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

…depth function

autometa/common/external/samtools.py

@@ -28,6 +28,7 @@
 import subprocess
 
 import pandas as pd
+import multiprocessing as mp
 
 logger = logging.getLogger(__name__)
 
@@ -55,22 +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
@@ -79,8 +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)