Merge pull request #73 from phac-nml/galaxy

Updated README and meta file for Bioconda to be v0.8.1

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:

ectyper/ectyper.py

@@ -15,6 +15,7 @@
                      genomeFunctions, predictionFunctions, subprocess_util,
                      __version__)
 
+
 # setup the application logging
 LOG = loggingFunctions.create_logger()
 

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':'-'

recipe/meta_bioconda.yaml

@@ -1,4 +1,4 @@
-{% set version = "0.8.0" %}
+{% set version = "0.8.1" %}
 
 about:
     license: Apache 2