Breaking the " same origin security policy" with CORS. An example with @GenomeBrowser / DAS.

Jerven Bolleman recently taught me about the CORS/Cross-origin resource sharing:

@yokofakun we support the CORS header. I have not looked at what jsonp needs will investigate

— Jerven Bolleman (@jervenbolleman) May 20, 2014

"Cross-origin resource sharing (CORS) is a mechanism that allows many resources (e.g. fonts, JavaScript, etc.) on a web page to be requested from another domain outside of the domain the resource originated from. In particular, JavaScript's AJAX calls can use the XMLHttpRequest mechanism. Such "cross-domain" requests would otherwise be forbidden by web browsers, per the same origin security policy."

I've created a page testing if some bioinformatics web-service support CORS. This page is available at : http://lindenb.github.io/pages/cors/index.html

Interestingly NCBI, Uniprot and UCSC support CORS. As an example, the following <form> fetches a DNA sequence using the DAS server of the UCSC and display it:

Position

The script:

That's it
Pierre

My tool to annotate VCF files.

The Variant Call Format is a text file format generated by many tools for NGS. It contains meta-information lines, a header line, and then data lines describing how the mutations were called. I don't like this format because it cannot be used to store some hierachical annotations (like json or xml), nevertheless it is a de facto standard.

I wrote a tool called vcfannotator to append a set of annotations from the UCSC database to a VCF file. As I wanted to keep this tool simple and without any dependencies, it only uses the flat files available from the download area at the UCSC.

This tools appends several informations:

• A prediction of the mutation: is it in the cDNA ? in an intron ? in an exon ? is it a non-synonymous mutation ? was a stop codon lost or gained ? is there any consequence on the splicing process ? Here, the UCSC DAS server and the KnonwGenes table are used to retrieve the genomic DNA and the structure of the gene.
• dbSNP: was this mutation found before in dbSNP ?
• Personal genomes: was this mutation found before in Venter's genome ? In Watson's genome ? etc...
• The mapability (Uniqueness of Reference Genome ): gives an idea about how the context is unique in the genome
• genomicSuperDups: is this mutation located in a segmental genomic duplication ?
• tfbsConsSites: is this mutation located in the site of a transcription factor ?
• phastCons44way: how is the mutation conserved within a multiple alignments of 44 vertebrate genomes to the human genome ?

The tool is available on github at: https://github.com/lindenb/jsandbox in jsandbox/src/sandbox/VCFAnnotator.java.

Compilation

> cd jsandbox
> ant vcfannotator

Execution & Options

> java -jar dist/vcfannotator.jar -h
VCF annotator
Pierre Lindenbaum PhD. 2010. http://plindenbaum.blogspot.com
Options:
-b ucsc.build default:hg18
-m mapability.
-g genomicSuperDups
-p basic prediction
-c phastcons prediction (phastCons44way)
-t transcription factors sites prediction
-pg personal genomes
-snp <id> add ucsc <id> must be present in "http://hgdownload.cse.ucsc.edu/goldenPath/<ucscdb>/database/<id>.txt.gz" e.g. snp129
-log <level> one value from java.util.logging.Level default:OFF
-proxyHost <host>
-proxyPort <port>

Example

Input

##fileformat=VCFv3.2
##fileDate=20091120
##source=gigabayes
##reference=ncbi36
##phasing=none
#CHROM POS ID REF ALT QUAL FILTER INFO
1 1105366 . T C 99 0 NS=471;DP=16179;AC=8;AN=942;HWE=0.0685233
1 1105373 . C T 99 0 NS=469;DP=15318;AC=5;AN=938;HWE=0.0267954
1 1108138 rs61733845 C T 99 0 NS=450;DP=16134;AC=110;AN=900;dbSNP;HWE=0.930276
1 1109206 . G A 99 0 NS=696;DP=54701;AC=2;AN=1392;HWE=0.0028777
1 1109262 . C T 99 0 NS=696;DP=55783;AC=12;AN=1392;HWE=0.104349
1 1110233 . C G 99 0 NS=694;DP=34301;AC=43;AN=1388;HWE=4.91397
1 1110240 . T A 99 0 NS=695;DP=35846;AC=3;AN=1390;HWE=0.00648883
1 1110294 rs1320571 G A 99 0 NS=608;DP=36050;AC=246;AN=1216;dbSNP;HM;HWE=3.05358
1 1110351 . A C 99 0 NS=696;DP=26284;AC=15;AN=1392;HWE=0.163402
1 1110358 . T C 99 0 NS=694;DP=24596;AC=24;AN=1388;HWE=0.422309
1 1110366 . G A 99 0 NS=697;DP=22511;AC=16;AN=1394;HWE=0.185781
1 3537495 . C T 99 0 NS=697;DP=25302;AC=15;AN=1394;HWE=0.163165
1 3537910 . G A 99 0 NS=605;DP=15896;AC=34;AN=1210;HWE=0.46683
1 3537996 rs2760321 T C 99 0 NS=571;DP=15376;AC=1040;AN=1142;dbSNP;HM;HWE=4.28852
(...)

