From f088ae9c1cb46dc4e251268702a5a87cd8d22f80 Mon Sep 17 00:00:00 2001
From: Martin Hunt <mh12@sanger.ac.uk>
Date: Tue, 17 Feb 2015 08:58:19 +0000
Subject: [PATCH 01/10] Do not require velvet

---
 ariba/tests/cluster_test.py | 16 ++++++++--------
 setup.py                    |  6 +-----
 2 files changed, 9 insertions(+), 13 deletions(-)

diff --git a/ariba/tests/cluster_test.py b/ariba/tests/cluster_test.py
index e9db8ea3..af46113e 100644
--- a/ariba/tests/cluster_test.py
+++ b/ariba/tests/cluster_test.py
@@ -71,14 +71,14 @@ def test_set_assembly_kmer(self):
         clean_cluster_dir(cluster_dir)
 
 
-    def test_assemble_with_velvet(self):
-        '''test _assemble_with_velvet'''
-        cluster_dir = os.path.join(data_dir, 'cluster_test_assemble_with_velvet')
-        clean_cluster_dir(cluster_dir, exclude=set(['gene.reads_mapped.unsorted.bam']))
-        c = cluster.Cluster(cluster_dir)
-        c._assemble_with_velvet()
-        self.assertEqual(c.status_flag.to_number(), 0)
-        clean_cluster_dir(cluster_dir, exclude=set(['gene.reads_mapped.unsorted.bam']))
+    #def test_assemble_with_velvet(self):
+    #    '''test _assemble_with_velvet'''
+    #    cluster_dir = os.path.join(data_dir, 'cluster_test_assemble_with_velvet')
+    #    clean_cluster_dir(cluster_dir, exclude=set(['gene.reads_mapped.unsorted.bam']))
+    #    c = cluster.Cluster(cluster_dir)
+    #    c._assemble_with_velvet()
+    #    self.assertEqual(c.status_flag.to_number(), 0)
+    #    clean_cluster_dir(cluster_dir, exclude=set(['gene.reads_mapped.unsorted.bam']))
 
 
     def test_assemble_with_spades(self):
diff --git a/setup.py b/setup.py
index 4c50e353..595ea63d 100644
--- a/setup.py
+++ b/setup.py
@@ -11,6 +11,7 @@
     'SSPACE_Basic_v2.0.pl',
     'samtools',
     'smalt',
+    'spades.py',
 ]
 
 print('Checking that dependencies are found in path...')
@@ -27,11 +28,6 @@
     sys.exit(1)
 
 
-if not(  (shutil.which('velveth') and shutil.which('velvetg')) or shutil.which('spades.py')  ):
-    print('Must have velvet (velveth and velvetg) or spades.py installed. Cannot continue', file=sys.stderr)
-    sys.exit(1)
-
-
 print('... all dependencies found')
 
 

From d3f030be6c32a3c1f38eb5ce3c0069350948ffc2 Mon Sep 17 00:00:00 2001
From: Martin Hunt <mh12@sanger.ac.uk>
Date: Tue, 17 Feb 2015 13:02:32 +0000
Subject: [PATCH 02/10] Use spades by default ; check dependencies

---
 ariba/__init__.py       |  1 +
 ariba/cluster.py        |  6 +--
 ariba/clusters.py       |  3 ++
 ariba/external_progs.py | 87 +++++++++++++++++++++++++++++++++++++++++
 ariba/tasks/run.py      | 30 ++++++++------
 5 files changed, 112 insertions(+), 15 deletions(-)
 create mode 100644 ariba/external_progs.py

diff --git a/ariba/__init__.py b/ariba/__init__.py
index bc52112f..2c86f770 100644
--- a/ariba/__init__.py
+++ b/ariba/__init__.py
@@ -3,6 +3,7 @@
     'cluster',
     'clusters',
     'common',
+    'external_progs',
     'flag',
     'histogram',
     'link',
diff --git a/ariba/cluster.py b/ariba/cluster.py
index 37eff498..7f432940 100644
--- a/ariba/cluster.py
+++ b/ariba/cluster.py
@@ -20,7 +20,6 @@ def __init__(self,
       nucmer_min_id=90,
       nucmer_min_len=50,
       nucmer_breaklen=50,
-      spades='spades.py',
       spades_only_assembler=False,
       sspace_k=20,
       reads_insert=500,
@@ -36,6 +35,7 @@ def __init__(self,
       bcftools_exe='bcftools',
       gapfiller_exe='GapFiller.pl',
       samtools_exe='samtools',
+      spades_exe='spades.py',
       sspace_exe='SSPACE_Basic_v2.0.pl',
       velvet_exe='velvet', # prefix of velvet{g,h}
     ):
@@ -71,8 +71,8 @@ def __init__(self,
         self._set_assembly_kmer(assembly_kmer)
         self.assembler = assembler
         assert self.assembler in ['velvet', 'spades']
-        self.spades = spades
         self.spades_only_assembler = spades_only_assembler
+        self.spades_exe = spades_exe
 
