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flexible find exe #113

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flexible find exe #113

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2d5f022
flexible find exe
Dec 19, 2020
acbfeb7
close log prior to passing args to species_pileup via utility.parallel
Dec 19, 2020
80b689d
fixed indentation error; added pop of log from args
Dec 19, 2020
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13 changes: 7 additions & 6 deletions midas/run/snps.py
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Original file line number Diff line number Diff line change
Expand Up @@ -160,20 +160,19 @@ def keep_read(aln):
else:
aln_stats['mapped_reads'] += 1
return True
def species_pileup(args, species_id, contigs):

# Set global variables for read filtering
global global_args # need global for keep_read function
global_args = args

# summary stats
global aln_stats
aln_stats = {'genome_length':0,
'total_depth':0,
'covered_bases':0,
'aligned_reads':0,
'mapped_reads':0}
'total_depth':0,
'covered_bases':0,
'aligned_reads':0,
'mapped_reads':0}

# open outfiles
out_path = '%s/snps/output/%s.snps.gz' % (args['outdir'], species_id)
Expand Down Expand Up @@ -220,6 +219,8 @@ def pysam_pileup(args, species, contigs):
start = time()
print("\nCounting alleles")
args['log'].write("\nCounting alleles\n")
args['log'].close()
args.pop('log', None)

# run pileups per species in parallel
argument_list = []
Expand Down
27 changes: 14 additions & 13 deletions midas/utility.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
# Freely distributed under the GNU General Public License (GPLv3)

import io, os, stat, sys, resource, gzip, platform, bz2, Bio.SeqIO
from distutils.spawn import find_executable

__version__ = '1.3.0'

Expand Down Expand Up @@ -106,23 +107,23 @@ def init_worker():
pool.join()
sys.exit("\nKeyboardInterrupt")

def find_exe(exe, path):
""" Finding executable """
if find_executable(exe) is None:
exe = os.path.join(path, exe)
if not os.path.isfile(exe):
sys.exit("\nError: File not found: %s\n" % exe)
if find_executable(exe) is None:
sys.exit("\nError: Executable not found: %s\n" % exe)
return exe

def add_executables(args):
""" Identify relative file and directory paths """
src_dir = os.path.dirname(os.path.abspath(__file__))
main_dir = os.path.dirname(src_dir)
args['stream_seqs'] = '/'.join([src_dir, 'run', 'stream_seqs.py'])
args['hs-blastn'] = '/'.join([main_dir, 'bin', platform.system(), 'hs-blastn'])
args['bowtie2-build'] = '/'.join([main_dir, 'bin', platform.system(), 'bowtie2-build'])
args['bowtie2'] = '/'.join([main_dir, 'bin', platform.system(), 'bowtie2'])
args['samtools'] = '/'.join([main_dir, 'bin', platform.system(), 'samtools'])

for arg in ['hs-blastn', 'stream_seqs', 'bowtie2-build', 'bowtie2', 'samtools']:
if not os.path.isfile(args[arg]):
sys.exit("\nError: File not found: %s\n" % args[arg])

for arg in ['hs-blastn', 'bowtie2-build', 'bowtie2', 'samtools']:
if not os.access(args[arg], os.X_OK):
sys.exit("\nError: File not executable: %s\n" % args[arg])
args['stream_seqs'] = find_exe('stream_seqs.py', os.path.join(src_dir, 'run'))
for exe in ['hs-blastn', 'bowtie2-build', 'bowtie2', 'samtools']:
args[exe] = find_exe(exe, os.path.join(main_dir, 'bin', platform.system()))

import subprocess as sp

Expand Down