spatula.cpp

#include "spatula.h"
#include "qgenlib/commands.h"
#include "qgenlib/qgen_utils.h"

int32_t cmdMatchTag(int32_t argc, char **argv);
int32_t cmdSearchTag(int32_t argc, char **argv);
int32_t cmdMakeSpatialDGE(int32_t argc, char **argv);
int32_t cmdMatchSpatialBarcodes(int32_t argc, char **argv);
int32_t cmdMergeMatchedTags(int32_t argc, char **argv);
int32_t cmdBuildSpatialBarcodeDict(int32_t argc, char **argv);
int32_t cmdReformatFASTQs(int32_t argc, char **argv);
int32_t cmdFilterFASTQs(int32_t argc, char **argv);
int32_t cmdReformatFASTQsMT(int32_t argc, char **argv);
int32_t cmdDGE2SDGE(int32_t argc, char **argv);
int32_t cmdSGE2TSV(int32_t argc, char **argv);
int32_t cmdMEX2SpTSV(int32_t argc, char **argv);
int32_t cmdPixel2SpTSV(int32_t argc, char **argv);
int32_t cmdMEXSubset(int32_t argc, char **argv);
int32_t cmdSpTSV2MEX(int32_t argc, char **argv);
int32_t cmdSpTSV2Model(int32_t argc, char **argv);
int32_t cmdConvertSGE(int32_t argc, char **argv);
int32_t cmdFilterTSV(int32_t argc, char **argv);
int32_t cmdSegmentSGE(int32_t argc, char **argv);
int32_t cmdDrawSGE(int32_t argc, char **argv);
int32_t cmdDrawTSV(int32_t argc, char **argv);
int32_t cmdSubsetSGE(int32_t argc, char **argv);
int32_t cmdCombineSGE(int32_t argc, char **argv);
int32_t cmdEvalDupsSBCD(int32_t argc, char **argv);
int32_t cmdDrawXY(int32_t argc, char **argv);
int32_t cmdDraw3way(int32_t argc, char **argv);
int32_t cmdPngMono2RGBA(int32_t argc, char **argv);
int32_t cmdCombineSBCD(int32_t argc, char **argv);
int32_t cmdHist(int32_t argc, char **argv);
int32_t cmdFilterCommonBarcodes(int32_t argc, char **argv);
int32_t cmdStratifyFASTQByBarcodes(int32_t argc, char **argv);
int32_t cmdCustomDemuxFASTQ(int32_t argc, char **argv);
int32_t cmdJoinPixelTSV(int32_t argc, char **argv);
int32_t cmdPairPseudobulkFromDecode(int32_t argc, char **argv);
int32_t cmdPseudobulkFromDecode(int32_t argc, char **argv);
int32_t cmdDiffExpDecode(int32_t argc, char **argv);
int32_t cmdDiffExpModelMatrix(int32_t argc, char **argv);
int32_t cmdMergePseudobulk(int32_t argc, char **argv);
int32_t cmdReformatTsv(int32_t argc, char **argv);
int32_t cmdPastePixelTSV(int32_t argc, char **argv);
int32_t cmdAppendTopKTSV(int32_t argc, char **argv);
int32_t cmdJoinPixelDecode(int32_t argc, char **argv);
int32_t cmdMergeSpTSV(int32_t argc, char **argv);
int32_t cmdDrawPolygons(int32_t argc, char **argv);
int32_t cmdPixels2Cells(int32_t argc, char **argv);
int32_t cmdSplitMoleculeCounts(int32_t argc, char **argv);
int32_t cmdAssignFeature2Bin(int32_t argc, char **argv);
int32_t cmdSplitMol2Bin(int32_t argc, char **argv);
int32_t cmdTsvAddCellId(int32_t argc, char **argv);

int32_t main(int32_t argc, char **argv)
{
  commandHelp.copyright_str = "Copyright (c) 2022-2024 by Hyun Min Kang";

  commandList cl;

  BEGIN_LONG_COMMANDS(longCommandlines)
  //LONG_COMMAND_GROUP("Tools for Analyzing Spatial Barcodes", NULL)
  //LONG_COMMAND_GROUP("Spatial Barcodes ", NULL)