         self.bcftools_exe = bcftools_exe
 
@@ -185,7 +185,7 @@ def _assemble_with_velvet(self):
 
     def _assemble_with_spades(self, unittest=False):
         cmd = ' '.join([
-            self.spades,
+            self.spades_exe,
             '-1', self.reads1,
             '-2', self.reads2,
             '-o', self.assembler_dir,
diff --git a/ariba/clusters.py b/ariba/clusters.py
index 31c4116b..63d2795b 100644
--- a/ariba/clusters.py
+++ b/ariba/clusters.py
@@ -33,6 +33,7 @@ def __init__(self,
       bcftools_exe='bcftools',
       gapfiller_exe='GapFiller.pl',
       samtools_exe='samtools',
+      spades_exe='spades.py',
       sspace_exe='SSPACE_Basic_v2.0.pl',
       velvet_exe='velvet', # prefix of velvet{g,h}
     ):
@@ -83,6 +84,7 @@ def __init__(self,
         self.gapfiller_exe = os.path.realpath(self.gapfiller_exe) # otherwise gapfiller dies loading packages
 
         self.samtools_exe = samtools_exe
+        self.spades_exe = spades_exe
 
         self.sspace_exe = shutil.which(sspace_exe)
         if self.sspace_exe is None:
@@ -248,6 +250,7 @@ def _init_and_run_clusters(self):
                 bcftools_exe=self.bcftools_exe,
                 gapfiller_exe=self.gapfiller_exe,
                 samtools_exe=self.samtools_exe,
+                spades_exe=self.spades_exe,
                 sspace_exe=self.sspace_exe,
                 velvet_exe=self.velvet,
             )
diff --git a/ariba/external_progs.py b/ariba/external_progs.py
new file mode 100644
index 00000000..f345efd3
--- /dev/null
+++ b/ariba/external_progs.py
@@ -0,0 +1,87 @@
+import shutil
+import subprocess
+import os
+from distutils.version import LooseVersion
+import re
+import sys
+import pyfastaq
+from ariba import common
+
+class Error (Exception): pass
+
+def is_in_path(prog):
+    return shutil.which(prog) is not None
+
+
+prog_to_version_cmd = {
+    'bcftools': ('bcftools', re.compile('^Version: ([0-9\.]+)')),
+    'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version ([0-9\.]+)')),
+    'smalt': ('smalt version', re.compile('^Version: ([0-9\.]+)')),
+    'spades': ('spades.py', re.compile('^SPAdes genome assembler v.([0-9\.]+)')),
+    'samtools': ('samtools', re.compile('^Version: ([0-9\.]+)')),
+    'sspace': (None, re.compile('^Usage: .*pl \[SSPACE_(.*)\]')),
+    'gapfiller': (None, re.compile('^Usage: .*pl \[GapFiller_(.*)\]'))
+}
+
+
+def get_version(prog, path=None):
+    assert prog in prog_to_version_cmd
+    if path is None:
+        path = prog
+    if not is_in_path(path):
+        raise Error('Error getting version of ' + path + ' - not found in path.')
+
+    if prog in ['sspace', 'gapfiller']:
+        cmd = 'perl ' + os.path.realpath(shutil.which(path))
+        regex = prog_to_version_cmd[prog][1]
+    else:
+        cmd, regex = prog_to_version_cmd[prog]
+
+    cmd_output = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
+    cmd_output = common.decode(cmd_output[0]).split('\n')[:-1] + common.decode(cmd_output[1]).split('\n')[:-1]
+    for line in cmd_output:
+        hits = regex.search(line)
+        if hits:
+            return hits.group(1)
+    return 'UNKNOWN ...\n I tried running this to get the version: "' + cmd + '"\n and the output didn\'t match this regular expression: "' + regex.pattern + '"'
+
+
+
+def check_versions(opts, verbose=False):
+    if verbose:
+        print('\nChecking depencies and their versions ...\n')
+        print('tool', 'path', 'version', sep='\t')
+
+    l = [
+        ('bcftools', opts.bcftools),
+        ('nucmer', None),
+        ('smalt', opts.smalt),
+        ('spades', opts.spades),
+        ('samtools', opts.samtools),
+        ('sspace', opts.sspace),
+        ('gapfiller', opts.gapfiller),
+    ]
+     
+    min_versions = {
+        'bcftools': '1.2',
+        'samtools': '1.2',
+        'nucmer': '3.1',
+        'spades': '3.5.0',
+        'smalt': '0.7.6',
+    }
+
+    errors = []
+
+    for t in l:
+        version = get_version(t[0], path=t[1])
+        if verbose:
+            print(t[0], t[1], version, sep='\t')
+
+        if t[0] in min_versions and LooseVersion(version) < LooseVersion(min_versions[t[0]]):
+            errors.append(' '.join(['Found version', version, 'of', t[0], 'which is too low! Please update to at least', min_versions[t[0]]]))
+
+    if len(errors):
+        for e in errors:
+            print(e, file=sys.stderr)
+        raise Error('Cannot continue. Some dependencies need updating')
+
diff --git a/ariba/tasks/run.py b/ariba/tasks/run.py
index fbe17dc3..f1692e91 100644
--- a/ariba/tasks/run.py
+++ b/ariba/tasks/run.py
@@ -22,26 +22,31 @@ def run():
     nucmer_group.add_argument('--nucmer_min_len', type=int, help='Minimum alignment length (delta-filter -i) [%(default)s]', default=50, metavar='INT')
     nucmer_group.add_argument('--nucmer_breaklen', type=int, help='Value to use for -breaklen when running nucmer [%(default)s]', default=50, metavar='INT')
 
