tbtools-cli 1.2.0__py3-none-any.whl

tbtools_cli-1.2.0.data/data/tbtools_cli/bridges/StructAnnoCompareCli.java

@@ -0,0 +1,66 @@
+import biocjava.bioDoer.StructAnnoCompare.StructAnnoCompareConfig;
+import biocjava.bioDoer.StructAnnoCompare.StructAnnoCompareResult;
+import biocjava.bioDoer.StructAnnoCompare.StructAnnoCompareService;
+
+import java.io.File;
+import java.nio.file.Path;
+
+/**
+ * tbplot annoCompare — 注释版本对比管线 CLI（08/31 第五十二波）
+ *
+ * 用法: StructAnnoCompareCli <before.gff3> <after.gff3> <outDir> [runName] [reciprocalOverlap] [boundaryTol] [cdsChangePct] [utrChangePct] [geneScope] [overlapMode]
+ *   before/after.gff3: 同一基因组两个版本的注释
+ *   outDir: 输出目录（自动建）
+ *   runName: 运行名（默认 "annoCompare"）
+ *   reciprocalOverlap: 双向重叠阈值（默认 0.5）
+ *   boundaryTol: 边界容差（默认 100）
+ *   cdsChangePct / utrChangePct: CDS/UTR 变化百分比阈值（默认 0.1 / 0.1）
+ *   geneScope: all|mrna_only（默认 all）
+ *   overlapMode: reciprocal|any（默认 reciprocal）
+ *
+ * 产物: <runName>_change_summary.csv / _change_log.csv / tracks/*_annotation_changes.bed /
+ *       curation_summary_table.csv / curation_core_metrics.csv / figures/*_curation_summary_jigplot.{png,pdf,svg} /
+ *       figures/*_ABCD_single_species_jigplot.{png,pdf,svg}
+ *
+ * 引擎: StructAnnoCompareService.run(StructAnnoCompareConfig)（纯 headless，无弹窗）
+ */
+public class StructAnnoCompareCli {
+    public static void main(String[] args) throws Exception {
+        if (args.length < 3) {
+            System.err.println("用法: StructAnnoCompareCli <before.gff3> <after.gff3> <outDir> [runName] [reciprocalOverlap] [boundaryTol] [cdsChangePct] [utrChangePct] [geneScope] [overlapMode]");
+            System.exit(1);
+        }
+        String before = args[0];
+        String after = args[1];
+        String outDir = args[2];
+        String runName = args.length > 3 ? args[3] : "annoCompare";
+        double recOverlap = args.length > 4 ? Double.parseDouble(args[4]) : 0.5;
+        int boundaryTol = args.length > 5 ? Integer.parseInt(args[5]) : 100;
+        double cdsPct = args.length > 6 ? Double.parseDouble(args[6]) : 0.1;
+        double utrPct = args.length > 7 ? Double.parseDouble(args[7]) : 0.1;
+        String geneScope = args.length > 8 ? args[8] : "all";
+        String overlapMode = args.length > 9 ? args[9] : "reciprocal";
+
+        StructAnnoCompareConfig cfg = new StructAnnoCompareConfig();
+        cfg.setBeforeGff(Path.of(before));
+        cfg.setAfterGff(Path.of(after));
+        cfg.setOutputDir(Path.of(outDir));
+        cfg.setRunName(runName);
+        cfg.setReciprocalOverlap(recOverlap);
+        cfg.setBoundaryTol(boundaryTol);
+        cfg.setCdsChangePct(cdsPct);
+        cfg.setUtrChangePct(utrPct);
+        cfg.setGeneScope(geneScope);
+        cfg.setOverlapMode(overlapMode);
+        cfg.setGenerateVisualization(true);
+        cfg.setLogConsumer(System.err::println);
+
+        StructAnnoCompareResult r = new StructAnnoCompareService().run(cfg);
+        System.err.println("[tbplot] summary: " + r.getSummaryPath());
+        System.err.println("[tbplot] change log: " + r.getChangeLogPath() + " (" + r.getChangeLogEntries() + " 条)");
+        System.err.println("[tbplot] curation core: " + r.getCurationCoreMetricsPath());
+        if (r.getFigurePng() != null) System.err.println("[tbplot] curation figure: " + r.getFigurePng());
+        if (r.getAbcdFigurePng() != null) System.err.println("[tbplot] ABCD figure: " + r.getAbcdFigurePng());
+        System.exit(0);
+    }
+}

