Vv", "Optional comma-separated comparative/outgroup species codes."],
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["Required_Pfams", "PF03106", "Optional Pfam accession(s) for identify."],
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]
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for row in analysis_rows:
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analysis.append(row)
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for cell in analysis[1]:
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cell.font = Font(bold=True)
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cell.fill = PatternFill("solid", fgColor="E2F0D9")
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cell.alignment = Alignment(horizontal="center")
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analysis.column_dimensions["A"].width = 24
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analysis.column_dimensions["B"].width = 22
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analysis.column_dimensions["C"].width = 76
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readme = wb.create_sheet("README")
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for row in CONFIG_README_ROWS:
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readme.append(row)
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readme["A1"].font = Font(bold=True, size=14)
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for cell in readme[5]:
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cell.font = Font(bold=True)
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cell.fill = PatternFill("solid", fgColor="E2F0D9")
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readme.column_dimensions["A"].width = 24
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readme.column_dimensions["B"].width = 46
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readme.column_dimensions["C"].width = 52
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readme.column_dimensions["D"].width = 12
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readme.column_dimensions["E"].width = 34
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for row in readme.iter_rows():
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for cell in row:
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cell.alignment = Alignment(wrap_text=True, vertical="top")
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return wb
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