From dd71c99aa0dbaabd37eacea023d6d9ea9b22eaaa Mon Sep 17 00:00:00 2001 From: Vedanth Date: Fri, 29 Dec 2023 16:23:45 +0530 Subject: [PATCH] hamronized resfinder.resfinder.orfs.tsv from raw directory. changed input gene col for hamronized in normalizers --- argnorm/normalizers.py | 2 +- docs/index.md | 6 +++--- examples/hamronized/resfinder.resfinder.orfs.tsv | 14 ++++++++++++++ 3 files changed, 18 insertions(+), 4 deletions(-) create mode 100644 examples/hamronized/resfinder.resfinder.orfs.tsv diff --git a/argnorm/normalizers.py b/argnorm/normalizers.py index 2faee70..c051e8d 100644 --- a/argnorm/normalizers.py +++ b/argnorm/normalizers.py @@ -275,7 +275,7 @@ def _set_input_gene_col(self): Always adapt this method to the input data format. """ if self.is_hamronized: - self._input_gene_col = '' # TODO add here. + self._input_gene_col = 'gene_symbol' # TODO add here. else: self._input_gene_col = 'Accession no.' diff --git a/docs/index.md b/docs/index.md index 5d7d59a..1a38d8f 100644 --- a/docs/index.md +++ b/docs/index.md @@ -2,7 +2,7 @@ [![Python package](https://github.com/BigDataBiology/argNorm/actions/workflows/python-package.yml/badge.svg)](https://github.com/BigDataBiology/argNorm/actions/workflows/python-package.yml) [![Downloads](https://pepy.tech/badge/argNorm)](https://pepy.tech/project/argNorm) -![](https://img.shields.io/badge/status-alpha-red?style=flat) +![](https://img.shields.io/badge/status-alpha-red?style=flat) Antibiotic resistance gene (ARG) normalization by mapping to the [antibiotic resistance ontology (ARO)](https://obofoundry.org/ontology/aro.html) by CARD. @@ -15,7 +15,7 @@ Thus, `argNorm` normalizes the _output vocabulary_ of these tools by mapping all This is a beta-quality implementation (subject to changes and some bugs may remain), but you're welcomed to try it and provide feedback. -We welcome your feedback on the [Issues Page](https://github.com/BigDataBiology/argNorm/issues). +We welcome your feedback on the [Issues Page](https://github.com/BigDataBiology/argNorm/issues). ## Supported tools @@ -83,4 +83,4 @@ argnorm resfinder -i examples/raw/resfinder.resfinder.reads.tsv -o outputs/raw/r argnorm amrfinderplus -i examples/raw/amrfinderplus.ncbi.orfs.tsv -o outputs/raw/amrfinderplus.ncbi.orfs.tsv -``` +``` \ No newline at end of file diff --git a/examples/hamronized/resfinder.resfinder.orfs.tsv b/examples/hamronized/resfinder.resfinder.orfs.tsv new file mode 100644 index 0000000..759efb0 --- /dev/null +++ b/examples/hamronized/resfinder.resfinder.orfs.tsv @@ -0,0 +1,14 @@ +input_file_name gene_symbol gene_name reference_database_name reference_database_version reference_accession analysis_software_name analysis_software_version genetic_variation_type antimicrobial_agent coverage_percentage coverage_depth coverage_ratio drug_class input_gene_length input_gene_start input_gene_stop input_protein_length input_protein_start input_protein_stop input_sequence_id nucleotide_mutation nucleotide_mutation_interpretation predicted_phenotype predicted_phenotype_confidence_level amino_acid_mutation amino_acid_mutation_interpretation reference_gene_length reference_gene_start reference_gene_stop reference_protein_length reference_protein_start reference_protein_stop resistance_mechanism strand_orientation sequence_identity +resfinder.resfinder.orfs.tsv aph(3')-III aph(3')-III resfinder 4.1.0 M26832 resfinder 0.0.1 gene_presence_detected 100.0 Aminoglycoside resistance 204 998 k119_48139 flag=1 multi=7.0000 len=1034 795 + 100.0 +resfinder.resfinder.orfs.tsv ant(6)-Ia ant(6)-Ia resfinder 4.1.0 KF864551 resfinder 0.0.1 gene_presence_detected 100.0 Aminoglycoside resistance 617 1483 k119_64006 flag=0 multi=37.0000 len=1517 867 - 100.0 +resfinder.resfinder.orfs.tsv erm(B) erm(B) resfinder 4.1.0 U18931 resfinder 0.0.1 gene_presence_detected 100.0 Macrolide resistance 24647 25384 k119_84636 flag=0 multi=44.9396 len=29273 738 + 100.0 +resfinder.resfinder.orfs.tsv lnu(C) lnu(C) resfinder 4.1.0 AY928180 resfinder 0.0.1 gene_presence_detected 100.0 Lincosamide resistance 231 725 k119_46979 flag=1 multi=6.0000 len=2214 495 + 98.99 +resfinder.resfinder.orfs.tsv erm(F) erm(F) resfinder 4.1.0 M17808 resfinder 0.0.1 gene_presence_detected 100.0 Macrolide resistance 73 873 k119_66841 flag=0 multi=55.0000 len=875 801 + 100.0 +resfinder.resfinder.orfs.tsv cat cat resfinder 4.1.0 M35190 resfinder 0.0.1 gene_presence_detected 100.0 Phenicol resistance 1975 2598 k119_95290 flag=3 multi=26.0047 len=5640 624 + 96.96 +resfinder.resfinder.orfs.tsv tet(Q) tet(Q) resfinder 4.1.0 L33696 resfinder 0.0.1 gene_presence_detected 99.94807892004154 Tetracycline resistance 8574 10499 k119_48273 flag=0 multi=99.8140 len=13795 1927 - 90.61 +resfinder.resfinder.orfs.tsv tet(X) tet(X) resfinder 4.1.0 M37699 resfinder 0.0.1 gene_presence_detected 100.0 Tetracycline resistance 12370 13536 k119_48273 flag=0 multi=99.8140 len=13795 1167 + 99.91 +resfinder.resfinder.orfs.tsv tet(O) tet(O) resfinder 4.1.0 M20925 resfinder 0.0.1 gene_presence_detected 100.0 Tetracycline resistance 978 2897 k119_60190 flag=1 multi=13.0000 len=3573 1920 - 99.43 +resfinder.resfinder.orfs.tsv tet(Q) tet(Q) resfinder 4.1.0 L33696 resfinder 0.0.1 gene_presence_detected 100.0 Tetracycline resistance 11179 13104 k119_36643 flag=0 multi=62.4691 len=39287 1926 + 99.69 +resfinder.resfinder.orfs.tsv tet(32) tet(32) resfinder 4.1.0 EF626943 resfinder 0.0.1 gene_presence_detected 100.0 Tetracycline resistance 121 2040 k119_69070 flag=0 multi=12.9788 len=11428 1920 + 99.74 +resfinder.resfinder.orfs.tsv tet(W) tet(W) resfinder 4.1.0 AJ427422 resfinder 0.0.1 gene_presence_detected 100.0 Tetracycline resistance 21199 23118 k119_9485 flag=0 multi=25.2509 len=23983 1920 + 100.0 +resfinder.resfinder.orfs.tsv tet(40) tet(40) resfinder 4.1.0 FJ158002 resfinder 0.0.1 gene_presence_detected 100.0 Tetracycline resistance 160 1380 k119_2904 flag=1 multi=9.0000 len=1720 1221 - 99.84