From 455db7c7dea20770e1cf8561ff9b601a9256df26 Mon Sep 17 00:00:00 2001 From: Martin Hunt Date: Tue, 14 Jul 2015 09:18:38 +0100 Subject: [PATCH 1/3] Use untrusted-contigs instead of trusted-contigs with spades --- ariba/cluster.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ariba/cluster.py b/ariba/cluster.py index caf6dc1b..dd10077f 100644 --- a/ariba/cluster.py +++ b/ariba/cluster.py @@ -289,7 +289,7 @@ def _assemble_with_spades(self, unittest=False): '-o', self.assembler_dir, '-k', str(self.assembly_kmer), '--threads', str(self.threads), - '--trusted-contigs', self.gene_fa, + '--untrusted-contigs', self.gene_fa, ]) if self.spades_other is not None: cmd += ' ' + self.spades_other From 48f934c61aa9cce42ff1850dbda564e62646d27f Mon Sep 17 00:00:00 2001 From: Martin Hunt Date: Tue, 14 Jul 2015 09:19:16 +0100 Subject: [PATCH 2/3] Quote contig names --- ariba/faidx.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ariba/faidx.py b/ariba/faidx.py index a9939abe..cefd7c60 100644 --- a/ariba/faidx.py +++ b/ariba/faidx.py @@ -13,7 +13,7 @@ def write_fa_subset(seq_names, infile, outfile, samtools_exe='samtools', verbose common.syscall(' '.join([ samtools_exe + ' faidx', infile, - name, + '"' + name + '"', '>>', outfile ])) From 21e18e42077e89e2bcf8ffe64f86110f5dbf85ce Mon Sep 17 00:00:00 2001 From: Martin Hunt Date: Tue, 14 Jul 2015 09:20:54 +0100 Subject: [PATCH 3/3] version bump --- ariba/common.py | 2 +- setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/ariba/common.py b/ariba/common.py index 16d0e4cf..4f0f5b84 100644 --- a/ariba/common.py +++ b/ariba/common.py @@ -1,7 +1,7 @@ import sys import subprocess -version = '0.4.0' +version = '0.4.1' def syscall(cmd, allow_fail=False, verbose=False): if verbose: diff --git a/setup.py b/setup.py index 740e5441..47617b41 100644 --- a/setup.py +++ b/setup.py @@ -7,7 +7,7 @@ setup( name='ariba', - version='0.4.0', + version='0.4.1', description='ARIBA: Antibiotic Resistance Identification By Assembly', packages = find_packages(), author='Martin Hunt',