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fcyufcyu
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1 parent d8413d6 commit 87bf339

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‎.github/workflows/build.yml‎

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,74 @@
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name: build
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on:
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push:
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workflow_dispatch:
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permissions:
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contents: read
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jobs:
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build:
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name: ${{ matrix.goos }}/${{ matrix.goarch }}
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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include:
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- goos: linux
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goarch: amd64
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ext: ''
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- goos: windows
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goarch: amd64
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ext: '.exe'
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steps:
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- name: Check out code
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uses: actions/checkout@v4
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- name: Set up Go
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uses: actions/setup-go@v5
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with:
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go-version: '1.25'
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- name: Get dependencies
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run: go mod download
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- name: Unzip embedded bindata
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run: |
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unzip -o lib/dat/bindata.go.zip -d lib/dat/
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unzip -o lib/ext/cdhit/unix/bindata.go.zip -d lib/ext/cdhit/unix/
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unzip -o lib/ext/cdhit/win/bindata.go.zip -d lib/ext/cdhit/win/
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unzip -o lib/ext/comet/unix/bindata.go.zip -d lib/ext/comet/unix/
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unzip -o lib/ext/comet/win/bindata.go.zip -d lib/ext/comet/win/
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unzip -o lib/ext/interprophet/unix/bindata.go.zip -d lib/ext/interprophet/unix/
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unzip -o lib/ext/interprophet/win/bindata.go.zip -d lib/ext/interprophet/win/
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unzip -o lib/ext/peptideprophet/unix/bindata.go.zip -d lib/ext/peptideprophet/unix/
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unzip -o lib/ext/peptideprophet/win/bindata.go.zip -d lib/ext/peptideprophet/win/
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unzip -o lib/ext/proteinprophet/unix/bindata.go.zip -d lib/ext/proteinprophet/unix/
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unzip -o lib/ext/proteinprophet/win/bindata.go.zip -d lib/ext/proteinprophet/win/
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unzip -o lib/ext/ptmprophet/unix/bindata.go.zip -d lib/ext/ptmprophet/unix/
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unzip -o lib/ext/ptmprophet/win/bindata.go.zip -d lib/ext/ptmprophet/win/
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unzip -o lib/obo/unimod/bindata.go.zip -d lib/obo/unimod/
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unzip -o lib/pip/bindata.go.zip -d lib/pip/
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- name: Build
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env:
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CGO_ENABLED: '0'
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GOOS: ${{ matrix.goos }}
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GOARCH: ${{ matrix.goarch }}
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run: |
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BUILD=$(date +%Y%m%d%H%M)
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VERSION="${GITHUB_REF_NAME}-${GITHUB_SHA::7}"
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OUTPUT="philosopher-${GOOS}-${GOARCH}${{ matrix.ext }}"
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go build -trimpath \
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-ldflags "-w -s -X main.version=${VERSION} -X main.build=${BUILD}" \
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-o "${OUTPUT}" main.go
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ls -lh "${OUTPUT}"
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- name: Upload artifact
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uses: actions/upload-artifact@v4
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with:
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name: philosopher-${{ matrix.goos }}-${{ matrix.goarch }}
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path: philosopher-${{ matrix.goos }}-${{ matrix.goarch }}${{ matrix.ext }}
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if-no-files-found: error

‎lib/id/pep.go‎

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Original file line numberDiff line numberDiff line change
@@ -88,6 +88,7 @@ type PeptideIdentification struct {
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SPRank float64
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Hyperscore float64
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Nextscore float64
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BCS int
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SpectralSim float64
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Rtscore float64
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IMscore float64
@@ -496,6 +497,9 @@ func processSpectrumQuery(sq spc.SpectrumQuery, mods mod.Modifications, decoyTag
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} else if string(j.Name) == "nextscore" {
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value, _ := strconv.ParseFloat(j.Value, 64)
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psm.Nextscore = value
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} else if string(j.Name) == "bcs" {
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value, _ := strconv.Atoi(j.Value)
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psm.BCS = value
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} else if string(j.Name) == "spectralsim" {
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value, _ := strconv.ParseFloat(j.Value, 64)
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psm.SpectralSim = value

‎lib/rep/psm.go‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -57,6 +57,7 @@ func (evi *Evidence) AssemblePSMReport(pep id.PepIDList, decoyTag string) {
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p.SPRank = i.SPRank
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p.Hyperscore = i.Hyperscore
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p.Nextscore = i.Nextscore
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p.BCS = i.BCS
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p.SpectralSim = i.SpectralSim
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p.Rtscore = i.Rtscore
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p.IMscore = i.IMscore
@@ -237,7 +238,7 @@ func (evi PSMEvidenceList) PSMReport(workspace, brand, decoyTag string, channels
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header += "\tIMScore"
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}
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header += "\tExpectation\tHyperscore\tNextscore\tProbability\tQvalue\tNumber of Enzymatic Termini\tNumber of Missed Cleavages\tProtein Start\tProtein End\tIntensity\tAssigned Modifications\tObserved Modifications"
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header += "\tExpectation\tHyperscore\tNextscore\tBCS\tProbability\tQvalue\tNumber of Enzymatic Termini\tNumber of Missed Cleavages\tProtein Start\tProtein End\tIntensity\tAssigned Modifications\tObserved Modifications"
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if hasClass {
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header += "\tClass"
@@ -611,11 +612,12 @@ func (evi PSMEvidenceList) PSMReport(workspace, brand, decoyTag string, channels
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)
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}
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line = fmt.Sprintf("%s\t%.14f\t%.4f\t%.4f\t%.4f\t%.14f\t%d\t%d\t%d\t%d\t%.4f\t%s\t%s",
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line = fmt.Sprintf("%s\t%.14f\t%.4f\t%.4f\t%d\t%.4f\t%.14f\t%d\t%d\t%d\t%d\t%.4f\t%s\t%s",
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line,
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i.Expectation,
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i.Hyperscore,
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i.Nextscore,
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i.BCS,
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i.Probability,
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i.Qvalue,
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i.NumberOfEnzymaticTermini,

‎lib/rep/rep.go‎

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@@ -155,6 +155,7 @@ type PSMEvidence struct {
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SPRank float64
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Hyperscore float64
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Nextscore float64
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BCS int
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SpectralSim float64
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Rtscore float64
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IMscore float64

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