resolved #19 removed run function, removed intermedediate files and r…

…enamed stderr and stdout

autometa/common/external/samtools.py

@@ -3,19 +3,15 @@
 """
 Copyright 2020 Ian J. Miller, Evan R. Rees, Kyle Wolf, Siddharth Uppal,
 Shaurya Chanana, Izaak Miller, Jason C. Kwan
-
 This file is part of Autometa.
-
 Autometa is free software: you can redistribute it and/or modify
 it under the terms of the GNU Affero General Public License as published by
 the Free Software Foundation, either version 3 of the License, or
 (at your option) any later version.
-
 Autometa is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 GNU Affero General Public License for more details.
-
 You should have received a copy of the GNU Affero General Public License
 along with Autometa. If not, see <http://www.gnu.org/licenses/>.
 
@@ -35,42 +31,8 @@
 logger = logging.getLogger(__name__)
 
 
-def run(cmd, bam):
-    """
-    Run `cmd` via subprocess.
-    
-    Parameters
-    ----------
-    cmd : str
-        Executable input str
-    bam : str
-        </path/to/output/alignment.bam>
-    
-    Returns
-    -------
-    bool
-        True if retcode == 0. i.e. function run successfully.
-    
-    Raises
-    ------
-    ChildProcessError
-        Function did not run successfully, returns retcode.
-    """
-
-    logger.debug(f'cmd: {cmd}')
-    log_samtools_dir = os.path.dirname(bam)
-    tempdir = tempfile.mkdtemp(suffix=None, prefix='samtools', dir=log_samtools_dir)
-    samtools_stderr=os.path.join(tempdir, 'samtools_stderr')
-    samtools_stdout=os.path.join(tempdir, 'samtools_stdout')
-    with open(samtools_stdout, 'w') as stdout, open(samtools_stderr, 'w') as stderr:
-        retcode = subprocess.call(cmd, stdout=stdout, stderr=stderr, shell=True)
-        if retcode != 0:
-            raise ChildProcessError(f'Samtools not successfully run, retcode: {retcode}')
-        shutil.rmtree(tempdir, ignore_errors=True)
-        return True
-
 def sort(sam, bam, nproc=mp.cpu_count()):
-    """ 
+    """
     Views then sorts sam file by leftmost coordinates and outputs to bam.
     
     Parameters
@@ -81,11 +43,33 @@ def sort(sam, bam, nproc=mp.cpu_count()):
         </path/to/output/alignment.bam>
     nproc : int, optional
         Number of processors to be used. By default uses all the processors of the system 
-    """
     
-    cmd = f'samtools view -@{nproc} -bS {sam} | samtools sort -@{nproc} -o {bam}'
-    run(cmd,bam)
+    Raises
+    ------
+    ChildProcessError
+        Samtools did not run successfully, returns retcode.
+    
+    """
 
+    cmd = f'samtools view -@{nproc} -bS {sam} | samtools sort -@{nproc} -o {bam}'
+    logger.debug(f'cmd: {cmd}')
+    samtools_out_dir = os.path.dirname(bam)
+    tempdir = tempfile.mkdtemp(suffix=None, prefix='samtools', dir=samtools_out_dir)
+    os.chdir(tempdir)
+    samtools_err = os.path.join(samtools_out_dir, 'samtools.err')
+    samtools_out = os.path.join(samtools_out_dir, 'samtools.out')
+    with open(samtools_out, 'w') as stdout, open(samtools_err, 'w') as stderr:
+        try:
+            retcode = subprocess.call(cmd, stdout=stdout, stderr=stderr, shell=True)
+            if retcode != 0:
+                raise ChildProcessError(f'Samtools not successfully run, retcode: {retcode}')
+        except ChildProcessError as err:
+            raise err     
+        finally:
+            shutil.rmtree(tempdir, ignore_errors=True)
+    os.remove(samtools_err)
+    os.remove(samtools_out)
+
 def main(args):
     sort(args.sam, args.bam, args.nproc)
 
@@ -100,5 +84,4 @@ def main(args):
     parser.add_argument('--bam', help='</path/to/output/alignment.bam>', type=str)
     parser.add_argument('--nproc', help='Number of processors to use', default=mp.cpu_count(), type=int)
     args = parser.parse_args()
-    main(args)
-
+    main(args)