[galaxy-dev] [hg] galaxy 2659: Added a new option to 'fetch closest features'...

9 Sep 2009

details:   http://www.bx.psu.edu/hg/galaxy/rev/ba2412c2a4d9
changeset: 2659:ba2412c2a4d9
user:      guru
date:      Wed Sep 02 13:36:16 2009 -0400
description:
Added a new option to 'fetch closest features' tool to return the closest feature either upstream or downstream.

3 file(s) affected in this change:

test-data/closest_features_either.interval
tools/new_operations/flanking_features.py
tools/new_operations/flanking_features.xml

diffs (524 lines):

diff -r 0cb12b9d9d4d -r ba2412c2a4d9 test-data/closest_features_either.interval

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closest_features_either.interval	Wed Sep 02 13:36:16 2009 -0400
@@ -0,0 +1,424 @@
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+chr22	31776507	31781507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+	chr22	31768507	31773507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31780507	31785507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+	chr22	31772507	31777507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31784507	31789507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+	chr22	31776507	31781507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31788507	31793507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+	chr22	31780507	31785507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31792507	31797507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+	chr22	31784507	31789507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31796507	31801507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+	chr22	31788507	31793507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31800507	31805507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+	chr22	31792507	31797507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31804507	31809507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+	chr22	31796507	31801507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31808507	31813507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+	chr22	31800507	31805507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31812507	31817507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+	chr22	31804507	31809507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31816507	31821507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+	chr22	31808507	31813507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
+chr22	31820507	31825507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+	chr22	31812507	31817507	uc003bnx.1_cds_2_0_chr22_29227_f	0	+
diff -r 0cb12b9d9d4d -r ba2412c2a4d9 tools/new_operations/flanking_features.py
--- a/tools/new_operations/flanking_features.py	Tue Sep 01 17:01:44 2009 -0400
+++ b/tools/new_operations/flanking_features.py	Wed Sep 02 13:36:16 2009 -0400
@@ -62,12 +62,16 @@
 def proximal_region_finder(readers, region, comments=True):
     primary = readers[0]
     features = readers[1]
+    either = False
     if region == 'Upstream':
         up, down = True, False
     elif region == 'Downstream':
         up, down = False, True
     else:
         up, down = True, True
+        if region == 'Either':
+            either = True
+        
     # Read features into memory:
     rightTree = quicksect.IntervalTree()
     for item in features:
@@ -107,14 +111,29 @@
                         res_ind = ends.index(max(ends)) #fetch the index of the closest interval i.e. the interval with the max end from the results_up list
                     else:
                         res_ind = 0
-                    map(outfields.append, result_up[res_ind].other)
-                    yield outfields
+                    if not(either):
+                        map(outfields.append, result_up[res_ind].other)
+                        yield outfields
                 
                 if result_down:    
                     outfields = list(interval)
-                    map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval
+                    if not(either):
+                        map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval
+                        yield outfields
+                
+                if either:
+                    if result_up and result_down:
+                        if abs(start - int(result_up[res_ind].end)) <= abs(end - int(result_down[-1].start)):
+                            map(outfields.append, result_up[res_ind].other)
+                        else:
+                            map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval
+                    elif result_up:
+                        map(outfields.append, result_up[res_ind].other)
+                    else:
+                        map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval
                     yield outfields
-                
+                    
+                        
 def main():
     options, args = doc_optparse.parse( __doc__ )
     try:
diff -r 0cb12b9d9d4d -r ba2412c2a4d9 tools/new_operations/flanking_features.xml
--- a/tools/new_operations/flanking_features.xml	Tue Sep 01 17:01:44 2009 -0400
+++ b/tools/new_operations/flanking_features.xml	Wed Sep 02 13:36:16 2009 -0400
@@ -1,10 +1,11 @@
-<tool id="flanking_features_1" name="Fetch closest feature" version="2.0.0">
+<tool id="flanking_features_1" name="Fetch closest feature" version="3.0.0">
   <description>  for every interval</description>
   <command interpreter="python">flanking_features.py $input1 $input2 $out_file1 $direction -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol}</command>
   <inputs>
     <param format="interval" name="input1" type="data" label="For every interval in"/>
-    <param format="interval" name="input2" type="data" label="Fetch features from"/>
-    <param name="direction" type="select" label="Location of the flanking features">
+    <param format="interval" name="input2" type="data" label="Fetch closest feature(s) from"/>
+    <param name="direction" type="select" label="Located">
+      <option value="Either">Either Upstream or Downstream</option>
       <option value="Both">Both Upstream and Downstream</option>
       <option value="Upstream">Upstream</option>
       <option value="Downstream">Downstream</option>
@@ -14,13 +15,19 @@
     <data format="interval" name="out_file1" />
   </outputs>
   <tests>
-  	<test>
-  	  <param name="input1" value="4_windows.bed"/>
+    <test>
+      <param name="input1" value="4_windows.bed"/>
+      <param name="input2" value="4_windows_2.bed"/>
+      <param name="direction" value="Either"/>
+      <output name="out_file1" file="closest_features_either.interval"/>
+    </test>
+    <test>
+      <param name="input1" value="4_windows.bed"/>
       <param name="input2" value="4_windows_2.bed"/>
       <param name="direction" value="Both"/>
       <output name="out_file1" file="closest_features.interval"/>
-  	</test>
-  	<test>
+    </test>
+    <test>
       <param name="input1" value="4_windows.bed"/>
       <param name="input2" value="4_windows_2.bed"/>
       <param name="direction" value="Upstream"/>

    

[galaxy-dev] [hg] galaxy 2659: Added a new option to 'fetch closest features'...

Greg Von Kuster