Mercurial > repos > bgruening > eden_cluster_motif_finder

changeset 2:295e085b8d60 draft default tip

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Uploaded
author bgruening
date Thu, 12 Jun 2014 12:22:56 -0400
parents f8111c9f037d
children
files eden_cluster_motif_finder.py eden_cluster_splitter.pyc eden_iterative_motif_finder.pyc eden_utilities.py eden_utilities.pyc eden_wrapper.pyc motif_finder.xml tool_dependencies.xml
diffstat 8 files changed, 18 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/eden_cluster_motif_finder.py	Thu Jun 12 11:38:08 2014 -0400
+++ b/eden_cluster_motif_finder.py	Thu Jun 12 12:22:56 2014 -0400
@@ -40,8 +40,10 @@
                 motif_count = seq.count(motif)
                 if motif_count > 0:
                     res = '%s\t%s\t%s\t%s\n' % (record.id, motif_id, motif, motif_count)
-                    print res,
-    
+                    args.motif_file.write(res)
+
+    args.motif_file.close()
+
 
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description='Extract motifs patterns with EDeN.')
Binary file eden_cluster_splitter.pyc has changed
Binary file eden_iterative_motif_finder.pyc has changed
--- a/eden_utilities.py	Thu Jun 12 11:38:08 2014 -0400
+++ b/eden_utilities.py	Thu Jun 12 12:22:56 2014 -0400
@@ -59,7 +59,7 @@
             dest="fraction_center_scan",
             type=int, 
             help='Fraction of total number of instances which is used to compute densities.', 
-            default=1.0)
+            default=1)
         
     if mode == 'eden_iterative_motif_finder' or  mode == 'eden_cluster_motif' :
         parser.add_argument("-f", "--output-file", 
@@ -83,4 +83,10 @@
             help='Number of negative instances per order per positive instance.', 
             default=3)
 
-    return parser
\ No newline at end of file
+    if mode == 'eden_cluster_motif' :
+        parser.add_argument("--motif-file", 
+            dest="motif_file", 
+            type=argparse.FileType('w'),
+            default=sys.stdout,
+            help="Path to the output motif file.")
+    return parser
Binary file eden_utilities.pyc has changed
Binary file eden_wrapper.pyc has changed
--- a/motif_finder.xml	Thu Jun 12 11:38:08 2014 -0400
+++ b/motif_finder.xml	Thu Jun 12 12:22:56 2014 -0400
@@ -2,7 +2,7 @@
     <description>based on EDeN</description>
     <requirements>
         <requirement type="package" version="1.63">biopython</requirement>
-        <requirement type="package" version="1.3.5">eden</requirement>
+        <requirement type="package" version="10">eden</requirement>
     </requirements>
     <command interpreter="python">
         eden_cluster_motif_finder.py
@@ -10,7 +10,7 @@
         --input-file $infile
         --radius $radius
         --distance $distance
-        --output-dir ./
+        --output-dir "./foo"
         --num-nearest-neighbors $num_nearest_neighbors
         --neighborhood-intersection-size $neighborhood_intersection_size
         --fraction-center-scan $fraction_center_scan
@@ -18,7 +18,7 @@
         --max-order $max_order
         --min-motif-size $min_motif_size
         --num-negative-repetitions $num_negative_repetitions
-        > $output
+        --motif-file $output
     </command>
     <inputs>
         <param name="infile" type="data" format="fasta" label="sequences" help="in FASTA format (--input-file)"/>
@@ -27,7 +27,7 @@
         <param name="num_nearest_neighbors" type="integer" value="10" label="Number of nearest neighbors used in the density estimation" help="(--num-nearest-neighbors)" />
         <param name="neighborhood_intersection_size" type="integer" value="5" label="Number of nearest neighbors that must be shared in neighborhood in order to trigger neighborhood joining."
             help="(--neighborhood-intersection-size)" />
-        <param name="fraction_center_scan" type="float" value="1.0" label="Fraction of total number of instances which is used to compute densities" help="(--fraction-center-scan)" />
+        <param name="fraction_center_scan" type="integer" value="1" label="Fraction of total number of instances which is used to compute densities" help="(--fraction-center-scan)" />
         <param name="max_order" type="integer" value="3" label="Size of the order for negative shuffling" help="(--max_order)" />
         <param name="min_motif_size" type="integer" value="4" label="Size of the smallest returned motif" help="(--min-motif-size)" />
         <param name="num_negative_repetitions" type="integer" value="3" label="Size of the smallest returned motif" help="(--num-negative-repetitions)" />
--- a/tool_dependencies.xml	Thu Jun 12 11:38:08 2014 -0400
+++ b/tool_dependencies.xml	Thu Jun 12 12:22:56 2014 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="eden" version="1.3.5">
-        <repository changeset_revision="dc13e98b0e3d" name="package_eden_1_3" owner="rnateam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="eden" version="10">
+        <repository changeset_revision="d1fd8665ea78" name="package_eden_latest" owner="bgruening" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="biopython" version="1.63">
         <repository changeset_revision="d8b200f1f5a5" name="package_biopython_1_63" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" />