Command:

java -jar dist/vcfannotator.jar -pg -m -g -p -c -t -snp snp130 -log ALL input.vcf
## wait !

Result

##fileformat=VCFv3.2
##fileDate=20091120
##source=gigabayes
##reference=ncbi36
##phasing=none
##SNP130=table snp130 from UCSC
##INFO=NA12878,1,String,"NA12878's Personal genome"
##INFO=NA12891,1,String,"NA12891's Personal genome"
(...)
chr1 1108138 rs61733845 C T 99 0 NS=450;DP=16134;AC=110;AN=900;dbSNP;HWE=0.930276;MAPABILITY_WGENCODEBROADMAPABILITYALIGN36MER=1;MAPABILITY_WGENCODEDUKEUNIQUENESS20=1;MAPABILITY_WGENCODEDUKEUNIQUENESS24=1;MAPABILITY_WGENCODEDUKEUNIQUENESS35=1;phastCons44way=1.000;PREDICTION=geneSymbol:TTLL10|wild.codon:TGC|wild.aa:C|pos.cdna:935|kgId:uc001acy.1|position.protein:312|strand:+|mut.aa:C|mut.codon:TGT|exon.name:Exon 11|type:EXON_CODING_SYNONYMOUS;PREDICTION=geneSymbol:TTLL10|wild.codon:TGC|wild.aa:C|pos.cdna:716|kgId:uc001acz.1|position.protein:239|strand:+|mut.aa:C|mut.codon:TGT|exon.name:Exon 7|type:EXON_CODING_SYNONYMOUS
(...)
chr1 1110351 . A C 99 0 NS=696;DP=26284;AC=15;AN=1392;HWE=0.163402;MAPABILITY_WGENCODEBROADMAPABILITYALIGN36MER=1;MAPABILITY_WGENCODEDUKEUNIQUENESS20=1;MAPABILITY_WGENCODEDUKEUNIQUENESS24=1;MAPABILITY_WGENCODEDUKEUNIQUENESS35=1;phastCons44way=1.000;PREDICTION=geneSymbol:TTLL10|wild.codon:AAG|wild.aa:K|splicing:SPLICING_DONOR|pos.cdna:1399|kgId:uc001acy.1|position.protein:467|strand:+|mut.aa:T|mut.codon:ACG|exon.name:Exon 13|type:EXON_CODING_NON_SYNONYMOUS;PREDICTION=geneSymbol:TTLL10|wild.codon:AAG|wild.aa:K|pos.cdna:1180|kgId:uc001acz.1|position.protein:394|strand:+|mut.aa:T|mut.codon:ACG|exon.name:Exon 9|type:EXON_CODING_NON_SYNONYMOUS
(...)
chr1 113068276 . C G 99 0 NS=697;DP=12774;AC=7;AN=1394;HWE=0.0353282;MAPABILITY_WGENCODEBROADMAPABILITYALIGN36MER=1;MAPABILITY_WGENCODEDUKEUNIQUENESS20=1;MAPABILITY_WGENCODEDUKEUNIQUENESS24=1;MAPABILITY_WGENCODEDUKEUNIQUENESS35=1;phastCons44way=1.000;PREDICTION=geneSymbol:FAM19A3|wild.codon:CCA|wild.aa:P|pos.cdna:451|kgId:uc001ecu.1|position.protein:151|strand:+|mut.aa:R|mut.codon:CGA|exon.name:Exon 4|type:EXON_CODING_NON_SYNONYMOUS;PREDICTION=geneSymbol:FAM19A3|wild.codon:ACC|wild.aa:T|pos.cdna:383|kgId:uc001ecv.1|position.protein:128|strand:+|mut.aa:T|mut.codon:ACG|exon.name:Exon 4|type:EXON_CODING_SYNONYMOUS
(...)