  //LONG_COMMAND_GROUP("Tools for Analyzing Seq-Scope-specific Spatial Gene Expression (SGE)", NULL)
  LONG_COMMAND_GROUP("Seq-Scope Tools", NULL)
  LONG_COMMAND("build-sbcds", &cmdBuildSpatialBarcodeDict, "Create spatial barcode dictionary based from HDMI FASTQ arrays")
  LONG_COMMAND("convert-sge", &cmdConvertSGE, "Convert SGE into plain various formats")
  LONG_COMMAND("combine-sbcds", &cmdCombineSBCD, "Combine multiple SBCD files")
  LONG_COMMAND("combine-sge", &cmdCombineSGE, "Combine multiple SGE files")
  LONG_COMMAND("dge2sdge", &cmdDGE2SDGE, "Convert DGE (from STARsolo) into SGE format (same as dge2sge)")
  LONG_COMMAND("dge2sge", &cmdDGE2SDGE, "Convert DGE (from STARsolo) into SGE format (same as dge2sdge)")
  LONG_COMMAND("eval-dups-sbcds", &cmdEvalDupsSBCD, "Evaluate duplicates in spatial barcodes")
  LONG_COMMAND("filter-tsv", &cmdFilterTSV, "Filter TSV based on spatial coordinates or gene list")
  LONG_COMMAND("make-sdge", &cmdMakeSpatialDGE, "Make spatial DGE files from STARsolo output")
  LONG_COMMAND("match-sbcds", &cmdMatchSpatialBarcodes, "Match the FASTQ file containing spatial barcodes with the spatial barcode dictionary")
  LONG_COMMAND("match-tag", &cmdMatchTag, "Match tags from FASTQ")
  LONG_COMMAND("merge-matched-tags", &cmdMergeMatchedTags, "Merged matched tags generated by match-tag command")
  LONG_COMMAND("search-tag", &cmdSearchTag, "Search tags from FASTQ")
  LONG_COMMAND("sge2tsv", &cmdSGE2TSV, "Convert SGE (from sge2sdge) into plain TSV format (unsorted)")
  LONG_COMMAND("segment-sge", &cmdSegmentSGE, "Segment SGE based on custom, grid, or hexagonal masks")
  LONG_COMMAND("subset-sge", &cmdSubsetSGE, "Subset Spatial SGE based on bounding box")

  //LONG_COMMAND_GROUP("Tools for Analyzing FICTURE-specific Gene Expression data", NULL)
  LONG_COMMAND_GROUP("FICTURE Tools", NULL)
  LONG_COMMAND("append-topk-tsv", &cmdAppendTopKTSV, "Append topK and topP columns to the input TSV file")
  LONG_COMMAND("diffexp-model-matrix", &cmdDiffExpModelMatrix, "Perform differential expression test from model matrix")
  LONG_COMMAND("diffexp-decode", &cmdDiffExpDecode, "Perform differential expression test and create pseudobulk data from pixel-level decoding output")
  LONG_COMMAND("join-pixel-decode", &cmdJoinPixelDecode, "Join pixel-level-decode output from FICTURE2 with raw transcript-level TSV files")
  LONG_COMMAND("join-pixel-tsv", &cmdJoinPixelTSV, "Join pixel-level output from FICTURE with raw transcript-level TSV files")
  LONG_COMMAND("merge-pseudobulk", &cmdMergePseudobulk, "Merge multiple pseudobulk matrices into one")
  LONG_COMMAND("merge-sptsv", &cmdMergeSpTSV, "Merge multiple sparse TSV files into a single sparse TSV file")
  LONG_COMMAND("mex2sptsv", &cmdMEX2SpTSV, "Convert 10x Market Exchange (MEX) formatted DGE to Sparse TSV format in FICTURE2")
  LONG_COMMAND("paste-pixel-tsv", &cmdPastePixelTSV, "Paste pixel-level output from FICTURE2 with raw transcript-level TSV files")
  LONG_COMMAND("pseudobulk-from-decode", &cmdPseudobulkFromDecode, "Write pseudobulk matrix from pixel-level decode output")
  LONG_COMMAND("pair-pseudobulk-from-decode", &cmdPairPseudobulkFromDecode, "Write pairwise pseudobulk matrix from pixel-level decode output")
  LONG_COMMAND("pixel2sptsv", &cmdPixel2SpTSV, "Convert pixel-level TSV to Sparse TSV based on assigned cell IDs")
  LONG_COMMAND("subset-mex", &cmdMEXSubset, "Subset 10x Market Exchange (MEX) formatted DGE to specific features and barcodes")
  LONG_COMMAND("sptsv2mex", &cmdSpTSV2MEX, "Convert Sparse TSV format in FICTURE2 to 10x Market Exchange (MEX) formatted DGE")
  LONG_COMMAND("sptsv2model", &cmdSpTSV2Model, "Create model matrix from Sparse TSV format in FICTURE2 with cluster assignment")
  LONG_COMMAND("pixels2cells", &cmdPixels2Cells, "Assign pixels to cell IDs based on boundary polygons")
  LONG_COMMAND("tsv-add-cell-id", &cmdTsvAddCellId, "Annotate transcript TSV with cell IDs from boundary polygons (exact, multithreaded)")
  LONG_COMMAND("assign-feature2bin", &cmdAssignFeature2Bin, "Assign features (genes) into ordered bins based on total counts, writing the bin assignment as JSON")
  LONG_COMMAND("split-mol2bin", &cmdSplitMol2Bin, "Split a molecule TSV into per-bin files using a gene->bin assignment JSON (from assign-feature2bin)")
  LONG_COMMAND("split-molecule-counts", &cmdSplitMoleculeCounts, "(Deprecated: use assign-feature2bin + split-mol2bin) Split molecule counts into pixel-level bins based on gene names")