-    executables_group = parser.add_argument_group('executables locations')
-    executables_group.add_argument('--bcftools', help='Path to bcftools executable [%(default)s]', default='bcftools', metavar='PATH')
-    executables_group.add_argument('--gapfiller', help='Path to GapFiller.pl [%(default)s]', default='GapFiller.pl', metavar='PATH')
-    executables_group.add_argument('--samtools', help='Path to samtools executable [%(default)s]', default='samtools', metavar='PATH')
-    executables_group.add_argument('--sspace', help='Path to SSPACE_Basic_v2.0.pl [%(default)s]', default='SSPACE_Basic_v2.0.pl', metavar='PATH')
-    executables_group.add_argument('--velvet', help='Path to prefix of velvet{g,h} [%(default)s]', default='velvet', metavar='PATH')
+    assembly_group = parser.add_argument_group('Assembly options')
+    assembly_group.add_argument('--min_scaff_depth', type=int, help='Minimum number of read pairs needed as evidence for scaffold link between two contigs. This is also the value used for sspace -k when scaffolding [%(default)s]', default=10, metavar='INT')
+    allowed_assemblers = ['velvet', 'spades']
+    assembly_group.add_argument('--assembler', help='Assembler to use. Available options: ' + ','.join(allowed_assemblers) + ' [%(default)s]', choices=allowed_assemblers, default='spades', metavar='Assembler')
+    assembly_group.add_argument('--assembler_k', help='kmer size to use with assembler. Default is 2/3 of the read length', metavar='INT')
+    assembly_group.add_argument('--spades_only_assembler', action='store_true', help='Use --only-assembler when running SPAdes')
 
     other_group = parser.add_argument_group('Other options')
     other_group.add_argument('--genetic_code', type=int, help='Number of genetic code to use. Currently supported 1 (default) or 4', choices=[1,4], default=1, metavar='INT')
-    other_group.add_argument('--min_scaff_depth', type=int, help='Minimum number of read pairs needed as evidence for scaffold link between two contigs. This is also the value used for sspace -k when scaffolding [%(default)s]', default=10, metavar='INT')
-    allowed_assemblers = ['velvet', 'spades']
-    other_group.add_argument('--assembler', help='Assembler to use. Although SPAdes can be used, it is experimental and velvet is currently recommended. Available options: ' + ','.join(allowed_assemblers) + ' [%(default)s]', choices=allowed_assemblers, default='velvet', metavar='Assembler')
-    other_group.add_argument('--assembler_k', help='kmer size to use with assembler. Default is 2/3 of the read length', metavar='INT')
-    other_group.add_argument('--spades_only_assembler', action='store_true', help='Use --only-assembler when running SPAdes')
     other_group.add_argument('--threads', type=int, help='Number of threads for smalt and spades [%(default)s]', default=1, metavar='INT')
     other_group.add_argument('--assembled_threshold', type=float, help='If proportion of gene assembled (regardless of into how many contigs) is at least this value then the flag gene_assembled is set [%(default)s]', default=0.95, metavar='FLOAT (between 0 and 1)')
     other_group.add_argument('--unique_threshold', type=float, help='If proportion of bases in gene assembled more than once is <= this value, then the flag unique_contig is set [%(default)s]', default=0.03, metavar='FLOAT (between 0 and 1)')
     other_group.add_argument('--verbose', action='store_true', help='Be verbose')
-    options = parser.parse_args()
 
