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Delete q-value column in the decoy output to avoid a confusion.
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@fcyu
fcyu committed Apr 25, 2018
1 parent 3c8f9fd commit 40d33b2
Showing 1 changed file with 8 additions and 8 deletions.
16 changes: 8 additions & 8 deletions src/main/java/proteomics/ECL2.java
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Original file line number Diff line number Diff line change
Expand Up @@ -293,14 +293,14 @@ private static void saveTargetResult(Map<String, CalFDR.Entry> result, Map<Strin

if (dev) {
intraTargetWriter.write("scan_num,spectrum_id,spectrum_mz,spectrum_mass,peptide_mass,rt,C13_correction,charge,score,delta_C,ppm,peptide,protein,protein_annotation_1,protein_annotation_2,e_value,q_value,mgf_title,,MS1_pearson_correlation_coefficient,candidate_num,point_num,r_square,slope,intercept,start_idx,end_idx,chain_score_1,chain_rank_1,chain_score_2,chain_rank_2\n");
intraDecoyWriter.write("scan_num,spectrum_id,spectrum_mz,spectrum_mass,peptide_mass,rt,C13_correction,charge,score,delta_C,ppm,peptide,protein,protein_annotation_1,protein_annotation_2,e_value,q_value,mgf_title,,MS1_pearson_correlation_coefficient,candidate_num,point_num,r_square,slope,intercept,start_idx,end_idx,chain_score_1,chain_rank_1,chain_score_2,chain_rank_2\n");
intraDecoyWriter.write("scan_num,spectrum_id,spectrum_mz,spectrum_mass,peptide_mass,rt,C13_correction,charge,score,delta_C,ppm,peptide,protein,protein_annotation_1,protein_annotation_2,e_value,mgf_title,,MS1_pearson_correlation_coefficient,candidate_num,point_num,r_square,slope,intercept,start_idx,end_idx,chain_score_1,chain_rank_1,chain_score_2,chain_rank_2\n");
interTargetWriter.write("scan_num,spectrum_id,spectrum_mz,spectrum_mass,peptide_mass,rt,C13_correction,charge,score,delta_C,ppm,peptide,protein,protein_annotation_1,protein_annotation_2,e_value,q_value,mgf_title,,MS1_pearson_correlation_coefficient,candidate_num,point_num,r_square,slope,intercept,start_idx,end_idx,chain_score_1,chain_rank_1,chain_score_2,chain_rank_2\n");
interDecoyWriter.write("scan_num,spectrum_id,spectrum_mz,spectrum_mass,peptide_mass,rt,C13_correction,charge,score,delta_C,ppm,peptide,protein,protein_annotation_1,protein_annotation_2,e_value,q_value,mgf_title,,MS1_pearson_correlation_coefficient,candidate_num,point_num,r_square,slope,intercept,start_idx,end_idx,chain_score_1,chain_rank_1,chain_score_2,chain_rank_2\n");
interDecoyWriter.write("scan_num,spectrum_id,spectrum_mz,spectrum_mass,peptide_mass,rt,C13_correction,charge,score,delta_C,ppm,peptide,protein,protein_annotation_1,protein_annotation_2,e_value,mgf_title,,MS1_pearson_correlation_coefficient,candidate_num,point_num,r_square,slope,intercept,start_idx,end_idx,chain_score_1,chain_rank_1,chain_score_2,chain_rank_2\n");
} else {
intraTargetWriter.write("scan_num,spectrum_id,spectrum_mz,spectrum_mass,peptide_mass,rt,C13_correction,charge,score,delta_C,ppm,peptide,protein,protein_annotation_1,protein_annotation_2,e_value,q_value,mgf_title,\n");
intraDecoyWriter.write("scan_num,spectrum_id,spectrum_mz,spectrum_mass,peptide_mass,rt,C13_correction,charge,score,delta_C,ppm,peptide,protein,protein_annotation_1,protein_annotation_2,e_value,q_value,mgf_title,\n");
intraDecoyWriter.write("scan_num,spectrum_id,spectrum_mz,spectrum_mass,peptide_mass,rt,C13_correction,charge,score,delta_C,ppm,peptide,protein,protein_annotation_1,protein_annotation_2,e_value,mgf_title,\n");
interTargetWriter.write("scan_num,spectrum_id,spectrum_mz,spectrum_mass,peptide_mass,rt,C13_correction,charge,score,delta_C,ppm,peptide,protein,protein_annotation_1,protein_annotation_2,e_value,q_value,mgf_title,\n");