Interestingly, for this last mutation chr1:113068276, there are two transcripts at the same position with two different translation frames, so there are two predictions: one synonymous mutation and one non-synonymous mutation.


That's it,

Pierre

A custom C++ streambuf for BIODAS-DNA/XML

(via cplusplus.com):streambuf objects are in charge of providing reading and writing functionality to/from certain types of character sequences, such as external files or strings. streambuf objects are usually associated with one specific character sequence, from which they read and write data through an internal memory buffer. The buffer is an array in memory which is expected to be synchronized when needed with the physical content of the associated character sequence.
A streambuf contains a method named underflow called in order to make additional characters available for reading.

A first streambuf : reading the content of an URL

My first class extends std::streambuf and is a wrapper for the CURL C API. The source code is available on github at http://github.com/lindenb/cclindenb/blob/master/src/core/lindenb/net/curl_streambuf.h. Here, each time underflow is called, the CURL API is asked to download a new chunk of data from the URL and it becomes the new buffer for this streambuf.

Usage

#include "lindenb/net/curl_streambuf.h"

static const char *url1="http://genome.ucsc.edu/cgi-bin/das/hg19/dna?segment=chr1:100000,100100";

static void test0001()
{
lindenb::net::curl_streambuf curl(url1);
std::istream in(&curl);
std::string line;
while(std::getline(in,line,'\n'))
{
std::cout << line << std::endl;
}
}

Output

<?xml version="1.0" standalone="no"?>
<!DOCTYPE DASDNA SYSTEM "http://www.biodas.org/dtd/dasdna.dtd">
<DASDNA>
<SEQUENCE id="chr1" start="100000" stop="100100" version="1.00">
<DNA length="101">
cactaagcacacagagaataatgtctagaatctgagtgccatgttatcaa
attgtactgagactcttgcagtcacacaggctgacatgtaagcatcgcca
t
</DNA>
</SEQUENCE>
</DASDNA>

A second streambuf : extracting the DNA from a BIODAS/DNA XML

For this second streambuf, I've used the Pull-Parser of libxml. This class is available at http://github.com/lindenb/cclindenb/blob/master/src/core/lindenb/bio/das/dna_streambuf.h. Here, the first time underflow is called, the instance of streambuf creates a new xmlTextReaderPtr skipping all the XML elements until it finds a new tag <DNA>. The internal buffer for this streambuf is then filled, during the remaining calls of underflow, with the text content of the DNA until it reaches the closing tag </DNA>

Usage

#include <fstream>
#include "lindenb/bio/das/dna_streambuf.h"
#include "lindenb/net/curl_streambuf.h"

static const char *url1="http://genome.ucsc.edu/cgi-bin/das/hg19/dna?segment=chr1:100000,100100";

static void test0002()
{
lindenb::net::curl_streambuf curl(url1);
std::istream in_net(&curl);
lindenb::bio::das::dna_streambuf dasdna(in_net);
std::istream in_das(&dasdna);
for(;;)
{
int c=in_das.get();
if(c==-1) break;
std::cout << (char)c;
}

}

Output

cactaagcacacagagaataatgtctagaatctgagtgccatgttatcaaattgtactgagactcttgcagtcacacaggctgacatgtaagcatcgccat

That's it
Pierre

Consequences : SNP, cDNA, proteins, etc....

This post is about Consequences, a tool finding the consequences of a set of mutations mapped on the human genome. It was motivated by a recent post of FriendFeed, Daniel MacArthur asked:“Given a list of human b36 coordinates for a list of genic SNPs (most not in dbSNP), what would be the quickest way to get a list of the genes they're found in and, if possible, the amino acid position they would affect?”.

About one year ago, I wrote a tool named "Consequences" answering this question but the sources are somewhere in a tar.gz , burned in an old CD, in a cardboard, in my cellar... so it was faster to re-write this simple code from scratch. The result should be fine but please, tell me if you find a bug.

