Mercurial > repos > onnodg > blast_annotations_processor
changeset 1:2acf82433aa4 draft default tip
planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit d771f9fbfd42bcdeda1623d954550882a0863847-dirty
| author | onnodg |
|---|---|
| date | Mon, 20 Oct 2025 12:26:51 +0000 |
| parents | a3989edf0a4a |
| children | |
| files | __pycache__/__init__.cpython-313.pyc __pycache__/blast_annotations_processor.cpython-313.pyc blast_annotations_processor.xml test-data/sorted_test.fasta test-data/sorted_test.tabular test-data/sync_test.xlsx tests/__pycache__/test_blast_annotations_processor.cpython-313-pytest-8.4.2.pyc |
| diffstat | 7 files changed, 49 insertions(+), 26 deletions(-) [+] |
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--- a/blast_annotations_processor.xml Tue Oct 14 09:08:30 2025 +0000 +++ b/blast_annotations_processor.xml Mon Oct 20 12:26:51 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="blast_annotation_processor" name="BLAST Annotation Processor" version="1.0.0"> +<tool id="blast_annotation_processor" name="BLAST Annotation Processor" version="1.0.1"> <description>Process BLAST annotation results with taxonomic analysis</description> <requirements> @@ -57,7 +57,7 @@ <option value="eval_plot">E-value distribution plot</option> <option value="taxa_output">Taxonomic report (Kraken2-like format)</option> <option value="circle_data">Circular taxonomic datafile</option> - <option value="header_anno">Header annotations table</option> + <option value="header_anno">Annotations per header (in Excel)</option> <option value="anno_stats">Annotation statistics</option> </param> @@ -165,38 +165,61 @@ - **Circular taxonomic data**: Json data to generate a circular sunburst-style diagram showing taxonomic composition across all taxonomic levels (Kingdom -> Species). -- **Header annotations table**: Excel workbook listing each sequence header with its taxonomic assignment and E-value. +- **Annotations per header**: Excel workbook listing each sequence header with its taxonomic assignment and E-value. - **Annotation statistics**: Summary statistics about annotation success rates and sequence counts. **Parameters:** -- **Uncertain threshold**: When multiple conflicting taxonomic assignments exist for a sequence, this threshold determines whether to use the most common assignment (if it exceeds the threshold) or mark it as "Uncertain taxa". +- **Uncertain threshold**: Treshold for lca. When multiple conflicting taxonomic assignments exist for a sequence, this threshold determines whether to use the most common assignment (if it exceeds the threshold) or mark it as "Uncertain taxa". - **E-value threshold**: Sequences with E-values higher than this threshold are filtered out from the analysis. - **Use read counts**: Determines whether circular data reflects the abundance of reads (checked) or just count unique taxonomic assignments (unchecked). -#Query ID #Subject #Subject accession #Subject Taxonomy ID #Identity percentage - #Coverage #evalue #bitscore #Source #Taxonomy + **Expected Input Format:** The annotated BLAST file should be in tabular format with at least 7 columns: -1. Query ID -2. Subject ID -3. Subject accession -4. Subject Taxonomy ID -5. Identity percentage -6. Coverage -7. Evalue -8. Bitscore -9. Source -10. Taxonomy + +- 1. Query ID + +- 2. Subject ID + +- 3. Subject accession + +- 4. Subject Taxonomy ID + +- 5. Identity percentage + +- 6. Coverage + +- 7. Evalue + +- 8. Bitscore + +- 9. Source + +- 10. Taxonomy **Note:** This tool processes files that have been deduplicated and contain read count information in the sequence headers in the format: `sequence_name(count_number)`. +------------- + +.. class:: infomark + **Credits** -Authors = Onno de Gorter, 2025. + Based on a script by Nick Kortleven, translated, modified and wrapped by Onno de Gorter, -Developed for the New light on old remedies project, a PhD research by Anja Fischer +Developed for the New light on old remedies project, a PhD research by Anja Fischer. + +Link to the project website: + +* https://ahm.uva.nl/funded-research-projects/new-lights-on-old-remedies/new-lights-on-old-remedies.html + ]]></help> + <creator> + <organization name="Naturalis Biodiversity Center" url="https://www.naturalis.nl/en/science" /> + <person givenName="Onno" familyName="de Gorter" url="https://github.com/Onnodg"/> + <person givenName="Nick" familyName="Kortleven" url="https://github.com/tombkingsts" /> + </creator> </tool> \ No newline at end of file
--- a/test-data/sorted_test.fasta Tue Oct 14 09:08:30 2025 +0000 +++ b/test-data/sorted_test.fasta Mon Oct 20 12:26:51 2025 +0000 @@ -1,4 +1,4 @@ ->read1(100) count=100; -ATCG ->read2(50) count=50; -GCTA +>read1(100) count=100; +ATCG +>read2(50) count=50; +GCTA
--- a/test-data/sorted_test.tabular Tue Oct 14 09:08:30 2025 +0000 +++ b/test-data/sorted_test.tabular Mon Oct 20 12:26:51 2025 +0000 @@ -1,4 +1,4 @@ -#Query ID #Subject #Subject accession #Subject Taxonomy ID #Identity percentage #Coverage #evalue #bitscore #Source #Taxonomy - read1(100) subject1 95.0 100 50 75 1e-50 200 database1 Viridiplantae / Streptophyta / Magnoliopsida / Fagales / Juglandaceae / Uncertain taxa / Uncertain taxa -read1(100) subject2 90.0 95 45 70 1e-5 180 database1 Viridiplantae / Streptophyta / Magnoliopsida / Rosales / Rosaceae / Sorbus / Sorbus aucuparia -read2(50) subject3 85.0 90 40 65 1e-3 160 database2 Viridiplantae / Streptophyta / Magnoliopsida / Solanales / Solanaceae / Uncertain taxa / Uncertain taxa +#Query ID #Subject #Subject accession #Subject Taxonomy ID #Identity percentage #Coverage #evalue #bitscore #Source #Taxonomy + read1(100) subject1 95.0 100 50 75 1e-50 200 database1 Viridiplantae / Streptophyta / Magnoliopsida / Fagales / Juglandaceae / Uncertain taxa / Uncertain taxa +read1(100) subject2 90.0 95 45 70 1e-5 180 database1 Viridiplantae / Streptophyta / Magnoliopsida / Rosales / Rosaceae / Sorbus / Sorbus aucuparia +read2(50) subject3 85.0 90 40 65 1e-3 160 database2 Viridiplantae / Streptophyta / Magnoliopsida / Solanales / Solanaceae / Uncertain taxa / Uncertain taxa