tbtools_cli-1.2.0.data/data/tbtools_cli/bridges/SubmitSMARTCli.java

@@ -0,0 +1,30 @@
+/**
+ * tbplot smart — SMART 域注释 CLI（插件 P00060 CLI 化）
+ *
+ * 用法: SubmitSMARTCli <in.fa> <out.txt> [--pfam] [--signalp] [--disembl] [--schnipsel] [--rep]
+ *   开关默认全开；关闭传 --no-xxx 不需要（默认全 true）
+ *
+ * ⚠️ 联网：POST 到 EMBL ismart.embl.de/smart/show_motifs.pl（约 10-60s）。
+ * 输出: 每行 query + 域位置 + 域类型（Pfam:XXX / low_complexity_region 等）。
+ */
+public class SubmitSMARTCli {
+    public static void main(String[] args) throws Exception {
+        if (args.length < 2) {
+            System.err.println("用法: SubmitSMARTCli <in.fa> <out.txt>");
+            System.exit(1);
+        }
+        Object s = Class.forName("BatchSMART.submitSMART").getDeclaredConstructor().newInstance();
+        Class<?> c = s.getClass();
+        c.getMethod("setInFa", java.io.File.class).invoke(s, new java.io.File(args[0]));
+        c.getMethod("setOutTab", java.io.File.class).invoke(s, new java.io.File(args[1]));
+        c.getMethod("setDo_pfam", boolean.class).invoke(s, true);
+        c.getMethod("setDo_signalp", boolean.class).invoke(s, true);
+        c.getMethod("setDo_disembl", boolean.class).invoke(s, true);
+        c.getMethod("setDo_schnipsel", boolean.class).invoke(s, true);
+        c.getMethod("setDo_rep", boolean.class).invoke(s, true);
+        c.getMethod("setFinished", boolean.class).invoke(s, false);
+        c.getMethod("process").invoke(s);
+        System.err.println("[tbplot] SMART 注释完成: " + args[1]);
+        System.exit(0);
+    }
+}

