biopipen 0.25.0__py3-none-any.whl → 0.25.2__py3-none-any.whl

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Files changed (9) hide show
  1. biopipen/__init__.py +1 -1
  2. biopipen/scripts/scrna/celltypist-wrapper.py +4 -3
  3. biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.R +1 -1
  4. biopipen/scripts/tcr/Immunarch-basic.R +1 -1
  5. biopipen/scripts/tcr/Immunarch-diversity.R +1 -1
  6. {biopipen-0.25.0.dist-info → biopipen-0.25.2.dist-info}/METADATA +1 -1
  7. {biopipen-0.25.0.dist-info → biopipen-0.25.2.dist-info}/RECORD +9 -9
  8. {biopipen-0.25.0.dist-info → biopipen-0.25.2.dist-info}/WHEEL +0 -0
  9. {biopipen-0.25.0.dist-info → biopipen-0.25.2.dist-info}/entry_points.txt +0 -0
biopipen/__init__.py CHANGED
@@ -1 +1 @@
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- __version__ = "0.25.0"
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+ __version__ = "0.25.2"
biopipen/scripts/scrna/celltypist-wrapper.py CHANGED
@@ -37,9 +37,10 @@ if __name__ == "__main__":
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  )
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  out_adata = annotated.to_adata()
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- if over_clustering and args.majority_voting:
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- # rename majority_voting column to over_clustering
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- out_adata.obs[over_clustering] = out_adata.obs["majority_voting"]
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+ # leave as is
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+ # if over_clustering and args.majority_voting:
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+ # # rename majority_voting column to over_clustering
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+ # out_adata.obs[over_clustering] = out_adata.obs["majority_voting"]
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  if args.output.endswith(".h5ad"):
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  try:
biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.R CHANGED
@@ -100,7 +100,7 @@ do_one_subset <- function(s, subset_col, subset_prefix) {
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  pre_rank_matrix <- as.matrix(rowSums(abs(pca$rotation[, 1:selected_pcs, drop=FALSE])))
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  pre_rank_matrix <- as.list(as.data.frame(t(pre_rank_matrix)))
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- odir = file.path(subset_dir, paste0(grouping_prefix, group))
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+ odir = file.path(subset_dir, paste0(grouping_prefix, slugify(group)))
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  dir.create(odir, showWarnings = FALSE)
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  runFGSEA(
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  pre_rank_matrix,
biopipen/scripts/tcr/Immunarch-basic.R CHANGED
@@ -11,7 +11,7 @@ counts = {{envs.counts | r}}
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  # Fill up cases
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  fill_up_cases_basic = function(config) {
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- log_info("Filling up cases ...")
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+ log_debug("Filling up cases ...")
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  cases = config$cases
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  if (is.null(cases) || length(cases) == 0) {
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  cases$DEFAULT = list(by = config$by, devpars = config$devpars, subset = config$subset)
biopipen/scripts/tcr/Immunarch-diversity.R CHANGED
@@ -35,7 +35,7 @@ dir.create(div_dir, showWarnings = FALSE)
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  # Fill up the cases
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  update_case = function(case, name) {
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- log_info("Filling up case: {name} ...")
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+ log_debug("Filling up case: {name} ...")
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  case$subset <- case$subset %||% div_subset
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  case$method <- case$method %||% div_method
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  case$by <- case$by %||% div_by
{biopipen-0.25.0.dist-info → biopipen-0.25.2.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: biopipen
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- Version: 0.25.0
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+ Version: 0.25.2
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  Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
