from micall.core import project_config
from micall.utils.externals import Bowtie2, Bowtie2Build, LineCounter
BOWTIE_THREADS = 1 # Bowtie performance roughly scales with number of threads
BOWTIE_VERSION = '2.2.8' # version of bowtie2, used for version control
BOWTIE_PATH = 'bowtie2-align-s' # path to executable, so you can install more than one version
BOWTIE_BUILD_PATH = 'bowtie2-build-s'
# Read and reference gap open/extension penalties.
READ_GAP_OPEN = 10
READ_GAP_EXTEND = 3
REF_GAP_OPEN = 10
REF_GAP_EXTEND = 3
logger = logging.getLogger(__name__)
line_counter = LineCounter()
def prelim_map(fastq1,
fastq2,
prelim_csv,
nthreads=BOWTIE_THREADS,
rdgopen=READ_GAP_OPEN,
rfgopen=REF_GAP_OPEN,
stderr=sys.stderr,
gzip=False,
work_path='',
excluded_seeds=None):
""" Run the preliminary mapping step.
@param fastq1: the file name for the forward reads in FASTQ format
def __init__(self, parent, *args, **kwargs):
self.pssm = Pssm(
path_to_lookup=AssetWrapper('micall/g2p/g2p_fpr.txt').path,
path_to_matrix=AssetWrapper('micall/g2p/g2p.matrix').path)
tk.Frame.__init__(self, parent, *args, **kwargs)
self.parent = parent
parent.report_callback_exception = self.report_callback_exception
self.rundir = None # path to MiSeq run folder containing data
self.workdir = gettempdir() # default to temp directory
os.chdir(self.workdir)
self.line_counter = LineCounter()
self.run_info = None
self.target_files = []
self.button_frame = tk.Frame(self)
self.button_frame.pack(side='top')
self.console_frame = tk.Frame(self)
self.console_frame.pack(side='top', fill='both', expand=True)
try:
with open(MiCall.CONFIG_FILE, 'rU') as f:
self.config = json.load(f)
except:
self.config = {}
self.nthreads = self.config.get('threads', None)
if not self.nthreads:
self.nthreads = int(round(cpu_count() * 0.5))
self.config['threads'] = self.nthreads
self.write_config()
self.button_run = tk.Button(self.button_frame,
text="Run",
command=self.process_files)
self.button_run.grid(row=0, column=1, sticky='W')
self.progress_bar = Progressbar(self.button_frame,
orient='horizontal',
length=500,
mode='determinate')
self.progress_bar.grid(row=1, columnspan=5)
scrollbar = tk.Scrollbar(self.console_frame)
scrollbar.pack(side=tk.RIGHT, fill=tk.Y)
self.console = tk.Text(self.console_frame,
bg='black',
fg='white',
yscrollcommand=scrollbar.set)
self.console.pack(side=tk.LEFT, fill=tk.BOTH)
self.console.tag_configure('ERROR', foreground="red")
scrollbar.config(command=self.console.yview)
# redirect stderr to Text widget
#sys.stderr = Redirector(self.console)
self.write('Welcome to MiCall v{}, running with {} threads.\n'.format(
pipeline_version, self.nthreads))