tbtools_cli-1.2.0.data/data/tbtools_cli/bridges/SuperCircosCli.java

@@ -0,0 +1,330 @@
+import biocjava.bioDoer.JIGplotToolkit.Circos.SuperCircos.JIGSuperCircos;
+import biocjava.bioDoer.JIGplotToolkit.Circos.SuperCircos.JIGSuperCircosControl;
+import biocjava.bioDoer.JIGplotToolkit.Circos.SuperCircos.JIGSuperTrack;
+import biocjava.bioDoer.JIGplotToolkit.Circos.LinkObj;
+import biocjava.bioDoer.JIGplotToolkit.Circos.chrFeature;
+import jigplot.engine.JIGBasePanel;
+import jigplot.engine.JIGSubPanel;
+import jigplot.engine.JIGConstants;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+
+/**
+ * SuperCircos CLI — 多轨道环形图
+ * 
+ * 用法:
+ *   java -cp JAR:tbplot SuperCircosCli <config.cfg> <outFile> [width] [height]
+ * 
+ * 配置格式（行导向，# 注释）:
+ *   [chrLen] <file>                    # 染色体长度文件: ChrName\tStart-End 或 ChrName\tLength
+ *   [link] <file>                      # 连接文件: ChrA\tStartA\tEndA\tChrB\tStartB\tEndB\t[Color]
+ *   [gene] <file>                      # 基因位置文件: Chr\tGeneName\tStart\tEnd
+ *   [track] <type> <file> <startPos> <endPos> <color1> <color2> <color3> <binSize> [fillColor] [drawColor]
+ *     type: Tile|Triangle|HeatMap|Point|Line|Bar|Arrow
+ *     color: RGB 格式 "255,0,0" 或 颜色名 RED|ORANGE|BLUE|YELLOW|CYAN|GREEN|BLACK|WHITE|GRAY|DARK_GRAY|LIGHT_GRAY
+ *   [width] <int>                      # 画布宽度 (默认 800)
+ *   [height] <int>                     # 画布高度 (默认 800)
+ *   [linkColor] <r,g,b>               # 连线颜色
+ *   [linkStroke] <float>              # 连线粗细 (默认 1.0)
+ *   [chrFillColor] <r,g,b>            # 染色体填充色
+ *   [chrLabelColor] <r,g,b>           # 染色体标签色
+ *   [chrLabelFont] <name> <style> <size>  # 染色体标签字体
+ *   [geneLabelShow] true|false        # 是否显示基因标签
+ *   [chrLabelShow] true|false         # 是否显示染色体标签
+ *   [chrBarShow] true|false           # 是否显示染色体条
+ *   [tickShow] true|false             # 是否显示刻度
+ *   [majorTickInterval] <int>         # 主刻度间隔 (bp)
+ *   [minorTickInterval] <int>         # 次刻度间隔 (bp)
+ *   [startAngle] <int>                # 起始角度
+ *   [endAngle] <int>                  # 结束角度
+ *   [circlize] true|false             # 是否环形
+ */
+public class SuperCircosCli {
+    
+    public static void main(String[] args) throws Exception {
+        if (args.length < 2) {
+            System.err.println("用法: SuperCircosCli <config.cfg> <outFile> [width] [height]");
+            System.exit(1);
+        }
+        
+        String configFile = args[0];
+        String outFile = args[1];
+        int width = 800;
+        int height = 800;
+        if (args.length > 2) width = Integer.parseInt(args[2]);
+        if (args.length > 3) height = Integer.parseInt(args[3]);
+        
+        // 解析配置
+        java.io.BufferedReader br = new java.io.BufferedReader(new java.io.FileReader(configFile));
+        String line;
+        
+        File chrLenFile = null;
+        File linkFile = null;
+        File geneFile = null;
+        ArrayList<JIGSuperTrack> tracks = new ArrayList<JIGSuperTrack>();
+        
+        Color linkColor = Color.LIGHT_GRAY;
+        float linkStroke = 1.0f;
+        Color chrFillColor = new Color(240, 240, 240);
+        Color chrLabelColor = Color.ORANGE;
+        Font chrLabelFont = new Font("Arial", Font.BOLD, 14);
+        boolean geneLabelShow = true;
+        boolean chrLabelShow = true;
+        boolean chrBarShow = true;
+        boolean tickShow = true;
+        int majorTickInterval = 10000000;
+        int minorTickInterval = 2000000;
+        int startAngle = 0;
+        int endAngle = 360;
+        boolean circlize = true;
+        
+        while ((line = br.readLine()) != null) {
+            line = line.trim();
+            if (line.startsWith("#") || line.isEmpty()) continue;
+            
+            String[] parts = line.split("\\s+", 2);
+            String key = parts[0];
+            String value = parts.length > 1 ? parts[1].trim() : "";
+            
+            if (key.equals("[chrLen]")) {
+                chrLenFile = new File(value);
+            } else if (key.equals("[link]")) {
+                linkFile = new File(value);
+            } else if (key.equals("[gene]")) {
+                geneFile = new File(value);
+            } else if (key.equals("[track]")) {
+                // [track] <type> <file> <startPos> <endPos> <color1> <color2> <color3> <binSize> [fillColor] [drawColor]
+                String[] tParts = value.split("\\s+");
+                String trackType = tParts[0];
+                File trackFile = new File(tParts[1]);
+                int startPos = Integer.parseInt(tParts[2]);
+                int endPos = Integer.parseInt(tParts[3]);
+                Color c1 = parseColor(tParts[4]);
+                Color c2 = parseColor(tParts[5]);
+                Color c3 = parseColor(tParts[6]);
+                int binSize = Integer.parseInt(tParts[7]);
+                
+                JIGSuperTrack track = new JIGSuperTrack();
+                track.setInTabFile(trackFile);
