changeset 4:54358dfa62c0 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readfile.py	Fri Mar 28 13:41:22 2014 -0400
@@ -0,0 +1,19 @@
+#!/usr/bin/env python
+
+import io
+import urllib2, urllib, httplib
+def getListFromFile(file):
+    idlist=[]
+    for line in file:
+        if int(line):
+            idlist.append(line.strip())
+    return idlist
+
+def getresult(url):
+    try:
+        connection = urllib2.urlopen(url)
+    except urllib2.HTTPError, e:
+        return ""
+    else:
+        return connection.read().rstrip()
+        

Binary file readfile.pyc has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rest_tool.py	Fri Mar 28 13:41:22 2014 -0400
@@ -0,0 +1,54 @@
+#!/usr/bin/env python
+# Aufruf convert_graph.py --type type --operation op --id id --outfile outfile
+
+import sys, os
+import argparse
+
+import readfile
+
+txt_output=["cids", "summary", "synonyms" ]
+
+def main(args):
+    url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/"+args.type+"/"
+    if args.type == "assay":
+        url+="aid/"
+    elif args.type == "compound":
+        url+="cid/"
+    elif args.type == "substance":
+        url+="sid/"
+    if args.idfile is None:
+        idstring=str(args.id)
+    else:
+        idlist=readfile.getListFromFile(args.idfile)
+        idstring=",".join(idlist)
+    url+=idstring+"/"+args.operation+"/"
+    if args.operation in txt_output:
+        url+="txt"
+    else:
+        url+="csv"
+    print(url)
+    data=readfile.getresult(url)
+    outfile=args.outfile
+    outfile.write(data)
+    outfile.close()
+    
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--type', type=str,
+        help="That you want BioAssay Compund ...")
+    parser.add_argument('--id', type=str,
+        help="Specify the ID")
+    parser.add_argument('--operation', type=str,
+        help="Specify the operation")
+    parser.add_argument('--property-value', type=str,
+        help="Specify the property")
+    parser.add_argument('--outfile', type=argparse.FileType('w'),
+        help="Specify one output file")
+    parser.add_argument('--idfile', type=argparse.FileType('r'),
+        help="Specify a file with a list of ids, one per line")
+    if len(sys.argv) < 8:
+        print "Too few arguments..."
+        parser.print_help()
+        exit(1)
+    args = parser.parse_args()
+    main( args )

