add option bowtie2_preset; version bump

ariba/cluster.py

@@ -38,6 +38,7 @@ def __init__(self,
       gapfiller_exe='GapFiller.pl',
       samtools_exe='samtools',
       bowtie2_exe='bowtie2',
+      bowtie2_preset='very-sensitive-local',
       smalt_exe='smalt',
       spades_exe='spades.py',
       sspace_exe='SSPACE_Basic_v2.0.pl',
@@ -95,6 +96,7 @@ def __init__(self,
         self.samtools_exe = samtools_exe
         self.smalt_exe = smalt_exe
         self.bowtie2_exe = bowtie2_exe
+        self.bowtie2_preset = bowtie2_preset
 
         if self.assembler == 'velvet':
             self.velveth = velvet_exe + 'h'
@@ -156,6 +158,7 @@ def _get_total_alignment_score(self, gene_name):
             threads=self.threads,
             samtools=self.samtools_exe,
             bowtie2=self.bowtie2_exe,
+            bowtie2_preset=self.bowtie2_preset,
             verbose=self.verbose,
         ) 
 
@@ -229,6 +232,7 @@ def _assemble_with_velvet(self):
             sort=True,
             samtools=self.samtools_exe,
             bowtie2=self.bowtie2_exe,
+            bowtie2_preset=self.bowtie2_preset,
             verbose=self.verbose,
         )
 
@@ -1007,6 +1011,7 @@ def run(self):
                 sort=True,
                 samtools=self.samtools_exe,
                 bowtie2=self.bowtie2_exe,
+                bowtie2_preset=self.bowtie2_preset,
                 verbose=self.verbose,
             )
             self._parse_assembly_bam()

ariba/clusters.py

@@ -35,6 +35,7 @@ def __init__(self,
       samtools_exe='samtools',
       smalt_exe='smalt',
       bowtie2_exe='bowtie2',
+      bowtie2_preset='very-sensitive-local',
       spades_exe='spades.py',
       sspace_exe='SSPACE_Basic_v2.0.pl',
       velvet_exe='velvet', # prefix of velvet{g,h}
@@ -70,6 +71,7 @@ def __init__(self,
         self.max_insert = max_insert
         self.smalt_exe = smalt_exe
         self.bowtie2_exe = bowtie2_exe
+        self.bowtie2_preset = bowtie2_preset
 
         self.insert_hist_bin = 10
         self.insert_hist = histogram.Histogram(self.insert_hist_bin)
@@ -146,6 +148,7 @@ def _map_reads_to_clustered_genes(self):
             threads=self.threads,
             samtools=self.samtools_exe,
             bowtie2=self.bowtie2_exe,
+            bowtie2_preset=self.bowtie2_preset,
             verbose=self.verbose,
         )
 
@@ -292,6 +295,8 @@ def _init_and_run_clusters(self):
                 bcftools_exe=self.bcftools_exe,
                 gapfiller_exe=self.gapfiller_exe,
                 samtools_exe=self.samtools_exe,
+                bowtie2_exe=self.bowtie2_exe,
+                bowtie2_preset=self.bowtie2_preset,
                 spades_exe=self.spades_exe,
                 sspace_exe=self.sspace_exe,
                 velvet_exe=self.velvet,

ariba/common.py

@@ -1,7 +1,7 @@
 import sys
 import subprocess
 
-version = '0.2.0'
+version = '0.3.0'
 
 def syscall(cmd, allow_fail=False, verbose=False):
     if verbose:

ariba/mapping.py

@@ -15,6 +15,7 @@ def run_bowtie2(
       sort=False,
       samtools='samtools',
       bowtie2='bowtie2',
+      bowtie2_preset='very-sensitive-local',
       verbose=False
     ):
 
@@ -36,7 +37,7 @@ def run_bowtie2(
     map_cmd = ' '.join([
         bowtie2,
         '--threads', str(threads),
-        '--very-sensitive-local',
+        '--' + bowtie2_preset,
         '-X', str(max_insert),
         '-x', map_index,
         '-1', reads_fwd,

ariba/tasks/run.py

@@ -31,6 +31,8 @@ def run():
     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 1,4,11 [%(default)s]', choices=[1,4,11], default=11, metavar='INT')
     other_group.add_argument('--threads', type=int, help='Number of threads for bowtie2 and spades [%(default)s]', default=1, metavar='INT')
+    bowtie2_presets = ['very-fast-local', 'fast-local', 'sensitive-local', 'very-sensitive-local']
+    other_group.add_argument('--bowtie2_preset', choices=bowtie2_presets, help='Preset option for bowtie2 mapping [%(default)s]', default='very-sensitive-local', metavar='|'.join(bowtie2_presets))
     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('--clean', type=int, choices=[0,1,2], help='Specify how much cleaning to do. 0=none, 1=some, 2=only keep the report [%(default)s]', default=1, metavar='INT')
@@ -75,6 +77,7 @@ def run():
           gapfiller_exe=options.gapfiller,
           samtools_exe=options.samtools,
           bowtie2_exe=options.bowtie2,
+          bowtie2_preset=options.bowtie2_preset,
           spades_exe=options.spades,
           sspace_exe=options.sspace,
           velvet_exe=options.velvet,

setup.py

@@ -7,7 +7,7 @@
 
 setup(
     name='ariba',
-    version='0.2.0',
+    version='0.3.0',
     description='ARIBA: Antibiotic Resistance Identification By Assembly',
     packages = find_packages(),
     author='Martin Hunt',