Get COSMIC variants overlapping with a region using the Ensembl REST API

get_COSMIC.sh

# A bash function to retrieve COSMIC variants (ID, location(b38), consequence and phenotype) based on
# genomic location using Ensembl's REST API. 

# The first solution uses only bash's wget and Perl with using the JSON package, 
# while the second, more compact solution utilizes jq: https://stedolan.github.io/jq/manual/
# The output of the solutions are expected to be the same.

# Without jq:
function get_COSMIC { wget -q "http://rest.ensembl.org/overlap/region/human/${1}?feature=somatic_variation;content-type=application/json" -O - | perl -MJSON -lane 'foreach $v (@{decode_json($_)}){ print join "\t", $v->{id} if $v->{source} == "COSMIC"}' | while read ID; do wget -q "http://rest.ensembl.org/variation/human/${ID}?content-type=application/json&phenotypes=1" -O - | perl -MJSON -lane '$v = decode_json($_); $id = $v->{name}; $loc = $v->{mappings}->[0]->{location}; $cons = $v->{most_severe_consequence}; my @pheno = (); foreach $p (@{$v->{phenotypes}}){push @pheno, $p->{trait}}; $pheno = join "|", @pheno; $pheno =~ s/ +/_/g; print join "\t", $id, $cons, $pheno, $loc'; done; }

# With jq (v.1.5 or higher):
function get_COSMIC { wget -q "http://rest.ensembl.org/overlap/region/human/${1}?feature=somatic_variation;content-type=application/json" -O - | jq -r '.[] | .id' | while read ID; do wget -q "http://rest.ensembl.org/variation/human/${ID}?content-type=application/json&phenotypes=1" -O - | jq -r '"\(.name) \(.most_severe_consequence) \([.phenotypes[] | .trait ] | join("|") | gsub(" "; "_")) \(.mappings[0].location)"'; done; }

# Sample input:
region="7:140424943-140624564"

# Usage: 
get_COSMIC ${region}

## Sample output:
# COSM5904881  splice_region_variant    Skin_tumour                                   7:140425874-140425874
# COSM5482096  coding_sequence_variant  Large_intestine_tumour                        7:140425889-140425889
# COSM4492612  coding_sequence_variant  Skin_tumour                                   7:140425896-140425896
# COSM2861240  coding_sequence_variant  Large_intestine_tumour                        7:140425908-140425908
# COSM4804782  coding_sequence_variant  Liver_tumour                                  7:140425914-140425914
# COSM1312749  coding_sequence_variant  Urinary_tract_tumour                          7:140425923-140425923
# COSM356225   coding_sequence_variant  Lung_tumour                                   7:140425957-140425957
# COSM3634220  coding_sequence_variant  Large_intestine_tumour|Skin_tumour            7:140425965-140425965
# COSM4498272  coding_sequence_variant  Skin_tumour|Upper_aerodigestive_tract_tumour  7:140426012-140426012
# COSM1086225  coding_sequence_variant  Endometrium_tumour                            7:140426013-140426013