changeset 0:85440c755ba8 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vep_rest/tool_dependencies.xml	Sat Oct 18 03:58:04 2014 -0400
@@ -0,0 +1,7 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="requests" version="2.2.1">
+        <repository changeset_revision="570c2648d96d" name="package_requests_2_2_1" owner="saketkc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="0a9eff2b87c3" name="package_pyvcf_0_6_7" owner="saketkc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vep_rest/vep_rest.py	Sat Oct 18 03:58:04 2014 -0400
@@ -0,0 +1,120 @@
+#!/usr/bin/env python
+"""
+Script to interact with Ensemble Variant Effect Predictor(VEP)
+webservice
+
+
+The MIT License (MIT)
+
+Copyright (c) 2014  Saket Choudhary<[e-mail], [e-mail]>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+
+"""
+import argparse
+import requests
+import sys
+import time
+import vcf
+
+URL = 'http://grch37.rest.ensembl.org/vep/human/region/{}:{}-{}/{}?content-type=application/json&protein=1'
+
+class VEPRestClient:
+
+    def __init__(self, input_file, output_file):
+        self.pending_urls = []
+        vcf_reader = vcf.Reader(open(input_file, 'r'))
+        self.output_file = output_file
+        for record in vcf_reader:
+            url = URL.format(record.CHROM, record.POS, record.POS, ("").join([str(x) for x in record.ALT]))
+            key = "{}:{}-{}-{}".format(record.CHROM, record.POS, record.POS, ("").join([str(x) for x in record.ALT]))
+            self.pending_urls.append((key, url))
+
+    def submit(self):
+        protein_variants = {}
+        for record in self.pending_urls:
+            vcf_key = record[0]
+            url = record[1]
+            request = requests.get(url)
+            time_delay = None
+            try:
+                retry_delay = request.headers['Retry-After']
+                time_delay = retry_delay
+            except KeyError:
+                pass
+            response = None
+            if time_delay:
+                time.sleep(time_delay)
+                request = requests.get(url)
+            try:
+                response = request.json()[0]
+            except Exception as e:
+                #TODO Better error handling
+                print e
+            if not response:
+                continue
+            variants = response['transcript_consequences']
+            consequence = ""
+            for variant in variants:
+                consequence  = ""
+                protein_id = None
+                protein_start = None
+                try:
+                    protein_id  = variant['protein_id']
+                except KeyError:
+                    pass
+                try:
+                    protein_start = variant['protein_start']
+                except KeyError:
+                    pass
+                if protein_id:
+                    if protein_id.startswith('ENSP'):
+                        if variant['protein_id'] not in protein_variants.keys():
+                            protein_variants[protein_id] = []
+                            consequence += protein_id
+                        if protein_start:
+                            try:
+                                #TODO Better error handling
+                                amino_acid_original, amino_acid_substituted = variant['amino_acids'].split("/")
+                                substitution = amino_acid_original + str(protein_start) + amino_acid_substituted
+                                if "X" not  in substitution:
+                                    protein_variants[variant['protein_id']].append(substitution)
+                                    consequence += "  ," + substitution
+                            except:
+                                pass
+
+        output = ""
+        for key, value in protein_variants.iteritems():
+            if len(value)>0:
+                output += "{}   {}\n".format(key, (",").join(value))
+
+        with open(self.output_file, 'wb') as f:
+            f.write(output)
+
+
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--input_file", type=str, required=True, help="Input file location")
+    parser.add_argument("--output_file", type=str, required=True, help="Output file location")
+    args = parser.parse_args(sys.argv[1:])
+    vep = VEPRestClient(args.input_file, args.output_file)
+    vep.submit()
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vep_rest/vep_rest.xml	Sat Oct 18 03:58:04 2014 -0400
@@ -0,0 +1,55 @@
+<tool id="vep_rest" name="VEP Rest">
+    <description>VEP Web Service</description>
+    <requirements>
+        <requirement type="package" version="2.2.1">requests</requirement>
+        <requirement type="python-module">requests</requirement>
+        <requirement type="package" version="2.2.1">pyvcf</requirement>
+        <requirement type="python-module">pyvcf</requirement>
+    </requirements>
+    <command interpreter="python">
+        vep_rest.py --input_file $input --output_file $output
+    </command>
+    <inputs>
+        <param name="input" format="vcf" type="data" label="Input variants" />
+    </inputs>
+    <outputs>
+        <data name="output" format="txt"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="vep_input.vcf"/>
+            <output name="output" file="vep_output.txt"/>
+        </test>
+    </tests>
+    <help>
+
+
+    **What it does**
+
+        This script calls VEP Rest webserice for GRCh37(http://grch37.rest.ensembl.org/) to fetch
+        consequences of  variations in the proteins ONLY. Variations in transcripts are IGNORED.
+
+        Input is a VCF file.[http://samtools.github.io/hts-specs/VCFv4.2.pdf]
+
+        Output is a text file with each line beginning with Protein identifier followed by comma separated substituions.
+        Example:
+
+        ENSP00000393181, S52C,G66W,P77S,R85K,V92M,L107I
+        ENSP00000471152, G45R,R42T,A40T,G19E,L11F,T3M
+        ENSP00000411579, S52C,G66W,P77S,R85K,V92M,L107I,E124A,E137K,R153H,R156P,E170K,S171L,P172R
+        ENSP00000349216, R9K,V16M,L31I,E48A,E61K,R77H,R80P,E94K,S95L,P96R
+        ENSP00000342313, S52C,G66W,P77S,R85K,V92M,L107I,E124A,E137K,R153H,R156P,E170K,S171L,P172R
+
+
+    **Citations**
+
+        If you use this tool in Galaxy, please cite :
+            McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F.
+            Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor.
+            Bioinformatics 26(16):2069-70(2010)
+            doi:10.1093/bioinformatics/btq330
+
+
+    </help>
+</tool>
+