diff --git a/README.md b/README.md index cc2f5da..3a5ba08 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ [![Master branch build status](https://api.travis-ci.org/phac-nml/ecoli_serotyping.svg?branch=master "Master Build Status")](https://travis-ci.org/phac-nml/ecoli_serotyping) # ECTyper (an easy typer) -**ecyper** is a standalone serotyping module for _Escherichia coli_. It supports _fasta_ and _fastq_ file formats. +**ectyper** is a standalone serotyping module for _Escherichia coli_. It supports _fasta_ and _fastq_ file formats. # Dependencies: - python >=3.5 @@ -48,7 +48,7 @@ usage: ectyper [-h] [-V] -i INPUT [-c CORES] [-d PERCENTIDENTITY] [-l PERCENTLENGTH] [--verify] [-o OUTPUT] [-r REFSEQ] [-s] -ectyper v0.8.0 Prediction of Escherichia coli serotype from raw reads or +ectyper v0.8.1 Prediction of Escherichia coli serotype from raw reads or assembled genome sequences optional arguments: diff --git a/ectyper/ectyper.py b/ectyper/ectyper.py index c83a12a..7a8e812 100644 --- a/ectyper/ectyper.py +++ b/ectyper/ectyper.py @@ -15,6 +15,7 @@ genomeFunctions, predictionFunctions, subprocess_util, __version__) + # setup the application logging LOG = loggingFunctions.create_logger() diff --git a/ectyper/predictionFunctions.py b/ectyper/predictionFunctions.py index 17a9386..aabd03d 100644 --- a/ectyper/predictionFunctions.py +++ b/ectyper/predictionFunctions.py @@ -40,7 +40,6 @@ def predict_serotype(blast_output_file, ectyper_dict_file, args): for genome_name, per_genome_df in output_df.groupby('genome_name'): predictions_dict[genome_name] = get_prediction(per_genome_df, args) - LOG.info("Serotype prediction completed") LOG.debug("Predictions dict:\n{}".format(predictions_dict)) return predictions_dict @@ -60,9 +59,6 @@ def get_prediction(per_genome_df, args): LOG.debug("per_genome_df:\n{}".format(per_genome_df)) # The DataFrame is sorted in descending order by score - # Once we hit a wzx / wzy or wzm / wzt pair, O type is done - # Once we hit a flX gene, H type is done - serotype = { 'O':'-', 'H':'-' diff --git a/recipe/meta_bioconda.yaml b/recipe/meta_bioconda.yaml index 627b3b7..572e3d6 100644 --- a/recipe/meta_bioconda.yaml +++ b/recipe/meta_bioconda.yaml @@ -1,4 +1,4 @@ -{% set version = "0.8.0" %} +{% set version = "0.8.1" %} about: license: Apache 2