+                track.setInTrackType(parseTrackType(trackType));
+                track.setTrackStartPos(startPos);
+                track.setTrackEndPos(endPos);
+                track.setEleMentColorOne(c1);
+                track.setEleMentColorTwo(c2);
+                track.setEleMentColorThree(c3);
+                track.setBinSize(binSize);
+                
+                if (tParts.length > 8 && !tParts[8].equals("-")) {
+                    track.setFillColor(parseColor(tParts[8]));
+                }
+                if (tParts.length > 9 && !tParts[9].equals("-")) {
+                    track.setDrawColor(parseColor(tParts[9]));
+                }
+                tracks.add(track);
+            } else if (key.equals("[width]")) {
+                width = Integer.parseInt(value);
+            } else if (key.equals("[height]")) {
+                height = Integer.parseInt(value);
+            } else if (key.equals("[linkColor]")) {
+                linkColor = parseColor(value);
+            } else if (key.equals("[linkStroke]")) {
+                linkStroke = Float.parseFloat(value);
+            } else if (key.equals("[chrFillColor]")) {
+                chrFillColor = parseColor(value);
+            } else if (key.equals("[chrLabelColor]")) {
+                chrLabelColor = parseColor(value);
+            } else if (key.equals("[chrLabelFont]")) {
+                String[] fp = value.split("\\s+");
+                String fname = fp[0];
+                int fstyle = Integer.parseInt(fp[1]);
+                int fsize = Integer.parseInt(fp[2]);
+                chrLabelFont = new Font(fname, fstyle, fsize);
+            } else if (key.equals("[geneLabelShow]")) {
+                geneLabelShow = Boolean.parseBoolean(value);
+            } else if (key.equals("[chrLabelShow]")) {
+                chrLabelShow = Boolean.parseBoolean(value);
+            } else if (key.equals("[chrBarShow]")) {
+                chrBarShow = Boolean.parseBoolean(value);
+            } else if (key.equals("[tickShow]")) {
+                tickShow = Boolean.parseBoolean(value);
+            } else if (key.equals("[majorTickInterval]")) {
+                majorTickInterval = Integer.parseInt(value);
+            } else if (key.equals("[minorTickInterval]")) {
+                minorTickInterval = Integer.parseInt(value);
+            } else if (key.equals("[startAngle]")) {
+                startAngle = Integer.parseInt(value);
+            } else if (key.equals("[endAngle]")) {
+                endAngle = Integer.parseInt(value);
+            } else if (key.equals("[circlize]")) {
+                circlize = Boolean.parseBoolean(value);
+            }
+        }
+        br.close();
+        
+        // 构建 SuperCircos
+        JIGSuperCircos jsc = new JIGSuperCircos();
+        
+        // 读取 chrLen
+        if (chrLenFile != null) {
+            LinkedHashMap<String, long[]> chrLenMap = new LinkedHashMap<String, long[]>();
+            java.io.BufferedReader chrBr = new java.io.BufferedReader(new java.io.FileReader(chrLenFile));
+            String chrLine;
+            while ((chrLine = chrBr.readLine()) != null) {
+                if (chrLine.startsWith("#") || chrLine.trim().isEmpty()) continue;
+                String[] cols = chrLine.split("\t");
+                String[] rangeArr = cols[1].split("[-:]");
+                if (rangeArr.length < 2) {
+                    chrLenMap.put(cols[0], new long[]{0, Long.parseLong(cols[1])});
+                } else {
+                    chrLenMap.put(cols[0], new long[]{Long.parseLong(rangeArr[0]), Long.parseLong(rangeArr[1])});
+                }
+            }
+            chrBr.close();
+            jsc.setChrLen(chrLenMap);
+        }
+        
+        // 读取 link
+        if (linkFile != null) {
+            ArrayList<LinkObj> linkArr = new ArrayList<LinkObj>();
+            java.io.BufferedReader linkBr = new java.io.BufferedReader(new java.io.FileReader(linkFile));
+            String linkLine;
+            while ((linkLine = linkBr.readLine()) != null) {
+                if (linkLine.startsWith("#") || linkLine.trim().isEmpty()) continue;
+                String[] cols = linkLine.split("\t");
+                if (cols.length <= 5) continue;
+                LinkObj curLink = new LinkObj();
+                chrFeature fromFeature = new chrFeature();
+                fromFeature.chrName = cols[0];
+                fromFeature.startPos = Integer.parseInt(cols[1]);
+                fromFeature.endPos = Integer.parseInt(cols[2]);
+                chrFeature toFeature = new chrFeature();
+                toFeature.chrName = cols[3];
+                toFeature.startPos = Integer.parseInt(cols[4]);
+                toFeature.endPos = Integer.parseInt(cols[5]);
+                curLink.fromFeature = fromFeature;
+                curLink.toFeature = toFeature;
+                if (cols.length > 6) {
