ability to run multiple things with a csv added

Readme.md

@@ -1,7 +1,8 @@
 
 
 
-##### this is a simple wrapper around samtools to subset bam files to later view in Igv for less command line literate people
+##### this is a simple wrapper around samtools to subset bam files to later view in Igv for less command line literate people for visual validation of variants.
 
 additional objects are for the writer to improve software documentasion as well as use click to manage inputs
 
+The idea is to continue to add functionality, ideally being able

smallerbam.py

@@ -1,19 +1,25 @@
 import subprocess as sp
 import os
 import click
-
+import pandas as pd
 
 class StClass():
     """Main class for stuff """
-    p = os.path.dirname(os.path.realpath(__file__))
-    bashscript = str(p)+'/samtools_view.sh'
+
+    def __init__(self):
+        self.p = os.path.dirname(os.path.realpath(__file__))
+        self.bashscript = str(self.p)+'/samtools_view.sh'
 
     def runbams(self, bamfile, region, outputfile):
         """run samtools view"""
         sp.call(['{}'.format(self.bashscript),
                  '{}'.format(bamfile),
                  '{}'.format(region),
                  '{}'.format(outputfile)])
+    def runmultiple(self, csv):
+        file = pd.read_csv(csv, header=None)
+        for i, r in file.iterrows():
+            self.runbams(r[0], r[1], r[2])
 
 
 @click.command()
@@ -29,9 +35,18 @@ def runbams(self, bamfile, region, outputfile):
     '--outputfile', '-o',
     help='outputfile',
 )
-def main(inputfile, region, outputfile):
+@click.option(
+    '--csv', '-c',
+    help='if multiple files need to be created use a simple csv, no header, with first column being input file,'
+         ' second for region and third for outputfile '
+)
+
+def main(inputfile, region, outputfile, csv ):
     sc = StClass()
-    sc.runbams(inputfile, region, outputfile)
+    if csv:
+        sc.runmultiple(csv)
+    else:
+        sc.runbams(inputfile, region, outputfile)
 
 
 if __name__ == '__main__':