+    executables_group = parser.add_argument_group('executables locations')
+    executables_group.add_argument('--bcftools', help='Path to bcftools executable [%(default)s]', default='bcftools', metavar='PATH')
+    executables_group.add_argument('--gapfiller', help='Path to GapFiller executable [%(default)s]', default='GapFiller.pl', metavar='PATH')
+    executables_group.add_argument('--samtools', help='Path to samtools executable [%(default)s]', default='samtools', metavar='PATH')
+    executables_group.add_argument('--smalt', help='Path to SMALT executable [%(default)s]', default='smalt', metavar='PATH')
+    executables_group.add_argument('--spades', help='Path to SPAdes executable [%(default)s]', default='spades.py', metavar='PATH')
+    executables_group.add_argument('--sspace', help='Path to SSPACE executable [%(default)s]', default='SSPACE_Basic_v2.0.pl', metavar='PATH')
+    executables_group.add_argument('--velvet', help='Path to prefix of velvet{g,h} [%(default)s]', default='velvet', metavar='PATH')
+
+    options = parser.parse_args()
+    ariba.external_progs.check_versions(options, verbose=options.verbose)
     pyfastaq.sequences.codon2aa = pyfastaq.genetic_codes.codes[options.genetic_code]
 
     c = ariba.clusters.Clusters(
@@ -66,6 +71,7 @@ def run():
           bcftools_exe=options.bcftools,
           gapfiller_exe=options.gapfiller,
           samtools_exe=options.samtools,
+          spades_exe=options.spades,
           sspace_exe=options.sspace,
           velvet_exe=options.velvet,
         )

From 95e8d9a5a4ebfe7327552538235695c0fe46fd6b Mon Sep 17 00:00:00 2001
From: Martin Hunt <mh12@sanger.ac.uk>
Date: Tue, 17 Feb 2015 13:14:51 +0000
Subject: [PATCH 03/10] Add --spades_other option, remove
 --spades_only_assembler option

---
 ariba/cluster.py   | 8 ++++----
 ariba/clusters.py  | 6 +++---
 ariba/tasks/run.py | 6 +++---
 3 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/ariba/cluster.py b/ariba/cluster.py
index 7f432940..38ea162e 100644
--- a/ariba/cluster.py
+++ b/ariba/cluster.py
@@ -20,7 +20,6 @@ def __init__(self,
       nucmer_min_id=90,
       nucmer_min_len=50,
       nucmer_breaklen=50,
-      spades_only_assembler=False,
       sspace_k=20,
       reads_insert=500,
       sspace_sd=0.4,
@@ -38,6 +37,7 @@ def __init__(self,
       spades_exe='spades.py',
       sspace_exe='SSPACE_Basic_v2.0.pl',
       velvet_exe='velvet', # prefix of velvet{g,h}
+      spades_other=None,
     ):
 
         self.root_dir = os.path.abspath(root_dir)
@@ -71,8 +71,8 @@ def __init__(self,
         self._set_assembly_kmer(assembly_kmer)
         self.assembler = assembler
         assert self.assembler in ['velvet', 'spades']
-        self.spades_only_assembler = spades_only_assembler
         self.spades_exe = spades_exe
+        self.spades_other = spades_other
 
         self.bcftools_exe = bcftools_exe
 
@@ -192,8 +192,8 @@ def _assemble_with_spades(self, unittest=False):
             '-k', str(self.assembly_kmer),
             '--threads', str(self.threads),
         ])
-        if self.spades_only_assembler:
-            cmd += ' --only-assembler'
+        if self.spades_other is not None:
+            cmd += ' ' + self.spades_other
 