This tool takes as input a tab delimited file containing the following fields:

1. A Name for your SNP
2. the chromosome e.g. 'chr2' (at this time only one chromosome per input is supported)
3. the position on the chromosome. The first base is indexed at 0
4. The base observed ON THE PLUS STRAND OF THE GENOME

. The sequence of the chromosome is then downloaded using the DAS server of the UCSC, the genes are downloaded using the mysql server of the UCSC and the 'knownGene' table. Then, for each mutation, I simply look at the consequence of each mutation. Here is a sample of the output:

<consequences chrom="chr1">
<observed-mutation position="1116" name="snp1" base="A">
<gene name="uc001aaa.2" exon-count="3" strand="+" txStart="1115" txEnd="4121" cdsStart="1115" cdsEnd="1115">
<in-utr-3/>
</gene>
<gene name="uc009vip.1" exon-count="2" strand="+" txStart="1115" txEnd="4272" cdsStart="1115" cdsEnd="1115">
<in-utr-3/>
</gene>
</observed-mutation>
(...)
</observed-mutation>
<observed-mutation position="1149167" name="snp282" base="A">
<gene name="uc009vjv.1" exon-count="6" strand="-" txStart="1142150" txEnd="1157310" cdsStart="1142754" cdsEnd="1149171">
<in-exon name="Exon 2" codon-wild="CAG" codon-mut="TAG" aa-wild="Q" aa-mut="*" base-wild="C" base-mut="T" index-cdna="3" index-protein="1">
<wild-cDNA>ATG C AGCGCTGGATCATGGAGAAGACGGCCGAGCACTTCCAGGAGGCCATGGAGGAGAGCAAGACACACTTCCGCGCCGTGGACCCTGACGGGGACGGTCACGTGTCTTGGGACGAGTATAAGGTGAAGTTTTTGGCGAGTAAAGGCCATAGCGAGAAGGAGGTTGCCGACGCCATCAGGCTCAACGAGGAACTCAAAGTGGATGAGGAAACACAGGAAGTCCTGGAGAACCTGAAGGACCGCTGGTACCAGGCGGACAGCCCCCCTGCAGACCTGCTGCTGACGGAGGAGGAGTTCCTGTCGTTCCTCCACCCCGAGCACAGCCGGGGAATGCTCAGGTTCATGGTGAAGGAGATCGTCCGGGACCTGGACCAGGACGGTGACAAGCAGCTCTCTGTGCCCGAGTTCATCTCCCTGCCCGTGGGCACCGTGGAGAACCAGCAGGGCCAGGACATTGACGACAACTGGGTGAAAGACAGAAAAAAGGAGTTTGAGGAGCTCATTGACTCCAACCACGACGGCATCGTGACCGCCGAGGAGCTGGAGAGCTACATGGACCCCATGAACGAGTACAACGCGCTGAACGAGGCCAAGCAGATGATCGCCGTCGCCGACGAGAACCAGAACCACCACCTGGAGCCCGAGGAGGTGCTCAAGTACAGCGAGTTCTTCACGGGCAGCAAGCTGGTGGACTACGCGCGCAGCGTGCACGAGGAGTTTTGA</wild-cDNA>