interDecoyWriter.write("scan_num,spectrum_id,spectrum_mz,spectrum_mass,peptide_mass,rt,C13_correction,charge,score,delta_C,ppm,peptide,protein,protein_annotation_1,protein_annotation_2,e_value,q_value,mgf_title,\n");
interDecoyWriter.write("scan_num,spectrum_id,spectrum_mz,spectrum_mass,peptide_mass,rt,C13_correction,charge,score,delta_C,ppm,peptide,protein,protein_annotation_1,protein_annotation_2,e_value,mgf_title,\n");
}
List<CalFDR.Entry> entryList = new ArrayList<>(result.values());
entryList.sort(Comparator.reverseOrder());
Expand Down Expand Up @@ -329,27 +329,27 @@ private static void saveTargetResult(Map<String, CalFDR.Entry> result, Map<Strin
if (sqlResultSet.getInt("hitType") == 0) {
intraTargetWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1) + "\",\"" + String.join(";", proAnnotationList2) + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + "," + entry.qValue + ",\"" + sqlResultSet.getString("mgfTitle") + "\",," + sqlResultSet.getDouble("ms1PearsonCorrelationCoefficient") + "," + sqlResultSet.getInt("candidateNum") + "," + sqlResultSet.getInt("pointCount") + "," + sqlResultSet.getDouble("rSquare") + "," + sqlResultSet.getDouble("slope") + "," + sqlResultSet.getDouble("intercept") + "," + sqlResultSet.getInt("startIdx") + "," + sqlResultSet.getInt("endIdx") + "," + sqlResultSet.getDouble("chainScore1") + "," + sqlResultSet.getInt("chainRank1") + "," + sqlResultSet.getDouble("chainScore2") + "," + sqlResultSet.getInt("chainRank2") + "\n");
} else {
intraDecoyWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1) + "\",\"" + String.join(";", proAnnotationList2) + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + "," + entry.qValue + ",\"" + sqlResultSet.getString("mgfTitle") + "\",," + sqlResultSet.getDouble("ms1PearsonCorrelationCoefficient") + "," + sqlResultSet.getInt("candidateNum") + "," + sqlResultSet.getInt("pointCount") + "," + sqlResultSet.getDouble("rSquare") + "," + sqlResultSet.getDouble("slope") + "," + sqlResultSet.getDouble("intercept") + "," + sqlResultSet.getInt("startIdx") + "," + sqlResultSet.getInt("endIdx") + "," + sqlResultSet.getDouble("chainScore1") + "," + sqlResultSet.getInt("chainRank1") + "," + sqlResultSet.getDouble("chainScore2") + "," + sqlResultSet.getInt("chainRank2") + "\n");
intraDecoyWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1) + "\",\"" + String.join(";", proAnnotationList2) + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + ",\"" + sqlResultSet.getString("mgfTitle") + "\",," + sqlResultSet.getDouble("ms1PearsonCorrelationCoefficient") + "," + sqlResultSet.getInt("candidateNum") + "," + sqlResultSet.getInt("pointCount") + "," + sqlResultSet.getDouble("rSquare") + "," + sqlResultSet.getDouble("slope") + "," + sqlResultSet.getDouble("intercept") + "," + sqlResultSet.getInt("startIdx") + "," + sqlResultSet.getInt("endIdx") + "," + sqlResultSet.getDouble("chainScore1") + "," + sqlResultSet.getInt("chainRank1") + "," + sqlResultSet.getDouble("chainScore2") + "," + sqlResultSet.getInt("chainRank2") + "\n");
}
} else {
if (sqlResultSet.getInt("hitType") == 0) {
interTargetWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1) + "\",\"" + String.join(";", proAnnotationList2) + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + "," + entry.qValue + ",\"" + sqlResultSet.getString("mgfTitle") + "\",," + sqlResultSet.getDouble("ms1PearsonCorrelationCoefficient") + "," + sqlResultSet.getInt("candidateNum") + "," + sqlResultSet.getInt("pointCount") + "," + sqlResultSet.getDouble("rSquare") + "," + sqlResultSet.getDouble("slope") + "," + sqlResultSet.getDouble("intercept") + "," + sqlResultSet.getInt("startIdx") + "," + sqlResultSet.getInt("endIdx") + "," + sqlResultSet.getDouble("chainScore1") + "," + sqlResultSet.getInt("chainRank1") + "," + sqlResultSet.getDouble("chainScore2") + "," + sqlResultSet.getInt("chainRank2") + "\n");
