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2prev, show number of samples/studies found
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@mikessh
mikessh committed Mar 18, 2017
1 parent f80f88a commit c5929a1
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Showing 2 changed files with 44 additions and 20 deletions.
47 changes: 27 additions & 20 deletions src/BuildDatabase.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -335,20 +335,20 @@ def METADATA_LINES = ["name\ttype\tvisible\tsearchable\tautocomplete\tdata.type\
"complex.id\ttxt\t0\t0\t0\tcomplex.id\tcomplex.id\tTCR alpha and beta chain records having the same complex identifier belong to the same T-cell clone.",
"gene\ttxt\t1\t1\t1\tfactor\tGene\tTCR chain: alpha or beta.",
"cdr3\tseq\t1\t1\t0\tcdr3\tCDR3\tTCR complementarity determining region 3 (CDR3) amino acid sequence.",
"v.segm\ttxt\t1\t1\t1\tfactor\tV\tTCR Variable segment identifier.",
"j.segm\ttxt\t1\t1\t1\tfactor\tJ\tTCR Joining segment identifier.",
"species\ttxt\t1\t1\t1\tfactor\tSpecies\tParent species of a given TCR.",
"mhc.a\ttxt\t1\t1\t1\tfactor\tMHC.A\tFirst MHC chain identifier.",
"mhc.b\ttxt\t1\t1\t1\tfactor\tMHC.B\tSecond MHC chain identifier (set to beta2microglobulin for MHC class I).",
"mhc.class\ttxt\t1\t1\t1\tfactor\tMHC.class\tMHC class (I or II).",
"antigen.epitope\tseq\t1\t1\t1\tpeptide\tAntigen.Epitope\tAmino acid sequence of the antigen peptide.",
"antigen.gene\ttxt\t1\t1\t1\tfactor\tAntigen.Gene\tParent gene of the antigen peptide.",
"antigen.species\ttxt\t1\t1\t1\tfactor\tAntigen.Species\tParent species of the antigen peptide.",
"v.segm\ttxt\t1\t1\t1\tfactor\tV\tTCR Variable segment allele.",
"j.segm\ttxt\t1\t1\t1\tfactor\tJ\tTCR Joining segment allele.",
"species\ttxt\t1\t1\t1\tfactor\tSpecies\tTCR parent species.",
"mhc.a\ttxt\t1\t1\t1\tfactor\tMHC A\tFirst MHC chain allele.",
"mhc.b\ttxt\t1\t1\t1\tfactor\tMHC B\tSecond MHC chain allele (defaults to Beta2Microglobulin for MHC class I).",
"mhc.class\ttxt\t1\t1\t1\tfactor\tMHC class\tMHC class (I or II).",
"antigen.epitope\tseq\t1\t1\t1\tpeptide\tEpitope\tAmino acid sequence of the epitope.",
"antigen.gene\ttxt\t1\t1\t1\tfactor\tEpitope gene\tRepresentative parent gene of the epitope.",
"antigen.species\ttxt\t1\t1\t1\tfactor\tEpitope species\tRepresentative parent species of the epitope.",
"reference.id\ttxt\t1\t1\t1\turl\tReference\tPubmed reference / URL / or submitter details in case unpublished.",
"method\ttxt\t1\t0\t0\tmethod.json\tMethod\tDetails on method used to assay TCR specificity.",
"meta\ttxt\t1\t0\t0\tmeta.json\tMeta\tVarious meta-information: cell subset, donor status, etc.",
"cdr3fix\ttxt\t1\t0\t0\tfixer.json\tcdr3fix\tDetails on CDR3 sequence fixing (if applied) and consistency between V, J and reported CDR3 sequence.",
"vdjdb.score\ttxt\t1\t1\t0\tuint\tscore\tVDJdb confidence score, the higher is the score the more confidence we have in the antigen specificity annotation of a given TCR clonotype/clone. 0 score indicates that there are insufficient method details to draw any conclusion.",
"cdr3fix\ttxt\t1\t0\t0\tfixer.json\tCDR3fix\tDetails on CDR3 sequence fixing (if applied) and consistency between V, J and reported CDR3 sequence.",
"vdjdb.score\ttxt\t1\t1\t0\tuint\tScore\tVDJdb confidence score, the higher is the score the more confidence we have in the antigen specificity annotation of a given TCR clonotype/clone. Zero score indicates that there are insufficient method details to draw any conclusion.",
"web.method\ttxt\t0\t0\t1\t0\tfactor\tInternal",
"web.method.seq\ttxt\t0\t0\t1\t0\tfactor\tInternal",
"web.cdr3fix.nc\ttxt\t0\t0\t1\t0\tfactor\tInternal",
Expand Down Expand Up @@ -398,10 +398,16 @@ new File("../database/vdjdb.txt").withPrintWriter { pw ->

def methodAnnot = new JsonBuilder(METHOD_COLUMNS.collectEntries {
[(it.split("method.")[1]): row[it]]
}).toString(),
metaAnnot = new JsonBuilder(META_COLUMNS.collectEntries {
}).toString()

def metaAnnotMap = META_COLUMNS.collectEntries {
[(it.split("meta.")[1]): row[it]]
}).toString()
}

metaAnnotMap << [("samples.found"): scoreFactory.getSamplesDetected(row)]
metaAnnotMap << [("studies.found"): scoreFactory.getStudiesDetected(row)]

def metaAnnot = new JsonBuilder(metaAnnotMap).toString()

def complexId
if (row["cdr3.alpha"] == "" || row["cdr3.beta"] == "") {
Expand Down Expand Up @@ -474,19 +480,20 @@ new File("../database/vdjdb.txt").withPrintWriter { pw ->
println "Generating and writing slim database"

def SLIM_METADATA_LINES = [
"name\ttype",
"complex.id\ttxt",
"gene\ttxt",
"cdr3\tseq",
"species\ttxt",
"antigen.epitope\tseq",
"antigen.gene\ttxt",
"antigen.species\ttxt",
"complex.id\ttxt",
"v.segm\ttxt",
"j.segm\ttxt",
"species\ttxt",
"v.end\ttxt",
"j.start\ttxt",
"mhc.a\ttxt",
"mhc.b\ttxt",
"mhc.class\ttxt",
"antigen.epitope\tseq",
"antigen.gene\ttxt",
"antigen.species\ttxt",
"reference.id\ttxt",
"vdjdb.score\ttxt"
]
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17 changes: 17 additions & 0 deletions src/VdjdbScoreFactory.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -17,11 +17,20 @@

class VdjdbScoreFactory {
final Map<String, Integer> scoreMap = new HashMap<>()
final Map<String, List<String>> publicationMap = new HashMap<>()

VdjdbScoreFactory(Table masterTable) {
masterTable.each { row ->
def sign = getSignature(row)

// Assign publications
def pubList = publicationMap[sign]
if (pubList == null) {
publicationMap.put(sign, pubList = new ArrayList<String>())
}
pubList << row["reference.id"]

// Compute score
def score
if (row["meta.structure.id"].trim().length() > 0) {
score = 3 // we have structure, any questions? :)
Expand Down Expand Up @@ -167,6 +176,14 @@ class VdjdbScoreFactory {
scoreMap[getSignature(row)] ?: 0
}

int getSamplesDetected(Table.Row row) {
(publicationMap[getSignature(row)] ?: []).size()
}

int getStudiesDetected(Table.Row row) {
(publicationMap[getSignature(row)] ?: []).unique().size()
}

String getSignature(Table.Row row) {
SIGNATURE_COLS.collect { row[it] }.join("\t")
}
Expand Down

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