<mut-cDNA>ATG T AGCGCTGGATCATGGAGAAGACGGCCGAGCACTTCCAGGAGGCCATGGAGGAGAGCAAGACACACTTCCGCGCCGTGGACCCTGACGGGGACGGTCACGTGTCTTGGGACGAGTATAAGGTGAAGTTTTTGGCGAGTAAAGGCCATAGCGAGAAGGAGGTTGCCGACGCCATCAGGCTCAACGAGGAACTCAAAGTGGATGAGGAAACACAGGAAGTCCTGGAGAACCTGAAGGACCGCTGGTACCAGGCGGACAGCCCCCCTGCAGACCTGCTGCTGACGGAGGAGGAGTTCCTGTCGTTCCTCCACCCCGAGCACAGCCGGGGAATGCTCAGGTTCATGGTGAAGGAGATCGTCCGGGACCTGGACCAGGACGGTGACAAGCAGCTCTCTGTGCCCGAGTTCATCTCCCTGCCCGTGGGCACCGTGGAGAACCAGCAGGGCCAGGACATTGACGACAACTGGGTGAAAGACAGAAAAAAGGAGTTTGAGGAGCTCATTGACTCCAACCACGACGGCATCGTGACCGCCGAGGAGCTGGAGAGCTACATGGACCCCATGAACGAGTACAACGCGCTGAACGAGGCCAAGCAGATGATCGCCGTCGCCGACGAGAACCAGAACCACCACCTGGAGCCCGAGGAGGTGCTCAAGTACAGCGAGTTCTTCACGGGCAGCAAGCTGGTGGACTACGCGCGCAGCGTGCACGAGGAGTTTTGA</mut-cDNA>
<wild-protein>M Q RWIMEKTAEHFQEAMEESKTHFRAVDPDGDGHVSWDEYKVKFLASKGHSEKEVADAIRLNEELKVDEETQEVLENLKDRWYQADSPPADLLLTEEEFLSFLHPEHSRGMLRFMVKEIVRDLDQDGDKQLSVPEFISLPVGTVENQQGQDIDDNWVKDRKKEFEELIDSNHDGIVTAEELESYMDPMNEYNALNEAKQMIAVADENQNHHLEPEEVLKYSEFFTGSKLVDYARSVHEEF*</wild-protein>
<mut-protein>M * RWIMEKTAEHFQEAMEESKTHFRAVDPDGDGHVSWDEYKVKFLASKGHSEKEVADAIRLNEELKVDEETQEVLENLKDRWYQADSPPADLLLTEEEFLSFLHPEHSRGMLRFMVKEIVRDLDQDGDKQLSVPEFISLPVGTVENQQGQDIDDNWVKDRKKEFEELIDSNHDGIVTAEELESYMDPMNEYNALNEAKQMIAVADENQNHHLEPEEVLKYSEFFTGSKLVDYARSVHEEF*</mut-protein>
</in-exon>
</gene>
<gene name="uc009vjw.1" exon-count="7" strand="-" txStart="1142150" txEnd="1157310" cdsStart="1142150" cdsEnd="1142150">
<in-utr-5/>
</gene>
</observed-mutation>
(...)
<observed-mutation position="1205906" name="snp195" base="A">
<gene name="uc001adt.1" exon-count="18" strand="+" txStart="1205678" txEnd="1217272" cdsStart="1205904" cdsEnd="1216853">
<in-exon name="Exon 1" codon-wild="ATG" codon-mut="ATA" aa-wild="M" aa-mut="I" base-wild="G" base-mut="A" index-cdna="2" index-protein="0">
<wild-cDNA>AT G AGGGCAGTGCTGTCACAGAAGACAACACCGCTCCCTCGTTACCTGTGGCCCGGCCACCTCAGCGGCCCAAGGAGGCTCACCTGGTCATGGTGCAGTGACCACAGGACCCCCACATGCCGGGAGCTGGGTTCGCCCCACCCCACCCCCTGCACCGGGCCAGCGAGGGGATGGCCCAGAAGAGGGGGAGGACCATGTGGATTCACCAGTGCTGGACATGTGCTCTGTGGCTACCCCCTCTGCCTACTCTCTGGCCCGATACAGGGGTGTGGGACAGGCCTGGGTGACTCCAGCATGGCTTTCCTCTCCAGGACGTCACCGGTGGCAGCTGCTTCCTTCCAGAGCCGGCAGGAGGCCAGAGGCTCCATCCTGCTTCAGAGCTGCCAGCTGCCCCCGCAATGGCTGAGCACCGAAGCATGGACGGGAGAATGGAAGCAGCCACACGGGGGGGCTCTCACCTCCAGATCGCCTGGGCCTGTGGCTCCCCAGAGGCCCTGCCACCTGAAGGGATGGCAGCACAGACCCACTCAGCACAACGCTGCCTGCAAACAGGGCCAGGCTGCAGCCCAGACGCCCCCCAGGCCGGGGCCACCATCAGCACCACCACCACCACCCAAGGAGGGGCACCAGGAGGGGCTGGTGGAGCTGCCCGCCTCGTTCCGGGAGCTGCTCACCTTCTTCTGCACCAATGCCACCATCCACGGCGCCATCCGCCTGGTCTGCTCCCGCGGGAACCGCCTCAAGACGACGTCCTGGGGGCTGCTGTCCCTGGGAGCCCTGGTCGCGCTCTGCTGGCAGCTGGGGCTCCTCTTTGAGCGTCACTGGCACCGCCCGGTCCTCATGGCCGTCTCTGTGCACTCGGAGCGCAAGCTGCTCCCGCTGGTCACCCTGTGTGACGGGAACCCACGTCGGCCGAGTCCGGTCCTCCGCCATCTGGAGCTGCTGGACGAGTTTGCCAGGGAGAACATTGACTCCCTGTACAACGTCAACCTCAGCAAAGGCAGAGCCGCCCTCTCCGCCACTGTCCCCCGCCACGAGCCCCCCTTCCACCTGGACCGGGAGATCCGTCTGCAGAGGCTGAGCCACTCGGGCAGCCGGGTCAGAGTGGGGTTCAGACTGTGCAACAGCACGGGCGGCGACTGCTTTTACCGAGGCTACACGTCAGGCGTGGCGGCTGTCCAGGACTGGTACCACTTCCACTATGTGGATATCCTGGCCCTGCTGCCCGCGGCATGGGAGGACAGCCACGGGAGCCAGGACGGCCACTTCGTCCTCTCCTGCAGTTACGATGGCCTGGACTGCCAGGCCCGACAGTTCCGGACCTTCCACCACCCCACCTACGGCAGCTGCTACACGGTCGATGGCGTCTGGACAGCTCAGCGCCCCGGCATCACCCACGGAGTCGGCCTGGTCCTCAGGGTTGAGCAGCAGCCTCACCTCCCTCTGCTGTCCACGCTGGCCGGCATCAGGGTCATGGTTCACGGCCGTAACCACACGCCCTTCCTGGGGCACCACAGCTTCAGCGTCCGGCCAGGGACGGAGGCCACCATCAGCATCCGAGAGGACGAGGTGCACCGGCTCGGGAGCCCCTACGGCCACTGCACCGCCGGCGGGGAAGGCGTGGAGGTGGAGCTGCTACACAACACCTCCTACACCAGGCAGGCCTGCCTGGTGTCCTGCTTCCAGCAGCTGATGGTGGAGACCTGCTCCTGTGGCTACTACCTCCACCCTCTGCCGGCGGGGGCTGAGTACTGCAGCTCTGCCCGGCACCCTGCCTGGGGACACTGCTTCTACCGCCTCTACCAGGACCTGGAGACCCACCGGCTCCCCTGTACCTCCCGCTGCCCCAGGCCCTGCAGGGAGTCTGCATTCAAGCTCTCCACTGGGACCTCCAGGTGGCCTTCCGCCAAGTCAGCTGGATGGACTCTGGCCACGCTAGGTGAACAGGGGCTGCCGCATCAGAGCCACAGACAGAGGAGCAGCCTGGCCAAAATCAACATCGTCTACCAGGAGCTCAACTACCGCTCAGTGGAGGAGGCGCCCGTGTACTCGGTGCCGCAGCTGCTCTCGGCCATGGGCAGCCTCTGCAGCCTGTGGTTTGGGGCCTCCGTCCTCTCCCTCCTGGAGCTCCTGGAGCTGCTGCTCGATGCTTCTGCCCTCACCCTGGTGCTAGGCGGCCGCCGGCTCCGCAGGGCGTGGTTCTCCTGGCCCAGAGCCAGCCCTGCCTCAGGGGCGTCCAGCATCAAGCCAGAGGCCAGTCAGATGCCCCCGCCTGCAGGCGGCACGTCAGATGACCCGGAGCCCAGCGGGCCTCATCTCCCACGGGTGATGCTTCCAGGGGTTCTGGCGGGAGTCTCAGCCGAAGAGAGCTGGGCTGGGCCCCAGCCCCTTGAGACTCTGGACACCTGA</wild-cDNA>
