resolved KwanLab#19 added docstring (and liscence), fixed nproc and r…

…emoved depth function

autometa/common/external/samtools.py

@@ -1,6 +1,24 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
+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/>.
+
 Script containing wrapper functions for samtools
 """
 
@@ -10,6 +28,7 @@
 import subprocess
 
 import pandas as pd
+import multiprocessing as mp
 
 logger = logging.getLogger(__name__)
 
@@ -37,22 +56,31 @@ def run(cmd):
     logger.debug(f'cmd: {cmd}')
     with open(os.devnull, 'w') as stdout, open(os.devnull, 'w') as stderr:
         retcode = subprocess.call(cmd, stdout=stdout, stderr=stderr, shell=True)
-    if retcode:
+    if not retcode:
+        return True
+    else:
         logger.warning(f'args:{cmd} retcode:{retcode}')
         return False
-    return True
 
-def sort(sam, out, nproc=0):
+def sort(sam, out, nproc=mp.cpu_count()):
+    """
+    Views the sam file and then sorts the alighnments by leftmost coordinates.
+    
+    Parameters
+    ----------
+    sam : str
+        </path/to/alignment.sam>
+    out : str
+        </path/to/output/file
+    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 {out}'
     run(cmd)
 
-def depth(bam, records):
-    cmds = [f'samtools depth -r {record.id} {bam}' for record in records]
-    raise NotImplementedError
-
 def main(args):
-    sort(args.sam)
-    depth(args.bam, args.seqs)
+    sort(args.sam, args.out, args.nproc)
 
 if __name__ == '__main__':
     import argparse
@@ -61,8 +89,8 @@ def main(args):
         format='%(asctime)s : %(name)s : %(levelname)s : %(message)s',
         datefmt='%m/%d/%Y %I:%M:%S %p')
     parser = argparse.ArgumentParser()
-    parser.add_argument('--bam')
-    parser.add_argument('--sam')
-    parser.add_argument('--seqs')
+    parser.add_argument('--sam', help='</path/to/alignment.sam>')
+    parser.add_argument('--out', help='</path/to/output/file')
+    parser.add_argument('--nproc', help='Number of processors to use', default=mp.cpu_count(), type=int)
     args = parser.parse_args()
     main(args)