         cwd = os.getcwd()
         os.chdir(self.assembly_dir)
diff --git a/ariba/clusters.py b/ariba/clusters.py
index 63d2795b..a9bc993d 100644
--- a/ariba/clusters.py
+++ b/ariba/clusters.py
@@ -22,7 +22,7 @@ def __init__(self,
       smalt_k=13,
       smalt_s=2,
       smalt_min_id=0.9,
-      spades_only_assembler=False,
+      spades_other=None,
       max_insert=1000,
       min_scaff_depth=10,
       nucmer_min_id=90,
@@ -45,7 +45,7 @@ def __init__(self,
         self.assembler = assembler
         assert self.assembler in ['velvet', 'spades']
         self.assembly_kmer = assembly_kmer
-        self.spades_only_assembler = spades_only_assembler
+        self.spades_other = spades_other
 
         self.bam_prefix = os.path.join(self.outdir, 'map_all_reads')
         self.bam = self.bam_prefix + '.bam'
@@ -239,7 +239,6 @@ def _init_and_run_clusters(self):
                 nucmer_min_id=self.nucmer_min_id,
                 nucmer_min_len=self.nucmer_min_len,
                 nucmer_breaklen=self.nucmer_breaklen,
-                spades_only_assembler=self.spades_only_assembler,
                 sspace_k=self.min_scaff_depth,
                 reads_insert=self.insert_size,
                 sspace_sd=self.insert_sspace_sd,
@@ -253,6 +252,7 @@ def _init_and_run_clusters(self):
                 spades_exe=self.spades_exe,
                 sspace_exe=self.sspace_exe,
                 velvet_exe=self.velvet,
+                spades_other=self.spades_other
             )
 
             self.clusters[gene].run()
diff --git a/ariba/tasks/run.py b/ariba/tasks/run.py
index f1692e91..e1a233fc 100644
--- a/ariba/tasks/run.py
+++ b/ariba/tasks/run.py
@@ -23,11 +23,11 @@ def run():
     nucmer_group.add_argument('--nucmer_breaklen', type=int, help='Value to use for -breaklen when running nucmer [%(default)s]', default=50, metavar='INT')
 
     assembly_group = parser.add_argument_group('Assembly options')
-    assembly_group.add_argument('--min_scaff_depth', type=int, help='Minimum number of read pairs needed as evidence for scaffold link between two contigs. This is also the value used for sspace -k when scaffolding [%(default)s]', default=10, metavar='INT')
     allowed_assemblers = ['velvet', 'spades']
     assembly_group.add_argument('--assembler', help='Assembler to use. Available options: ' + ','.join(allowed_assemblers) + ' [%(default)s]', choices=allowed_assemblers, default='spades', metavar='Assembler')
+    assembly_group.add_argument('--min_scaff_depth', type=int, help='Minimum number of read pairs needed as evidence for scaffold link between two contigs. This is also the value used for sspace -k when scaffolding [%(default)s]', default=10, metavar='INT')
     assembly_group.add_argument('--assembler_k', help='kmer size to use with assembler. Default is 2/3 of the read length', metavar='INT')
-    assembly_group.add_argument('--spades_only_assembler', action='store_true', help='Use --only-assembler when running SPAdes')
+    assembly_group.add_argument('--spades_other', help='Put options string to be used with spades in quotes. This will NOT be sanity checked. Do not use -k or -t: for these options you should use the ariba run options --assembler_k and --threads')
 
     other_group = parser.add_argument_group('Other options')
     other_group.add_argument('--genetic_code', type=int, help='Number of genetic code to use. Currently supported 1 (default) or 4', choices=[1,4], default=1, metavar='INT')
@@ -65,7 +65,7 @@ def run():
           nucmer_min_id=options.nucmer_min_id,
           nucmer_min_len=options.nucmer_min_len,
           nucmer_breaklen=options.nucmer_breaklen,
-          spades_only_assembler=options.spades_only_assembler,
+          spades_other=options.spades_other,
           assembled_threshold=options.assembled_threshold,
           unique_threshold=options.unique_threshold,
           bcftools_exe=options.bcftools,

From 0cee26ef13f946cb2069e1f57c3b0ce99addc958 Mon Sep 17 00:00:00 2001
From: Martin Hunt <mh12@sanger.ac.uk>
Date: Tue, 17 Feb 2015 13:47:30 +0000
Subject: [PATCH 04/10] Improve verbose output; use --trusted-contigs