<mut-cDNA>AT A AGGGCAGTGCTGTCACAGAAGACAACACCGCTCCCTCGTTACCTGTGGCCCGGCCACCTCAGCGGCCCAAGGAGGCTCACCTGGTCATGGTGCAGTGACCACAGGACCCCCACATGCCGGGAGCTGGGTTCGCCCCACCCCACCCCCTGCACCGGGCCAGCGAGGGGATGGCCCAGAAGAGGGGGAGGACCATGTGGATTCACCAGTGCTGGACATGTGCTCTGTGGCTACCCCCTCTGCCTACTCTCTGGCCCGATACAGGGGTGTGGGACAGGCCTGGGTGACTCCAGCATGGCTTTCCTCTCCAGGACGTCACCGGTGGCAGCTGCTTCCTTCCAGAGCCGGCAGGAGGCCAGAGGCTCCATCCTGCTTCAGAGCTGCCAGCTGCCCCCGCAATGGCTGAGCACCGAAGCATGGACGGGAGAATGGAAGCAGCCACACGGGGGGGCTCTCACCTCCAGATCGCCTGGGCCTGTGGCTCCCCAGAGGCCCTGCCACCTGAAGGGATGGCAGCACAGACCCACTCAGCACAACGCTGCCTGCAAACAGGGCCAGGCTGCAGCCCAGACGCCCCCCAGGCCGGGGCCACCATCAGCACCACCACCACCACCCAAGGAGGGGCACCAGGAGGGGCTGGTGGAGCTGCCCGCCTCGTTCCGGGAGCTGCTCACCTTCTTCTGCACCAATGCCACCATCCACGGCGCCATCCGCCTGGTCTGCTCCCGCGGGAACCGCCTCAAGACGACGTCCTGGGGGCTGCTGTCCCTGGGAGCCCTGGTCGCGCTCTGCTGGCAGCTGGGGCTCCTCTTTGAGCGTCACTGGCACCGCCCGGTCCTCATGGCCGTCTCTGTGCACTCGGAGCGCAAGCTGCTCCCGCTGGTCACCCTGTGTGACGGGAACCCACGTCGGCCGAGTCCGGTCCTCCGCCATCTGGAGCTGCTGGACGAGTTTGCCAGGGAGAACATTGACTCCCTGTACAACGTCAACCTCAGCAAAGGCAGAGCCGCCCTCTCCGCCACTGTCCCCCGCCACGAGCCCCCCTTCCACCTGGACCGGGAGATCCGTCTGCAGAGGCTGAGCCACTCGGGCAGCCGGGTCAGAGTGGGGTTCAGACTGTGCAACAGCACGGGCGGCGACTGCTTTTACCGAGGCTACACGTCAGGCGTGGCGGCTGTCCAGGACTGGTACCACTTCCACTATGTGGATATCCTGGCCCTGCTGCCCGCGGCATGGGAGGACAGCCACGGGAGCCAGGACGGCCACTTCGTCCTCTCCTGCAGTTACGATGGCCTGGACTGCCAGGCCCGACAGTTCCGGACCTTCCACCACCCCACCTACGGCAGCTGCTACACGGTCGATGGCGTCTGGACAGCTCAGCGCCCCGGCATCACCCACGGAGTCGGCCTGGTCCTCAGGGTTGAGCAGCAGCCTCACCTCCCTCTGCTGTCCACGCTGGCCGGCATCAGGGTCATGGTTCACGGCCGTAACCACACGCCCTTCCTGGGGCACCACAGCTTCAGCGTCCGGCCAGGGACGGAGGCCACCATCAGCATCCGAGAGGACGAGGTGCACCGGCTCGGGAGCCCCTACGGCCACTGCACCGCCGGCGGGGAAGGCGTGGAGGTGGAGCTGCTACACAACACCTCCTACACCAGGCAGGCCTGCCTGGTGTCCTGCTTCCAGCAGCTGATGGTGGAGACCTGCTCCTGTGGCTACTACCTCCACCCTCTGCCGGCGGGGGCTGAGTACTGCAGCTCTGCCCGGCACCCTGCCTGGGGACACTGCTTCTACCGCCTCTACCAGGACCTGGAGACCCACCGGCTCCCCTGTACCTCCCGCTGCCCCAGGCCCTGCAGGGAGTCTGCATTCAAGCTCTCCACTGGGACCTCCAGGTGGCCTTCCGCCAAGTCAGCTGGATGGACTCTGGCCACGCTAGGTGAACAGGGGCTGCCGCATCAGAGCCACAGACAGAGGAGCAGCCTGGCCAAAATCAACATCGTCTACCAGGAGCTCAACTACCGCTCAGTGGAGGAGGCGCCCGTGTACTCGGTGCCGCAGCTGCTCTCGGCCATGGGCAGCCTCTGCAGCCTGTGGTTTGGGGCCTCCGTCCTCTCCCTCCTGGAGCTCCTGGAGCTGCTGCTCGATGCTTCTGCCCTCACCCTGGTGCTAGGCGGCCGCCGGCTCCGCAGGGCGTGGTTCTCCTGGCCCAGAGCCAGCCCTGCCTCAGGGGCGTCCAGCATCAAGCCAGAGGCCAGTCAGATGCCCCCGCCTGCAGGCGGCACGTCAGATGACCCGGAGCCCAGCGGGCCTCATCTCCCACGGGTGATGCTTCCAGGGGTTCTGGCGGGAGTCTCAGCCGAAGAGAGCTGGGCTGGGCCCCAGCCCCTTGAGACTCTGGACACCTGA</mut-cDNA>
