reportgen creates beautiful reports from clinseq data.
git clone https://bitbucket.org/twhitington/reportgen.git
pip install ./reportgen# Example execution with some dummy input files:
cat << EOF > meta.json
{
"personnummer": "19501010-1234",
"blood_sample_id": 123456,
"tumor_sample_id": 123456,
"blood_sample_date": "2016-04-29",
"tumor_sample_date": "2016-05-20",
"doctor": "Dr Namn Namnsson",
"doctor_address": "Onkologimottagningen\nStora Lasaretet\n123 45 Stadsby"
}
EOF
FIXME: THIS EXAMPLE IS WRONG; CONFORM WITH DEFINITION
cat << EOF > report.json
{
"PI3K_pathway": "Mutation class A",
"MSI_status": "MSS/MSI-L",
"KRAS": ["Mutated", "G12D"],
"BRAF": ["Not mutated", null],
"NRAS": ["Not determined", null]
}
EOF
reportgen meta.json report.jsonXXX
::= {[,]} # NOTE: I mean a comma-separated list, zero or more elements ::= "msiReport" : | "alasscaReport" : | "simpleSomaticMutationsReport" : ::= {} ::= "MSS/MSI-L" | "MSI-H" | ::= {} ::= "A" | "B" | ::= "NotDetermined" ::= "NotMutated" ::= "Mutated" ::= { : } ::= "ENSG"[0-9]{11} ::= [ | | , ] ::= {[ : ,]} # NOTE: I mean a comma-separated list, zero or more elements ::= # Not defined exactly yet. Some e.g.s: "KRAS_COMMON", "KRAS_UNCOMMON", "BRAF_COMMON" ::= [A-Z][0-9]+[A-Z] | [0-9]+
- Tom Whitington
- Daniel Klevebring