+                    curLink.color = parseColor(cols[6]);
+                } else {
+                    curLink.color = new Color(240, 240, 240);
+                }
+                linkArr.add(curLink);
+            }
+            linkBr.close();
+            jsc.setLinkedRegion(linkArr);
+        }
+        
+        // 读取 gene
+        if (geneFile != null) {
+            LinkedHashMap<String, ArrayList<chrFeature>> genePosMap = new LinkedHashMap<String, ArrayList<chrFeature>>();
+            java.io.BufferedReader geneBr = new java.io.BufferedReader(new java.io.FileReader(geneFile));
+            String geneLine;
+            while ((geneLine = geneBr.readLine()) != null) {
+                if (geneLine.startsWith("#") || geneLine.trim().isEmpty()) continue;
+                String[] cols = geneLine.split("\t");
+                if (cols.length <= 3) continue;
+                chrFeature gf = new chrFeature();
+                gf.chrName = cols[0];
+                gf.featureName = cols[1];
+                gf.startPos = Integer.parseInt(cols[2]);
+                gf.endPos = Integer.parseInt(cols[3]);
+                if (genePosMap.containsKey(gf.chrName)) {
+                    genePosMap.get(gf.chrName).add(gf);
+                } else {
+                    ArrayList<chrFeature> arr = new ArrayList<chrFeature>();
+                    arr.add(gf);
+                    genePosMap.put(gf.chrName, arr);
+                }
+            }
+            geneBr.close();
+            jsc.setGenePos(genePosMap);
+        }
+        
+        // 设置 track
+        if (!tracks.isEmpty()) {
+            jsc.setTrackArr(tracks);
+        }
+        
+        // 设置参数
+        jsc.setGraphWidth(width);
+        jsc.setGraphHeight(height);
+        jsc.setLinkColor(linkColor);
+        jsc.setLinkStrokeSize(linkStroke);
+        jsc.setChrFillColor(chrFillColor);
+        jsc.setChrLabelColor(chrLabelColor);
+        jsc.setChrLabelFont(chrLabelFont);
+        jsc.setShowGeneLabel(geneLabelShow);
+        jsc.setShowChrLabel(chrLabelShow);
+        jsc.setShowChrBar(chrBarShow);
+        jsc.setShowIntervalTick(tickShow);
+        jsc.setMajorTickInterval(majorTickInterval);
+        jsc.setMinorTickInterval(minorTickInterval);
+        jsc.setStartAngle(startAngle);
+        jsc.setEndAngle(endAngle);
+        jsc.setCirclize(circlize);
+        
+        // 调用 plot 获取 JIGSubPanel[]
+        JIGSubPanel[] subPanels = jsc.plot();
+        
+        // 构建 JIGBasePanel 并保存
+        JIGBasePanel basePanel = new JIGBasePanel(width, height);
+        for (JIGSubPanel sp : subPanels) {
+            basePanel.addSubPanel(sp);
+        }
+        
+        // 保存
+        if (outFile.toLowerCase().endsWith(".svg")) {
+            basePanel.save2SVG(new java.io.File(outFile));
+        } else if (outFile.toLowerCase().endsWith(".png")) {
+            basePanel.save2PNG(new java.io.File(outFile));
+        } else if (outFile.toLowerCase().endsWith(".pdf")) {
+            basePanel.save2PDF(new java.io.File(outFile));
+        } else {
+            basePanel.save2SVG(new java.io.File(outFile + ".svg"));
+        }
+        
+        System.err.println("SuperCircos saved: " + outFile);
+    }
+    
+    static Color parseColor(String s) {
+        s = s.trim();
+        if (s.contains(",")) {
+            String[] rgb = s.split(",");
+            return new Color(Integer.parseInt(rgb[0].trim()), Integer.parseInt(rgb[1].trim()), Integer.parseInt(rgb[2].trim()));
+        }
+        switch (s.toUpperCase()) {
+            case "RED": return Color.RED;
+            case "ORANGE": return Color.ORANGE;
+            case "BLUE": return Color.BLUE;
+            case "YELLOW": return Color.YELLOW;
+            case "CYAN": return Color.CYAN;
+            case "GREEN": return Color.GREEN;
+            case "BLACK": return Color.BLACK;
+            case "WHITE": return Color.WHITE;
+            case "GRAY": return Color.GRAY;
+            case "DARK_GRAY": return Color.DARK_GRAY;
+            case "LIGHT_GRAY": return Color.LIGHT_GRAY;
+            case "PINK": return Color.PINK;
+            case "MAGENTA": return Color.MAGENTA;
+            default:
+                try { return Color.decode(s); } catch (Exception e) { return Color.RED; }
+        }
+    }
+    
+    static JIGSuperTrack.TrackType parseTrackType(String s) {
+        switch (s.trim().toUpperCase()) {
+            case "TILE": return JIGSuperTrack.TrackType.Tile;
+            case "TRIANGLE": return JIGSuperTrack.TrackType.Triangle;
+            case "HEATMAP": return JIGSuperTrack.TrackType.HeatMap;
+            case "POINT": return JIGSuperTrack.TrackType.Point;
+            case "LINE": return JIGSuperTrack.TrackType.Line;
+            case "BAR": return JIGSuperTrack.TrackType.Bar;
+            case "ARROW": return JIGSuperTrack.TrackType.Arrow;
+            default: return JIGSuperTrack.TrackType.HeatMap;
+        }
+    }
+}

