From 01926ede0825c3ddfd70305871a9e992eea9a2ae Mon Sep 17 00:00:00 2001
From: Aron Skaftason <arontommi@gmail.com>
Date: Fri, 12 Jan 2018 11:48:31 +0100
Subject: [PATCH] now possible to run bed files in csv files

---
 .idea/workspace.xml       | 56 ++++++++++++++++++++-------------------
 smallerbams/smallerbam.py |  5 ++++
 2 files changed, 34 insertions(+), 27 deletions(-)

diff --git a/.idea/workspace.xml b/.idea/workspace.xml
index 051bc91..abb2e4b 100644
--- a/.idea/workspace.xml
+++ b/.idea/workspace.xml
@@ -24,17 +24,17 @@
         <entry file="file://$PROJECT_DIR$/smallerbams/samtools_view.sh">
           <provider selected="true" editor-type-id="text-editor">
             <state relative-caret-position="90">
-              <caret line="6" column="0" selection-start-line="6" selection-start-column="0" selection-end-line="6" selection-end-column="0" />
+              <caret line="6" column="27" selection-start-line="6" selection-start-column="27" selection-end-line="6" selection-end-column="27" />
               <folding />
             </state>
           </provider>
         </entry>
       </file>
-      <file leaf-file-name="smallerbam.py" pinned="false" current-in-tab="false">
+      <file leaf-file-name="smallerbam.py" pinned="false" current-in-tab="true">
         <entry file="file://$PROJECT_DIR$/smallerbams/smallerbam.py">
           <provider selected="true" editor-type-id="text-editor">
-            <state relative-caret-position="541">
-              <caret line="43" column="44" selection-start-line="43" selection-start-column="44" selection-end-line="43" selection-end-column="44" />
+            <state relative-caret-position="129">
+              <caret line="16" column="12" selection-start-line="16" selection-start-column="12" selection-end-line="16" selection-end-column="12" />
               <folding>
                 <element signature="e#0#23#0" expanded="true" />
               </folding>
@@ -42,7 +42,7 @@
           </provider>
         </entry>
       </file>
-      <file leaf-file-name="Readme.md" pinned="false" current-in-tab="true">
+      <file leaf-file-name="Readme.md" pinned="false" current-in-tab="false">
         <entry file="file://$PROJECT_DIR$/Readme.md">
           <provider selected="true" editor-type-id="split-provider[text-editor;MarkdownPreviewEditor]">
             <state split_layout="SPLIT">
@@ -72,14 +72,16 @@
         <option value="$PROJECT_DIR$/samtools_view.sh" />
         <option value="$PROJECT_DIR$/smallerbam.py" />
         <option value="$PROJECT_DIR$/Readme.md" />
+        <option value="$PROJECT_DIR$/smallerbams/samtools_view.sh" />
+        <option value="$PROJECT_DIR$/smallerbams/smallerbam.py" />
       </list>
     </option>
   </component>
   <component name="ProjectFrameBounds">
-    <option name="x" value="28" />
-    <option name="y" value="23" />
+    <option name="x" value="-2532" />
+    <option name="y" value="34" />
     <option name="width" value="1191" />
-    <option name="height" value="731" />
+    <option name="height" value="1009" />
   </component>
   <component name="ProjectLevelVcsManager" settingsEditedManually="false">
     <OptionsSetting value="true" id="Add" />
@@ -313,10 +315,10 @@
     <servers />
   </component>
   <component name="ToolWindowManager">
-    <frame x="28" y="23" width="1191" height="731" extended-state="0" />
-    <editor active="false" />
+    <frame x="-2532" y="34" width="1191" height="1009" extended-state="0" />
+    <editor active="true" />
     <layout>
-      <window_info id="Project" active="true" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="true" show_stripe_button="true" weight="0.26837608" sideWeight="0.5" order="0" side_tool="false" content_ui="combo" />
+      <window_info id="Project" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="true" show_stripe_button="true" weight="0.26837608" sideWeight="0.5" order="0" side_tool="false" content_ui="combo" />
       <window_info id="TODO" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="6" side_tool="false" content_ui="tabs" />
       <window_info id="Event Log" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="-1" side_tool="true" content_ui="tabs" />
       <window_info id="Version Control" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="-1" side_tool="false" content_ui="tabs" />
@@ -353,36 +355,36 @@
     <watches-manager />
   </component>
   <component name="editorHistoryManager">
+    <entry file="file://$PROJECT_DIR$/Readme.md">
+      <provider selected="true" editor-type-id="split-provider[text-editor;MarkdownPreviewEditor]">
+        <state split_layout="SPLIT">
+          <first_editor relative-caret-position="45">
+            <caret line="3" column="4" selection-start-line="3" selection-start-column="4" selection-end-line="3" selection-end-column="4" />
+            <folding />
+          </first_editor>
+          <second_editor>
+            <js_state />
+          </second_editor>
+        </state>
+      </provider>
+    </entry>
     <entry file="file://$PROJECT_DIR$/smallerbams/samtools_view.sh">
       <provider selected="true" editor-type-id="text-editor">
         <state relative-caret-position="90">
-          <caret line="6" column="0" selection-start-line="6" selection-start-column="0" selection-end-line="6" selection-end-column="0" />
+          <caret line="6" column="27" selection-start-line="6" selection-start-column="27" selection-end-line="6" selection-end-column="27" />
           <folding />
         </state>
       </provider>
     </entry>
     <entry file="file://$PROJECT_DIR$/smallerbams/smallerbam.py">
       <provider selected="true" editor-type-id="text-editor">
-        <state relative-caret-position="541">
-          <caret line="43" column="44" selection-start-line="43" selection-start-column="44" selection-end-line="43" selection-end-column="44" />
+        <state relative-caret-position="129">
+          <caret line="16" column="12" selection-start-line="16" selection-start-column="12" selection-end-line="16" selection-end-column="12" />
           <folding>
             <element signature="e#0#23#0" expanded="true" />
           </folding>
         </state>
       </provider>
     </entry>
-    <entry file="file://$PROJECT_DIR$/Readme.md">
-      <provider selected="true" editor-type-id="split-provider[text-editor;MarkdownPreviewEditor]">
-        <state split_layout="SPLIT">
-          <first_editor relative-caret-position="45">
-            <caret line="3" column="4" selection-start-line="3" selection-start-column="4" selection-end-line="3" selection-end-column="4" />
-            <folding />
-          </first_editor>
-          <second_editor>
-            <js_state />
-          </second_editor>
-        </state>
-      </provider>
-    </entry>
   </component>
 </project>
\ No newline at end of file
diff --git a/smallerbams/smallerbam.py b/smallerbams/smallerbam.py
index 36684e1..46c89cf 100644
--- a/smallerbams/smallerbam.py
+++ b/smallerbams/smallerbam.py
@@ -12,10 +12,15 @@ def __init__(self):
 
     def runbams(self, bamfile, region, outputfile):
         """run samtools view"""
+        if str(region).endswith('.bed'):
+            region = '-L ' + region
+        else:
+            pass
         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():