---
 ariba/cluster.py        | 23 +++++++++++++----------
 ariba/clusters.py       | 22 ++++++++++++++++++++--
 ariba/external_progs.py |  4 +++-
 3 files changed, 36 insertions(+), 13 deletions(-)

diff --git a/ariba/cluster.py b/ariba/cluster.py
index 38ea162e..6e762cab 100644
--- a/ariba/cluster.py
+++ b/ariba/cluster.py
@@ -140,6 +140,17 @@ def _set_assembly_kmer(self, k):
 
 
     def _assemble_with_velvet(self):
+        # map reads to reference gene to make BAM input to velvet columbus
+        mapping.run_smalt(
+            self.reads1,
+            self.reads2,
+            self.gene_fa,
+            self.gene_bam[:-4],
+            threads=self.threads,
+            sort=True,
+            verbose=self.verbose,
+        )
+
         cmd = ' '.join([
             self.velveth,
             self.assembler_dir,
@@ -191,6 +202,7 @@ 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,
         ])
         if self.spades_other is not None:
             cmd += ' ' + self.spades_other
@@ -659,16 +671,6 @@ def _make_report_lines(self):
 
 
     def run(self):
-        # map reads to reference gene
-        mapping.run_smalt(
-            self.reads1,
-            self.reads2,
-            self.gene_fa,
-            self.gene_bam[:-4],
-            threads=self.threads,
-            sort=True,
-        )
-
         if self.assembler == 'velvet':
             self._assemble_with_velvet()
         elif self.assembler == 'spades':
@@ -696,6 +698,7 @@ def run(self):
                 self.final_assembly_bam[:-4],
                 threads=self.threads,
                 sort=True,
+                verbose=self.verbose,
             )
             self._parse_assembly_bam()
 
diff --git a/ariba/clusters.py b/ariba/clusters.py
index a9bc993d..cf041ebc 100644
--- a/ariba/clusters.py
+++ b/ariba/clusters.py
@@ -108,7 +108,8 @@ def _map_reads(self):
             index_k=self.smalt_k,
             index_s=self.smalt_s,
             threads=self.threads,
-            minid=self.smalt_min_id
+            minid=self.smalt_min_id,
+            verbose=self.verbose,
         )
 
 
@@ -203,9 +204,11 @@ def _set_insert_size_data(self):
         (x, self.insert_size, pc95, self.insert_sspace_sd) = self.insert_hist.stats()
         self.insert_proper_pair_max = 1.1 * pc95
         if self.verbose:
+            print('\nInsert size information from reads mapped to reference genes:')
             print('Insert size:', self.insert_size, sep='\t')
             print('Insert sspace sd:', self.insert_sspace_sd, sep='\t')
             print('Max insert:', self.insert_proper_pair_max, sep='\t')
+            print()
 
 
     def _write_gene_fa(self, gene_name, outfile):
@@ -225,9 +228,12 @@ def _init_and_run_clusters(self):
         if len(self.cluster_to_dir) == 0:
             raise Error('Did not get any reads mapped to genes. Cannot continue')
 
+        counter = 0
+
         for gene in sorted(self.cluster_to_dir):
+            counter += 1
             if self.verbose:
-                print('Running', gene)
+                print('\nAssembling cluster', counter, 'of', str(len(self.cluster_to_dir)) + ':', gene)
             new_dir = self.cluster_to_dir[gene]
             self._write_gene_fa(gene, os.path.join(new_dir, 'gene.fa'))
             self.clusters[gene] = cluster.Cluster(
@@ -296,8 +302,20 @@ def _write_reports(self):
 
 
     def run(self):
+        if self.verbose:
+            print('{:_^79}'.format(' Mapping reads to reference genes '))
         self._map_reads()
+        if self.verbose:
+            print('Finished mapping\n')
+            print('{:_^79}'.format(' Generating clusters '))
         self._bam_to_clusters_reads()
         self._set_insert_size_data()
+        if self.verbose:
+            print('{:_^79}'.format(' Assembling each cluster '))
         self._init_and_run_clusters()
+        if self.verbose:
+            print('Finished assembling clusters\n')
+            print('{:_^79}'.format(' Writing report files '))
         self._write_reports()
+        if self.verbose:
+            print('Finished writing report files. All done!')
diff --git a/ariba/external_progs.py b/ariba/external_progs.py
index f345efd3..12cd9b0c 100644
--- a/ariba/external_progs.py
+++ b/ariba/external_progs.py
@@ -49,7 +49,7 @@ def get_version(prog, path=None):
 
 def check_versions(opts, verbose=False):
     if verbose:
-        print('\nChecking depencies and their versions ...\n')
+        print('{:_^79}'.format(' Checking dependencies and their versions '))
         print('tool', 'path', 'version', sep='\t')
 
     l = [
@@ -85,3 +85,5 @@ def check_versions(opts, verbose=False):
             print(e, file=sys.stderr)
         raise Error('Cannot continue. Some dependencies need updating')
 