tbtools_cli-1.2.0.data/data/tbtools_cli/bridges/TableColManipCli.java

@@ -0,0 +1,56 @@
+import java.io.File;
+import java.lang.reflect.Method;
+import java.util.ArrayList;
+
+/**
+ * TableColManipulator CLI bridge (engine 84)
+ * 表格列选择/筛选：根据列名从表中选择列输出
+ * Usage: TableColManipCli <inTable> <outTable> <colName1> [colName2 ...] [--sep tab|comma|space] [--header true|false] [--caseSensitive true|false]
+ *   inTable: 输入表格（支持 .gz）；colNames: 要保留的列名（表头）
+ */
+public class TableColManipCli {
+    public static void main(String[] args) throws Exception {
+        if (args.length < 3) {
+            System.err.println("Usage: TableColManipCli <inTable> <outTable> <colName1> [colName2...] [--sep tab|comma|space] [--header true|false] [--caseSensitive true|false]");
+            System.exit(1);
+        }
+        String inTable = args[0];
+        String outTable = args[1];
+        String sep = "tab";
+        boolean header = true;
+        boolean caseSensitive = false;
+        ArrayList<String> selCols = new ArrayList<>();
+        // 解析参数: colNames 直到 -- 前缀
+        int i = 2;
+        while (i < args.length) {
+            switch (args[i]) {
+                case "--sep": sep = args[++i]; break;
+                case "--header": header = Boolean.parseBoolean(args[++i]); break;
+                case "--caseSensitive": caseSensitive = Boolean.parseBoolean(args[++i]); break;
+                default: selCols.add(args[i]);
+            }
+            i++;
+        }
+        if (selCols.isEmpty()) {
+            System.err.println("至少需要一个列名");
+            System.exit(1);
+        }
+
+        Class<?> c = Class.forName("biocjava.bioDoer.Table.TableColManipulator");
+        Object o = c.getDeclaredConstructor().newInstance();
+        // ColSepType 枚举
+        Class<?> sepEnum = Class.forName("biocjava.bioDoer.Table.TableColManipulator$ColSepType");
+        String sepVal = sep.equals("comma") ? "comma" : sep.equals("space") ? "space" : "tab";
+        Object sepEnumVal = Enum.valueOf((Class) sepEnum, sepVal);
+        c.getMethod("setColumnSepType", sepEnum).invoke(o, sepEnumVal);
+        c.getMethod("setInFile", File.class).invoke(o, new File(inTable));
+        c.getMethod("setOutFile", File.class).invoke(o, new File(outTable));
+        c.getMethod("setContainHeader", boolean.class).invoke(o, header);
+        c.getMethod("setCaseSensitive", boolean.class).invoke(o, caseSensitive);
+        // setIdList 需要 ArrayList —— 传空列表
+        c.getMethod("setIdList", ArrayList.class).invoke(o, new ArrayList<String>());
+        c.getMethod("setSelectedCols", ArrayList.class).invoke(o, selCols);
+        c.getMethod("selectedLines").invoke(o);
+        System.out.println("[tbcli] TableColManipulator done: " + outTable);
+    }
+}

tbtools_cli-1.2.0.data/data/tbtools_cli/bridges/TableCollapseCli.java

@@ -0,0 +1,33 @@
+import java.io.File;
+
+/**
+ * tbplot tableCollapse — 表格按键折叠 CLI（08/29，第 63 引擎）
+ *
+ * 用法: TableCollapseCli <inTable> <keyColIndex> <outTable> [hasHeader true|false] [colSep]
+ *   inTable: 输入表格；keyColIndex: 折叠键列（0 起）
+ *   outTable: 按键折叠（同键行合并，值用分隔符连接）
+ *   hasHeader: 是否有表头（默认 true）
+ *   colSep: 分隔符（默认 \t）
+ *
+ * ⚠️ main() 硬编码路径——改走 setInTable/setKeyColumnIndex/setOutTable 等 setter + process()。
+ */
+public class TableCollapseCli {
+    public static void main(String[] args) throws Exception {
+        if (args.length < 3) {
+            System.err.println("用法: TableCollapseCli <inTable> <keyColIndex> <outTable> [hasHeader true|false] [colSep]");
+            System.exit(1);
+        }
+        Object o = Class.forName("biocjava.bioDoer.Table.TableCollasper")
+                .getDeclaredConstructor().newInstance();
+        Class<?> c = o.getClass();
+        c.getMethod("setInTable", File.class).invoke(o, new File(args[0]));
+        c.getMethod("setKeyColumnIndex", int.class).invoke(o, Integer.parseInt(args[1]));
+        c.getMethod("setOutTable", File.class).invoke(o, new File(args[2]));
+        boolean header = true;
+        if (args.length > 3) header = Boolean.parseBoolean(args[3]);
+        c.getMethod("setHeader", boolean.class).invoke(o, header);
+        c.getMethod("process").invoke(o);
+        System.err.println("[tbplot] 表格按键折叠完成: " + args[2]);
+        System.exit(0);
+    }
+}