  LONG_COMMAND_GROUP("FASTQ Tools", NULL)
  LONG_COMMAND("custom-demux-fastq", &cmdCustomDemuxFASTQ, "Demultiplex FASTQ files based in a customized manner")
  LONG_COMMAND("filter-common-barcodes", &cmdFilterCommonBarcodes, "Filter FASTQ files based on the frequency of barcodes")
  LONG_COMMAND("filter-fastqs", &cmdFilterFASTQs, "Filter FASTQs based on a pattern")
  LONG_COMMAND("reformat-fastqs", &cmdReformatFASTQs, "Reformat FASTQs to be ready for STARsolo alignment")
  LONG_COMMAND("reformat-fastqs-mt", &cmdReformatFASTQsMT, "Reformat FASTQs to be ready for STARsolo alignment (multithreaded/not working)")
  LONG_COMMAND("stratify-fastq-by-barcodes", &cmdStratifyFASTQByBarcodes, "Stratify FASTQ files by spatial barcodes and UMIs")

  LONG_COMMAND_GROUP("Image Tools", NULL)
  LONG_COMMAND("draw-3way", &cmdDraw3way, "Draw the 3-way image from the output of sttools pipeline")
  LONG_COMMAND("draw-sge", &cmdDrawSGE, "Draw the image of spatial gene expression (SGE) data")
  LONG_COMMAND("draw-xy", &cmdDrawXY, "Draw the image of points in 2D space")
  LONG_COMMAND("draw-tsv", &cmdDrawTSV, "Draw the image of TSV-formatted spatial gene expression data")
  LONG_COMMAND("draw-polygons", &cmdDrawPolygons, "Draw polygons based on JSON input")
  LONG_COMMAND("png-mono2rgba", &cmdPngMono2RGBA, "Convert a monochrome PNG image to RGBA format")

  LONG_COMMAND_GROUP("Other Tools", NULL)
  LONG_COMMAND("hist", &cmdHist, "Create a text-based histogram")
  LONG_COMMAND("reformat-tsv", &cmdReformatTsv, "Reformat TSV/CSV files by selecting or reordering columns")

  END_LONG_COMMANDS();

  cl.Add(new longCommands("Available Commands", longCommandlines));

  if (argc < 2)
  {
    printf("[spatula %s] -- spatial transcriptomics utilities\n\n", SPATULA_VERSION_STRING);
    fprintf(stderr, " Copyright (c) 2022-2026 by Hyun Min Kang\n");
    fprintf(stderr, " Licensed under the Apache License v2.0 http://www.apache.org/licenses/\n\n");
    fprintf(stderr, "To run a specific command      : %s [command] [options]\n", argv[0]);
    fprintf(stderr, "For detailed instructions, run : %s --help\n", argv[0]);
    cl.Status();
    return 1;
  }
  else
  {
    if (strcmp(argv[1], "--help") == 0)
    {
      cl.HelpMessage();
    }
    else
    {
      return cl.Read(argc, argv);
    }
  }
  return 0;
}