<wild-protein> M RAVLSQKTTPLPRYLWPGHLSGPRRLTWSWCSDHRTPTCRELGSPHPTPCTGPARGWPRRGGGPCGFTSAGHVLCGYPLCLLSGPIQGCGTGLGDSSMAFLSRTSPVAAASFQSRQEARGSILLQSCQLPPQWLSTEAWTGEWKQPHGGALTSRSPGPVAPQRPCHLKGWQHRPTQHNAACKQGQAAAQTPPRPGPPSAPPPPPKEGHQEGLVELPASFRELLTFFCTNATIHGAIRLVCSRGNRLKTTSWGLLSLGALVALCWQLGLLFERHWHRPVLMAVSVHSERKLLPLVTLCDGNPRRPSPVLRHLELLDEFARENIDSLYNVNLSKGRAALSATVPRHEPPFHLDREIRLQRLSHSGSRVRVGFRLCNSTGGDCFYRGYTSGVAAVQDWYHFHYVDILALLPAAWEDSHGSQDGHFVLSCSYDGLDCQARQFRTFHHPTYGSCYTVDGVWTAQRPGITHGVGLVLRVEQQPHLPLLSTLAGIRVMVHGRNHTPFLGHHSFSVRPGTEATISIREDEVHRLGSPYGHCTAGGEGVEVELLHNTSYTRQACLVSCFQQLMVETCSCGYYLHPLPAGAEYCSSARHPAWGHCFYRLYQDLETHRLPCTSRCPRPCRESAFKLSTGTSRWPSAKSAGWTLATLGEQGLPHQSHRQRSSLAKINIVYQELNYRSVEEAPVYSVPQLLSAMGSLCSLWFGASVLSLLELLELLLDASALTLVLGGRRLRRAWFSWPRASPASGASSIKPEASQMPPPAGGTSDDPEPSGPHLPRVMLPGVLAGVSAEESWAGPQPLETLDT*</wild-protein>
<mut-protein> I RAVLSQKTTPLPRYLWPGHLSGPRRLTWSWCSDHRTPTCRELGSPHPTPCTGPARGWPRRGGGPCGFTSAGHVLCGYPLCLLSGPIQGCGTGLGDSSMAFLSRTSPVAAASFQSRQEARGSILLQSCQLPPQWLSTEAWTGEWKQPHGGALTSRSPGPVAPQRPCHLKGWQHRPTQHNAACKQGQAAAQTPPRPGPPSAPPPPPKEGHQEGLVELPASFRELLTFFCTNATIHGAIRLVCSRGNRLKTTSWGLLSLGALVALCWQLGLLFERHWHRPVLMAVSVHSERKLLPLVTLCDGNPRRPSPVLRHLELLDEFARENIDSLYNVNLSKGRAALSATVPRHEPPFHLDREIRLQRLSHSGSRVRVGFRLCNSTGGDCFYRGYTSGVAAVQDWYHFHYVDILALLPAAWEDSHGSQDGHFVLSCSYDGLDCQARQFRTFHHPTYGSCYTVDGVWTAQRPGITHGVGLVLRVEQQPHLPLLSTLAGIRVMVHGRNHTPFLGHHSFSVRPGTEATISIREDEVHRLGSPYGHCTAGGEGVEVELLHNTSYTRQACLVSCFQQLMVETCSCGYYLHPLPAGAEYCSSARHPAWGHCFYRLYQDLETHRLPCTSRCPRPCRESAFKLSTGTSRWPSAKSAGWTLATLGEQGLPHQSHRQRSSLAKINIVYQELNYRSVEEAPVYSVPQLLSAMGSLCSLWFGASVLSLLELLELLLDASALTLVLGGRRLRRAWFSWPRASPASGASSIKPEASQMPPPAGGTSDDPEPSGPHLPRVMLPGVLAGVSAEESWAGPQPLETLDT*</mut-protein>
</in-exon>
</gene>
<gene name="uc001adu.1" exon-count="17" strand="+" txStart="1205678" txEnd="1217272" cdsStart="1209267" cdsEnd="1216853">
<in-utr-5/>
</gene>
</observed-mutation>
(...)
</consequences>

The source code is available here:

Consequences.java

A 'jar' is available for download at http://lindenb.googlecode.com/files/consequences.jar.
Running the tool:

java -cp {path}/mysql-connector-java-xxxx-bin.jar:consequences.jar org.lindenb.tinytools.Consequences your-list-of-snp.txt

Well, that is not big science but it might be helpful.
That's it.

Pierre