} else {
interDecoyWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1) + "\",\"" + String.join(";", proAnnotationList2) + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + "," + entry.qValue + ",\"" + sqlResultSet.getString("mgfTitle") + "\",," + sqlResultSet.getDouble("ms1PearsonCorrelationCoefficient") + "," + sqlResultSet.getInt("candidateNum") + "," + sqlResultSet.getInt("pointCount") + "," + sqlResultSet.getDouble("rSquare") + "," + sqlResultSet.getDouble("slope") + "," + sqlResultSet.getDouble("intercept") + "," + sqlResultSet.getInt("startIdx") + "," + sqlResultSet.getInt("endIdx") + "," + sqlResultSet.getDouble("chainScore1") + "," + sqlResultSet.getInt("chainRank1") + "," + sqlResultSet.getDouble("chainScore2") + "," + sqlResultSet.getInt("chainRank2") + "\n");
interDecoyWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1) + "\",\"" + String.join(";", proAnnotationList2) + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + ",\"" + sqlResultSet.getString("mgfTitle") + "\",," + sqlResultSet.getDouble("ms1PearsonCorrelationCoefficient") + "," + sqlResultSet.getInt("candidateNum") + "," + sqlResultSet.getInt("pointCount") + "," + sqlResultSet.getDouble("rSquare") + "," + sqlResultSet.getDouble("slope") + "," + sqlResultSet.getDouble("intercept") + "," + sqlResultSet.getInt("startIdx") + "," + sqlResultSet.getInt("endIdx") + "," + sqlResultSet.getDouble("chainScore1") + "," + sqlResultSet.getInt("chainRank1") + "," + sqlResultSet.getDouble("chainScore2") + "," + sqlResultSet.getInt("chainRank2") + "\n");
}
}
} else {
if (sqlResultSet.getString("clType").contentEquals("intra_protein")) {
if (sqlResultSet.getInt("hitType") == 0) {
intraTargetWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1) + "\",\"" + String.join(";", proAnnotationList2) + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + "," + entry.qValue + ",\"" + sqlResultSet.getString("mgfTitle") + "\"\n");
} else {
intraDecoyWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1) + "\",\"" + String.join(";", proAnnotationList2) + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + "," + entry.qValue + ",\"" + sqlResultSet.getString("mgfTitle") + "\",\n");
intraDecoyWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1) + "\",\"" + String.join(";", proAnnotationList2) + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + ",\"" + sqlResultSet.getString("mgfTitle") + "\",\n");
}
} else {
if (sqlResultSet.getInt("hitType") == 0) {
interTargetWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1) + "\",\"" + String.join(";", proAnnotationList2) + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + "," + entry.qValue + ",\"" + sqlResultSet.getString("mgfTitle") + "\",\n");
} else {
interDecoyWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1) + "\",\"" + String.join(";", proAnnotationList2) + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + "," + entry.qValue + ",\"" + sqlResultSet.getString("mgfTitle") + "\",\n");
interDecoyWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1) + "\",\"" + String.join(";", proAnnotationList2) + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + ",\"" + sqlResultSet.getString("mgfTitle") + "\",\n");
}
}
}
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