tbtools_cli-1.2.0.data/data/tbtools_cli/bridges/TargetScoreCli.java

@@ -0,0 +1,47 @@
+import java.io.File;
+
+/**
+ * tbplot targetScore — miRNA 靶标打分 CLI（08/29，第 55 引擎）
+ *
+ * 用法: TargetScoreCli <in.ssearch36.m10> <outTable> [--scoreCutOff N] [--maxMismatch N] [--recCom true|false] [--revTargetSo true|false]
+ *   in.m10: ssearch36 官方参数输出（-w 100 -W 25 -E 1 -m 10 -i -U <mirna.fa> <target.fa>）
+ *   outTable: 靶标表（miRNA  target  strand  beg  end  score  miRNAseq  targetseq  E  bits）
+ *
+ * ⚠️ 关键坑（08/29 实锤）：
+ *   1. 必须 setCurAligner(Ssearch36)——默认 Fasta36 会 NPE（frame null）
+ *   2. ssearch36 必须带 -i（reverse-complement）才有 sw_frame 行
+ *   3. 完整管线：ssearch36 -i -m 10 → TargetScoreCli → 靶标表
+ */
+public class TargetScoreCli {
+    public static void main(String[] args) throws Exception {
+        if (args.length < 2) {
+            System.err.println("用法: TargetScoreCli <in.ssearch36.m10> <outTable> [--scoreCutOff N] [--maxMismatch N] [--recCom true|false] [--revTargetSo true|false]");
+            System.exit(1);
+        }
+        String in = args[0];
+        String out = args[1];
+        double scoreCutOff = 5.0;
+        int maxMisM = 6;
+        boolean recCom = false, revTargetSo = false;
+        for (int i = 2; i < args.length; i++) {
+            if (args[i].equals("--scoreCutOff") && i+1 < args.length) scoreCutOff = Double.parseDouble(args[++i]);
+            else if (args[i].equals("--maxMismatch") && i+1 < args.length) maxMisM = Integer.parseInt(args[++i]);
+            else if (args[i].equals("--recCom") && i+1 < args.length) recCom = Boolean.parseBoolean(args[++i]);
+            else if (args[i].equals("--revTargetSo") && i+1 < args.length) revTargetSo = Boolean.parseBoolean(args[++i]);
+        }
+        Object o = Class.forName("biocjava.bioDoer.miRNA.TargetSoEngine").getDeclaredConstructor().newInstance();
+        Class<?> c = o.getClass();
+        Class<?> alignerCls = Class.forName("biocjava.bioDoer.miRNA.TargetSoEngine$aligner");
+        c.getMethod("setCurAligner", alignerCls)
+                .invoke(o, Enum.valueOf((Class) alignerCls, "Ssearch36"));
+        c.getMethod("setInFasta36m10File", File.class).invoke(o, new File(in));
+        c.getMethod("setScoreCutOff", double.class).invoke(o, scoreCutOff);
+        c.getMethod("setTotalMaxMisM", int.class).invoke(o, maxMisM);
+        c.getMethod("setOutTable", File.class).invoke(o, new File(out));
+        c.getMethod("setGenomeIsRecCom", boolean.class).invoke(o, recCom);
+        c.getMethod("setRevTargetSo", boolean.class).invoke(o, revTargetSo);
+        c.getMethod("process").invoke(o);
+        System.err.println("[tbplot] miRNA 靶标打分完成: " + out);
+        System.exit(0);
+    }
+}

