Mercurial > repos > jeremyjliu > region_motif_data_manager

changeset 8:b4c2836d2e4e draft

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Uploaded
author jeremyjliu
date Fri, 30 Jan 2015 13:47:29 -0500
parents 2c918b3a7e8c
children e4229c66d78d
files data_manager/data_manager_fetch_motifs.py data_manager/data_manager_fetch_motifs.xml tool_data_table_conf.xml.sample
diffstat 3 files changed, 19 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/data_manager_fetch_motifs.py	Thu Jan 29 00:00:12 2015 -0500
+++ b/data_manager/data_manager_fetch_motifs.py	Fri Jan 30 13:47:29 2015 -0500
@@ -1,5 +1,7 @@
 #!/usr/bin/env python
-#Dan Blankenberg
+# Jeremy Liu
+# February 2015
+# Adapted from Dan Blackenburg's sample data manager
 
 import sys
 import os
@@ -20,32 +22,35 @@
 
 def download_motif_databases( data_manager_dict, params, target_directory, motif_db ):
 
+    # Select download URL, file name, data table name, and path using motif_db selector variable
     if motif_db == "pouya":
-        BGZ = ['COMPBIO URL HERE',
+        BGZ = ['http://compbio.med.harvard.edu/motif-enrichment/pouya_motifs_bed.bgz',
                 "pouya_motifs.bed.bgz", "pouya_bgz", "Pouya Encode Motifs (hg19) BGZ"]
-        TBI = ['COMPBIO URL HERE',
+        TBI = ['http://compbio.med.harvard.edu/motif-enrichment/pouya_motifs_bed.bgz.tbi',
                 "pouya_motifs.bed.bgz.tbi", "pouya_tbi", "Pouya Encode Motifs (hg19) TBI"]
     elif motif_db == "jaspar":
-        BGZ = ['COMPBIO URL HERE',
-               "jaspar_jolma_motifs.bed.bgz", "jaspar_bgz", "Jaspar and Jolma Motifs (hg19) BGZ"]
-        TBI = ['COMPBIO URL HERE',
+        BGZ = ['http://compbio.med.harvard.edu/motif-enrichment/jaspar_jolma_motifs.bed.bgz',
+                "jaspar_jolma_motifs.bed.bgz", "jaspar_bgz", "Jaspar and Jolma Motifs (hg19) BGZ"]
+        TBI = ['http://compbio.med.harvard.edu/motif-enrichment/jaspar_jolma_motifs.bed.bgz.tbi',
                 "jaspar_jolma_motifs.bed.bgz.tbi", "jaspar_tbi", "Jaspar and Jolma Motifs (hg19) TBI"]
     elif motif_db == "mouse":
-        BGZ = ['COMPBIO URL HERE',
-                "mouse_motifs.bed.bgz", "mouse_bgz", "Mouse Motifs (mm9) BGZ"]
-        TBI = ['COMPBIO URL HERE',
-                "mouse_motifs.bed.bgz.tbi", "mouse_tbi", "Mouse Motifs (mm9) TBI"]
+        BGZ = ['http://compbio.med.harvard.edu/motif-enrichment/mm9_motifs_split.bed.bgz',
+                "mm9_motifs_split.bed.bgz", "mouse_bgz", "Mouse Motifs (mm9) BGZ"]
+        TBI = ['http://compbio.med.harvard.edu/motif-enrichment/mm9_motifs_split.bed.bgz.tbi',
+                "mm9_motifs_split.bed.bgz.tbi", "mouse_tbi", "Mouse Motifs (mm9) TBI"]
     else:
-        BGZ = ['http://gehlenborg.com/wp-content/uploads/motif/pouya_test_motifs.bed.bgz', 
+        BGZ = ['http://compbio.med.harvard.edu/motif-enrichment/pouya_test_motifs.bed.bgz', 
                "pouya_test_motifs.bed.bgz", "test_bgz", "Test Pouya Subset (hg19) BGZ"]
-        TBI = ['http://gehlenborg.com/wp-content/uploads/motif/pouya_test_motifs.bed.bgz.tbi',
+        TBI = ['http://compbio.med.harvard.edu/motif-enrichment/pouya_test_motifs.bed.bgz.tbi',
                "pouya_test_motifs.bed.bgz.tbi", "test_tbi", "Test Pouya Subset (hg19) TBI"]
 
+    # Save and add motif bgz file to motif_databases data table
     bgz_reader = urllib2.urlopen( BGZ[0] )
     bgz_data_table_entry = _stream_fasta_to_file( bgz_reader, target_directory, params,
                             BGZ[1], BGZ[2], BGZ[3] )
     _add_data_table_entry( data_manager_dict, 'motif_databases', bgz_data_table_entry )
 
+    # Save and add motif tbi file to motif_databases data table
     tbi_reader = urllib2.urlopen( TBI[0] )
     tbi_data_table_entry = _stream_fasta_to_file( tbi_reader, target_directory, params,
                             TBI[1], TBI[2], TBI[3] )
--- a/data_manager/data_manager_fetch_motifs.xml	Thu Jan 29 00:00:12 2015 -0500
+++ b/data_manager/data_manager_fetch_motifs.xml	Fri Jan 30 13:47:29 2015 -0500
@@ -19,6 +19,7 @@
         CBMI source and populates the "motif_databases" data table.
 
         **TO DO**
+        
         Ability to add motif database from local file, as the last step in 
         a MEME pipeline.
     </help>
--- a/tool_data_table_conf.xml.sample	Thu Jan 29 00:00:12 2015 -0500
+++ b/tool_data_table_conf.xml.sample	Fri Jan 30 13:47:29 2015 -0500
@@ -1,5 +1,5 @@
 <tables>
-    <!-- Locations of all motif database files under genome directory -->
+    <!-- Locations of motif database files -->
     <table name="motif_databases" comment_char="#">
         <columns>value, name, path</columns>
         <file path="tool-data/motif_databases.loc" />