+    if verbose:
+        print('\n... dependencies look OK.\n')

From b9bb4d4beb48161e70ed1264dd6accd26fa3cf7d Mon Sep 17 00:00:00 2001
From: Martin Hunt <mh12@sanger.ac.uk>
Date: Tue, 17 Feb 2015 14:03:29 +0000
Subject: [PATCH 05/10] Be verbose when required

---
 ariba/mapping.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/ariba/mapping.py b/ariba/mapping.py
index 3c2622eb..b4718830 100644
--- a/ariba/mapping.py
+++ b/ariba/mapping.py
@@ -15,7 +15,8 @@ def run_smalt(
       max_insert=1000,
       minid=0.9,
       sort=False,
-      extra_smalt_map_ops='-x'
+      extra_smalt_map_ops='-x',
+      verbose=False
     ):
     if extra_smalt_map_ops is None:
         extra_smalt_map_ops = ''
@@ -59,15 +60,15 @@ def run_smalt(
         intermediate_bam = final_bam
 
     map_cmd += ' -bS -T ' + ref_fa + '  - > ' + intermediate_bam
-    common.syscall(index_cmd)
-    common.syscall(map_cmd)
+    common.syscall(index_cmd, verbose=verbose)
+    common.syscall(map_cmd, verbose=verbose)
 
     if sort:
         threads = min(4, threads)
         thread_mem = int(500 / threads)
         sort_cmd = 'samtools sort -@' + str(threads) + ' -m ' + str(thread_mem) + 'M ' + intermediate_bam + ' ' + out_prefix
         index_cmd = 'samtools index ' + final_bam
-        common.syscall(sort_cmd)
-        common.syscall(index_cmd)
+        common.syscall(sort_cmd, verbose=verbose)
+        common.syscall(index_cmd, verbose=verbose)
     for fname in clean_files:
         os.unlink(fname)

From 848494f51a32584ff33f66c78b6739212ac095fe Mon Sep 17 00:00:00 2001
From: Martin Hunt <mh12@sanger.ac.uk>
Date: Tue, 17 Feb 2015 14:17:06 +0000
Subject: [PATCH 06/10] Only check path/version for assembler being used

---
 ariba/external_progs.py | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/ariba/external_progs.py b/ariba/external_progs.py
index 12cd9b0c..3ca89cc9 100644
--- a/ariba/external_progs.py
+++ b/ariba/external_progs.py
@@ -20,7 +20,9 @@ def is_in_path(prog):
     'spades': ('spades.py', re.compile('^SPAdes genome assembler v.([0-9\.]+)')),
     'samtools': ('samtools', re.compile('^Version: ([0-9\.]+)')),
     'sspace': (None, re.compile('^Usage: .*pl \[SSPACE_(.*)\]')),
-    'gapfiller': (None, re.compile('^Usage: .*pl \[GapFiller_(.*)\]'))
+    'gapfiller': (None, re.compile('^Usage: .*pl \[GapFiller_(.*)\]')),
+    'velvetg': ('velvetg', re.compile('Version ([0-9\.]+)')),
+    'velveth': ('velveth', re.compile('Version ([0-9\.]+)')),
 }
 
 
@@ -56,18 +58,27 @@ def check_versions(opts, verbose=False):
         ('bcftools', opts.bcftools),
         ('nucmer', None),
         ('smalt', opts.smalt),
-        ('spades', opts.spades),
         ('samtools', opts.samtools),
         ('sspace', opts.sspace),
         ('gapfiller', opts.gapfiller),
     ]
-     
+    
+    if opts.assembler == 'spades':
+        l.append(('spades', opts.spades))
+    elif opts.assembler == 'velvet':
+        l.append(('velvetg', opts.velvet + 'g'))
+        l.append(('velveth', opts.velvet + 'h'))
+    else:
+        raise Error('Assembler ' + opts.assembler + ' not recognised. Cannot continue')
+
     min_versions = {
         'bcftools': '1.2',
         'samtools': '1.2',
         'nucmer': '3.1',
         'spades': '3.5.0',
         'smalt': '0.7.6',
+        'velvetg': '1.2.07',
+        'velveth': '1.2.07',
     }
 
     errors = []