tbtools_cli-1.2.0.data/data/tbtools_cli/bridges/TauCalcCli.java

@@ -0,0 +1,28 @@
+import java.io.File;
+
+/**
+ * tbplot tauIndex — 组织特异性 τ 指数 CLI（08/29，第 59 引擎）
+ *
+ * 用法: TauCalcCli <inExpTab> <outTAU>
+ *   inExpTab: 表达矩阵（首列基因名 + 样本列）
+ *   outTAU: 每基因 Preferred Sample + TAU Index（0=均匀, 1=完全组织特异）
+ *
+ * ⚠️ main() 硬编码路径——改走 setInExpTab/setOutTAU + process()。
+ *    τ 指数：1 - Σ(1-x̂)/(n-1)，组织表达分析的通用特异性指标。
+ */
+public class TauCalcCli {
+    public static void main(String[] args) throws Exception {
+        if (args.length < 2) {
+            System.err.println("用法: TauCalcCli <inExpTab> <outTAU>");
+            System.exit(1);
+        }
+        Object o = Class.forName("biocjava.bioDoer.Table.TAUCalc")
+                .getDeclaredConstructor().newInstance();
+        Class<?> c = o.getClass();
+        c.getMethod("setInExpTab", File.class).invoke(o, new File(args[0]));
+        c.getMethod("setOutTAU", File.class).invoke(o, new File(args[1]));
+        c.getMethod("process").invoke(o);
+        System.err.println("[tbplot] τ 指数计算完成: " + args[1]);
+        System.exit(0);
+    }
+}

tbtools_cli-1.2.0.data/data/tbtools_cli/bridges/TaxonomyBatchCli.java

@@ -0,0 +1,72 @@
+import biocjava.bioWeb.NCBITaxonomy.NCBITaxonomy;
+import biocjava.bioWeb.NCBITaxonomy.Taxon;
+
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileReader;
+import java.io.FileWriter;
+
+/**
+ * tbplot taxparse — 物种名批量分类解析 CLI（GUI 逆向 #38，09/21）
+ *
+ * 用法: TaxonomyBatchCli <idList.txt> <out.xls>
+ *   idList: 每行一个物种名（首列；其余列原样透传）
+ *   out:    首列 + 9 级分类（superkingdom/kingdom/phylum/subphylum/order/
+ *           family/subfamily/tribe/genus）+ 透传列
+ *
+ * 引擎: NCBITaxonomy.process（GUI 逆向：TaxonomyParserGUIPanel $3 批量循环逻辑；
+ *   ⚠️ 联网 NCBI eutils esearch+efetch；注册表单次版为 tbtools tool NCBITaxonomy）
+ */
+public class TaxonomyBatchCli {
+    public static void main(String[] args) throws Exception {
+        if (args.length < 2) {
+            System.err.println("用法: TaxonomyBatchCli <idList.txt> <out.xls>");
+            System.exit(1);
+        }
+        File idFile = new File(args[0]);
+        File outFile = new File(args[1]);
+        if (!idFile.exists()) {
+            System.err.println("错误: 输入文件不存在: " + idFile.getAbsolutePath());
+            System.exit(2);
+        }
+        NCBITaxonomy nt = new NCBITaxonomy();
+        BufferedReader br = new BufferedReader(new FileReader(idFile));
+        BufferedWriter bw = new BufferedWriter(new FileWriter(outFile));
+        bw.write("Name\tSuperkingdom\tKingdom\tPhylum\tSubphylum\tOrder\tFamily\tSubfamily\tTribe\tGenus");
+        bw.newLine();
+        String inline;
+        int ok = 0, skip = 0;
+        while ((inline = br.readLine()) != null) {
+            if (inline.trim().isEmpty()) continue;
+            String[] columns = inline.split("\t");
+            Taxon curTaxon = nt.process(columns[0]);
+            if (!curTaxon.isExist()) {
+                System.err.println("Skipping line " + inline + " which can't be processed");
+                skip++;
+                continue;
+            }
+            StringBuilder sb = new StringBuilder();
+            sb.append(columns[0]).append("\t");
+            sb.append(curTaxon.getSuperkingdom()).append("\t");
+            sb.append(curTaxon.getKingdom()).append("\t");
+            sb.append(curTaxon.getPhylum()).append("\t");
+            sb.append(curTaxon.getSubphylum()).append("\t");
+            sb.append(curTaxon.getOrder()).append("\t");
+            sb.append(curTaxon.getFamily()).append("\t");
+            sb.append(curTaxon.getSubfamily()).append("\t");
+            sb.append(curTaxon.getTribe()).append("\t");
+            sb.append(curTaxon.getGenus());
+            for (int i = 1; i < columns.length; ++i) {
+                sb.append("\t").append(columns[i]);
+            }
+            bw.write(sb.toString());
+            bw.newLine();
+            ok++;
+        }
+        br.close();
+        bw.close();
+        System.err.println("[tbplot] 分类解析完成: " + ok + " 条成功" + (skip > 0 ? "，" + skip + " 条跳过" : "") + " → " + outFile.getAbsolutePath());
+        System.exit(0);
+    }
+}