Commit 0c1eaaa8 authored by Sascha Steinbiss's avatar Sascha Steinbiss
Browse files

New upstream version 2.12.0+ds

parent 313bcec6

README.md

+1 −1
Original line number Diff line number Diff line
@@ -5,7 +5,7 @@ Antimicrobial Resistance Identification By Assembly 
For how to use ARIBA, please see the [ARIBA wiki page][ARIBA wiki].



[![Build Status](https://travis-ci.org/sanger-pathogens/ariba.svg?branch=master)](https://travis-ci.org/sanger-pathogens/ariba)

[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg)](https://github.com/ssjunnebo/ariba/blob/master/LICENSE)

[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg)](https://github.com/sanger-pathogens/ariba/blob/master/LICENSE)

[![status](https://img.shields.io/badge/MGEN-10.1099%2Fmgen.0.000131-brightgreen.svg)](http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000131)



## Contents

ariba/assembly.py

+1 −1
Original line number Diff line number Diff line
@@ -59,7 +59,7 @@ class Assembly: 
        self.threads = threads



        if extern_progs is None:

            self.extern_progs = external_progs.ExternalProgs()

            self.extern_progs = external_progs.ExternalProgs(using_spades=self.assembler == 'spades')

        else:

            self.extern_progs = extern_progs

ariba/cdhit.py

+1 −1
Original line number Diff line number Diff line
@@ -27,7 +27,7 @@ class Runner: 
        self.length_diff_cutoff = length_diff_cutoff

        self.verbose = verbose

        self.min_cluster_number = min_cluster_number

        extern_progs = external_progs.ExternalProgs(fail_on_error=True)

        extern_progs = external_progs.ExternalProgs(fail_on_error=True, using_spades=False)

        self.cd_hit_est = extern_progs.exe('cdhit')

ariba/cluster.py

+1 −1
Original line number Diff line number Diff line
@@ -130,7 +130,7 @@ class Cluster: 
            self.log_fh = None



        if extern_progs is None:

            self.extern_progs = external_progs.ExternalProgs()

            self.extern_progs = external_progs.ExternalProgs(using_spades=self.assembler == 'spades')

        else:

            self.extern_progs = extern_progs

ariba/external_progs.py

+15 −2
Original line number Diff line number Diff line
@@ -20,10 +20,19 @@ prog_to_default = { 
prog_to_env_var = {x: 'ARIBA_' + x.upper() for x in prog_to_default if x not in {'nucmer'}}





# Nucmer 3.1 'nucmer --version' outputs this:

# nucmer

# NUCmer (NUCleotide MUMmer) version 3.1

#

# Numcer 4 'nucmer --version' outputs this:

# 4.0.0beta2

#

# ... make the regex permissive and hope things

# still work for later versions

prog_to_version_cmd = {

    'bowtie2': ('--version', re.compile('.*bowtie2.*version (.*)$')),

    'cdhit': ('', re.compile('CD-HIT version ([0-9\.]+) \(')),

    'nucmer': ('--version', re.compile('^NUCmer \(NUCleotide MUMmer\) version ([0-9\.]+)')),

    'nucmer': ('--version', re.compile('([0-9]+\.[0-9\.]+.*$)')),

    'spades': ('--version', re.compile('SPAdes\s+v([0-9\.]+)'))

}
@@ -40,11 +49,12 @@ prog_optional = set([ 
])



class ExternalProgs:

    def __init__(self, verbose=False, fail_on_error=True):

    def __init__(self, verbose=False, fail_on_error=True, using_spades=False):

        self.progs = {}

        self.version_report = []

        self.all_deps_ok = True

        self.versions = {}

        self.using_spades = using_spades



        if verbose:

            print('{:_^79}'.format(' Checking dependencies and their versions '))
@@ -53,6 +63,9 @@ class ExternalProgs: 
        warnings = []



        for prog in sorted(prog_to_default):

            if prog == 'spades' and not self.using_spades:

                continue



            msg_sink = errors

            if prog in prog_optional:

                msg_sink = warnings