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rest_tool.xml	Fri Mar 28 13:41:22 2014 -0400
@@ -0,0 +1,119 @@
+<tool id="rest_tool" name="Fetch Data from pubchem" version="0.1.0">
+    <description>Fetch pubchem data</description>
+    <version_command>echo "0.1.0"</version_command>
+    <requirements>
+        <requirement type="set_environment">REST_TOOL_SCRIPT_PATH</requirement>
+    </requirements>
+    <command interpreter="python">
+        #if $choose_action.action == 'specific_data':
+        rest_tool.py
+            #if $choose_action.field_or_file1.field_or_file1 == 'field':
+            --id $choose_action.field_or_file1.id1 
+            #else:
+            --idfile $choose_action.field_or_file1.file_ids_1
+            #end if
+            --type $choose_action.input_type 
+            
+            --operation $choose_action.operation_property.operation
+            #if $choose_action.operation_property.operation == 'property':
+                --property-value $choose_action.operation_property.property
+            #end if
+            
+            --outfile $output
+        #elif $choose_action.action == 'compounds_for_assay':
+            rest_tool_comp_for_assay.py
+            #if $choose_action.field_or_file2.field_or_file2 == 'field':
+            --aid $choose_action.field_or_file2.id2 
+            #else:
+            --aidfile $choose_action.field_or_file2.file_ids_2
+            #end if
+            --outfile $output
+        #elif $choose_action.action == 'assays_by_activity':
+            rest_tool_assay_by_activity_or_target.py --activity $choose_action.activity --outfile $output
+        #elif $choose_action.action == 'assays_by_targets':
+            rest_tool_assay_by_activity_or_target.py --targettype $choose_action.target_identifier_type --targetid $choose_action.target_id --outfile $output
+        #end if
+    </command>
+
+    <inputs>
+        <conditional name="choose_action">
+            <param name="action" multiple="false" type="select" label="Choose action">
+                <option value="specific_data">Get Data for specific Assay/Compound/Substance</option>
+                <option value="compounds_for_assay">Get all compound IDs to given BioAssays</option>
+                <option value="all_assay_with_compounds">Get all BioAssay IDs with Compound IDs</option>
+                <option value="assays_by_activity">Get BioAssays for activity</option>
+                <option value="assays_by_targets">Get BioAssays for targets</option>
+            </param>
+            <when value="specific_data">
+                <param name="input_type" multiple="false" type="select" label="Input Type">
+                    <option value="assay">BioAssay</option>
+                    <option value="compound">Compound</option>
+                    <option value="substance">Substance</option>
+                </param>
+                <conditional name="field_or_file1">
+                    <param name="field_or_file1" multiple="false" type="select" label="Specify the ID by">
+                        <option value="field">Textfield</option>
+                        <option value="file">File</option>
+                    </param>
+                    <when value="field">
+                        <param format="txt" name="id1" type="text" label="Enter the ID(s)" />
+                    </when>
+                    <when value="file">
+                        <param format="txt,csv" name="file_ids_1" type="data" label="Give the file" />
+                    </when>
+                </conditional>
+                
+                <conditional name="operation_property">
+                    <param name="operation" type="select" multiple="false" label="Operation">
+                    <option value="synonyms">Synonyms</option>
+                    <option value="cids">CIDs</option>
+                    <option value="property">Property</option>
+                    <option value="xrefs">XRefs</option>
+                    <option value="description">Discription</option>
+                    <option value="summary">Summary</option>
+                    </param>
+                    <when value="property">
+                        <param name="property" label="Specify Property" type="text" />
+                    </when>
+                </conditional>
+
+            </when>
+            <when value="compounds_for_assay">
+                <conditional name="field_or_file2">
+                    <param name="field_or_file2" multiple="false" type="select" label="Specify the ID by">
+                        <option value="field">Textfield</option>
+                        <option value="file">File</option>
+                    </param>
+                    <when value="field">
+                        <param format="txt" name="id2" type="text" label="Enter the ID(s)" />
+                    </when>
+                    <when value="file">
+                        <param format="txt,csv" name="file_ids_2" type="data" label="Give the file" />
+                    </when>
+                </conditional>
+            </when>
+            <when value="assays_by_activity">
+                <param format="txt" name="activity" type="text" label="Enter the activity " />
+            </when>
+            <when value="assays_by_targets">
+                <param name="target_identifier_type" multiple="false" type="select" label="Choose target identifier">
+                    <option value="gi">GI</option>
+                    <option value="geneid">Gene ID</option>
+                    <option value="genesymbol">Gene Symbol</option>
+                </param>
+                <param format="txt" name="target_id" type="text" label="Enter the target" />
+            </when>
+            
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="csv" name="output" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+**What it does**
+
+This tool fetches data from pubchem
+    </help>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rest_tool_assay_by_activity_or_target.py	Fri Mar 28 13:41:22 2014 -0400
@@ -0,0 +1,39 @@
+#!/usr/bin/env python
+# Aufruf convert_graph.py --aid list of ids --aid-from-file file
+
+import sys, os
+import argparse
+
+
+import readfile
+
+def main(args):
+    #search for acitivity or target
+    url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/"
+    if args.activity is None:
+        #target
+        url+="target/"+args.targettype+"/"+args.targetid
+    else:
+        url+="activity/"+args.activity
+    url+="/aids/txt"
+    data=readfile.getresult(url)
+    args.outfile.write(data)
+    args.outfile.close()
+    
+    
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--activity', type=str,
+        help="Activities you are looking for")
+    parser.add_argument('--targettype', type=str,
+        help="The target identifier type")
+    parser.add_argument('--targetid', type=str,
+        help="The specific target")
+    parser.add_argument('--outfile', type=argparse.FileType('w'),
+        help="Specify output file")
+    if len(sys.argv) < 2:
+        print "Too few arguments..."
+        parser.print_help()
+        exit(1)
+    args = parser.parse_args()
+    main( args )

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rest_tool_comp_for_assay.py	Fri Mar 28 13:41:22 2014 -0400
@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+# Aufruf convert_graph.py --aid list of ids --aid-from-file file
+
+import sys, os
+import networkx as nx
+import argparse
+import urllib2, urllib, httplib
+
+import readfile
+#supported graph_types
+#output_types = ["tsv", "csv", "png", "json", "txt", "xml", "sdf", "asnt", "asnb", "jsonp"]
+
+        
+#get the cids for bioassay aid
+def getCompoundList(aidlist):
+    aidliststring=",".join(aidlist)
+    url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/"+aidliststring+"/cids/txt"
+    data=readfile.getresult(url)
+    return data
+        
+def main(args):
+    if args.aidfile is None:
+        aidlist=args.aid.split(",")
+    else:
+        aidlist=readfile.getListFromFile(args.aidfile)
+    cids=getCompoundList(aidlist)
+    args.outfile.write(cids)
+    args.outfile.close()
+    
+    
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--aid', type=str,
+        help="AIDs of the BioAssay")
+    parser.add_argument('--aidfile', type=argparse.FileType('r'),
+        help="Specify a file with a list of aids, one per line")
+    parser.add_argument('--outfile', type=argparse.FileType('w'),
+        help="Specify output file")
+    if len(sys.argv) < 2:
+        print "Too few arguments..."
+        parser.print_help()
+        exit(1)
+    args = parser.parse_args()
+    main( args )

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Mar 28 13:41:22 2014 -0400
@@ -0,0 +1,5 @@
+<tool_dependency>
+    <set_environment version="1.0">
+        <environment_variable name="REST_TOOL_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
+</tool_dependency>