From a1dee8eac47a76b4d5f058c4e14114456dcd2efd Mon Sep 17 00:00:00 2001
From: Martin Hunt <mh12@sanger.ac.uk>
Date: Tue, 17 Feb 2015 14:20:01 +0000
Subject: [PATCH 07/10] Tweak usage

---
 scripts/ariba | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/ariba b/scripts/ariba
index 1316a7b3..2dfaa0d5 100755
--- a/scripts/ariba
+++ b/scripts/ariba
@@ -19,7 +19,7 @@ ordered_tasks = [
 
 
 def print_usage_and_exit():
-    print('Usage: ariba <command> [options]', file=sys.stderr)
+    print('Usage: ariba <command> [options] <required arguments>', file=sys.stderr)
     print('\nTo get minimal usage for a command use:\nariba command', file=sys.stderr)
     print('\nTo get full help for a command use one of:\nariba command -h\nariba command --help\n', file=sys.stderr)
     print('\nAvailable commands:\n', file=sys.stderr)

From 5e0c2c2564e47d19f3fcb74a7fd5dc647943e423 Mon Sep 17 00:00:00 2001
From: Martin Hunt <mh12@sanger.ac.uk>
Date: Tue, 17 Feb 2015 14:21:09 +0000
Subject: [PATCH 08/10] Do not check for spades

---
 setup.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/setup.py b/setup.py
index 595ea63d..75f24f65 100644
--- a/setup.py
+++ b/setup.py
@@ -11,7 +11,6 @@
     'SSPACE_Basic_v2.0.pl',
     'samtools',
     'smalt',
-    'spades.py',
 ]
 
 print('Checking that dependencies are found in path...')

From 1c436d57abfacac42f8dc4558cb05ce9d1c84131 Mon Sep 17 00:00:00 2001
From: Martin Hunt <mh12@sanger.ac.uk>
Date: Tue, 17 Feb 2015 14:27:02 +0000
Subject: [PATCH 09/10] Require smalt version 0.7.4 or higher

---
 ariba/external_progs.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ariba/external_progs.py b/ariba/external_progs.py
index 3ca89cc9..5a8d024c 100644
--- a/ariba/external_progs.py
+++ b/ariba/external_progs.py
@@ -76,7 +76,7 @@ def check_versions(opts, verbose=False):
         'samtools': '1.2',
         'nucmer': '3.1',
         'spades': '3.5.0',
-        'smalt': '0.7.6',
+        'smalt': '0.7.4',
         'velvetg': '1.2.07',
         'velveth': '1.2.07',
     }

From 3d0a3ba44b184edad3c9128e9ae6ec819715a708 Mon Sep 17 00:00:00 2001
From: Martin Hunt <mh12@sanger.ac.uk>
Date: Tue, 17 Feb 2015 14:27:39 +0000
Subject: [PATCH 10/10] Mummer, SPAdes dependency; tweak usage

---
 README.md | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index 55990e56..cee5f85b 100644
--- a/README.md
+++ b/README.md
@@ -11,8 +11,10 @@ Dependencies:
   * [samtools and bcftools] [samtools]  version >= 1.2
   * [SSPACE-basic scaffolder] [sspace]
   * [GapFiller] [gapfiller]
-  * [SMALT] [smalt]
-  * [Velvet] [velvet]
+  * [MUMmer] [mummer] vesrion >= 3.23
+  * [SMALT] [smalt] version >= 0.7.4
+  * Either [SPAdes] [spades] version >= 3.5.0 or [Velvet] [velvet] version >= 1.2.07
+    (SPAdes is recommended)
 
 Install with pip:
 
@@ -35,7 +37,7 @@ Usage
 The installation will put a single script called `ariba` in your path.
 The usage is:
 
-    ariba <command> [options]
+    ariba <command> [options] <required arguments>
 
 Run just `ariba` to get a list of tasks. Use `-h` or `--help`
 with a task to get the help, for example
@@ -48,8 +50,10 @@ To run the pipeline to identify the genes present in a pair of FASTQ files:
 
 
 
-  [smalt]: https://www.sanger.ac.uk/resources/software/smalt/
-  [sspace]: http://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE
   [gapfiller]: http://www.baseclear.com/genomics/bioinformatics/basetools/gapfiller
+  [mummer]: http://mummer.sourceforge.net/
   [samtools]: http://www.htslib.org/
+  [smalt]: https://www.sanger.ac.uk/resources/software/smalt/
+  [spades]: http://bioinf.spbau.ru/spades
+  [sspace]: http://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE
   [velvet]: http://www.ebi.ac.uk/~zerbino/velvet/