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  License: MIT
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  Author: pwwang
{biopipen-0.25.0.dist-info → biopipen-0.25.2.dist-info}/RECORD RENAMED
@@ -1,4 +1,4 @@
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- biopipen/__init__.py,sha256=Mu4JbSLl5nr-J2figk5hmW2mrw4skf_oeIzxbnpcgwY,23
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+ biopipen/__init__.py,sha256=NMzPG-AisbqV0qHNDcM-oIMtdXA6rLhjzeATPyNq6Nw,23
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  biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
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  biopipen/core/config.toml,sha256=Rn7Cta7WsMtmQkKGC4h9d5dU_STaIVBgR8UliiGgL6o,1757
@@ -149,12 +149,12 @@ biopipen/scripts/scrna/SeuratSubset.R,sha256=yVA11NVE2FSSw-DhxQcJRapns0tNNHdyDYi
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  biopipen/scripts/scrna/SeuratTo10X.R,sha256=T2nJBTwOe12AIKC2FZsMSv6xx3s-67CYZokpz5wshqY,2679
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  biopipen/scripts/scrna/TopExpressingGenes.R,sha256=J6tM54HStWkguUwFoIHRo_EAtCUKOuCBEfInzRfDYMQ,7703
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  biopipen/scripts/scrna/Write10X.R,sha256=OMhXvJwvaH-aWsMpijKrvXQVabc1qUu5ZEwiLAhkDeY,285
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- biopipen/scripts/scrna/celltypist-wrapper.py,sha256=Q2DIQA1N7inDdGk77bSxg7CJPQBKZgOLVNAgqDKYEZM,1698
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+ biopipen/scripts/scrna/celltypist-wrapper.py,sha256=f5M8f4rU5nC7l17RS0YVmUPpLLz4D6PIcgWtA77UExM,1722
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  biopipen/scripts/scrna/sctype.R,sha256=NaUJkABwF5G1UVm1CCtcMbwLSj94Mo24mbYCKFqo1Bw,6524
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  biopipen/scripts/scrna_metabolic_landscape/MetabolicFeatures.R,sha256=b77yG5FeRse3bNfFgLIEYGHNZzydAn1OeyyR_n5Ju60,4790
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  biopipen/scripts/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.R,sha256=ic8Fy8QqYDGh_izmvZVJ3KL66podg_CSF5ITL3FZsvo,5196
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  biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayActivity.R,sha256=95DLX1Rz0tobOuDZ8V9YdGgO0KiNthhccoeeOK21tno,16216
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- biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.R,sha256=EpV4Wqj1dLqtaJyIJo6dN6vxeRH6elLibbHpK_N37bE,9822
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+ biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.R,sha256=rQ9iwGh9FNRZlJJzM4QItdyXmebfzLAq05ZAjb1kGUw,9831
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  biopipen/scripts/tcgamaf/Maf2Vcf.py,sha256=Cxh7fiSNCxWDTfIJqZDOOnaSrw-85S_fH2U-PWY03hc,704
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  biopipen/scripts/tcgamaf/MafAddChr.py,sha256=V10HMisl12O3ZfXuRmFNdy5p-3mr43WCvy0GHxSpwfA,494
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  biopipen/scripts/tcgamaf/maf2vcf.pl,sha256=hJKcH-NbgWK6fmK7f3qex7ozJJl-PqCNPXqpwfcHwJg,22707
@@ -166,9 +166,9 @@ biopipen/scripts/tcr/GIANA/GIANA.py,sha256=0qLhgCWxT8K-4JvORA03CzBPTT5pd4Di5B_Dg
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  biopipen/scripts/tcr/GIANA/GIANA4.py,sha256=Z7Q3cUr1Pvmy4CFADN0P7i9g1-HbzWROMqk5HvL_F1Q,45762
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  biopipen/scripts/tcr/GIANA/Imgt_Human_TRBV.fasta,sha256=XUwDPXJxVH5O9Q0gCL6EILKXEwVyiAZXm4VS2vkPcnQ,15371
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  biopipen/scripts/tcr/GIANA/query.py,sha256=5NWSEDNrJomMt48tzLGpRwJTZB0zQxvMVTilyG8osX8,7298
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- biopipen/scripts/tcr/Immunarch-basic.R,sha256=g64RXmiPw73vbnwrKoRaNs1d3O6mRV9uhcAFkBV0g3U,3121
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+ biopipen/scripts/tcr/Immunarch-basic.R,sha256=3mLYkC10qA5jqxPO6ERMYBeeUJJ2x7XcvRC6IzTZw2w,3122
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  biopipen/scripts/tcr/Immunarch-clonality.R,sha256=48rbPCWka4eNEy-fjM0BlKDkMYdG2zlB8Sly1B4xdUI,3858
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- biopipen/scripts/tcr/Immunarch-diversity.R,sha256=C1qx50K2eIZ2c590jumGe1BpMmgohlaP-wVkmwzHa2E,28296
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+ biopipen/scripts/tcr/Immunarch-diversity.R,sha256=pSDZnJ2GvHjVFY-ah-Twz-cXfjiFcNBzfJ5wexQAiLw,28297
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  biopipen/scripts/tcr/Immunarch-geneusage.R,sha256=c0C8-KtKI2q6O9xZ9f5COefQbPlshT2hz1f36qpnW34,6817
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  biopipen/scripts/tcr/Immunarch-kmer.R,sha256=ttDKwPTde_DN2xekRF2LBrc_o8wQjxXa49VAzmUzQl8,6212
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  biopipen/scripts/tcr/Immunarch-overlap.R,sha256=GVt-qJPtd6NEe5njAqNStf2AP6pLkv7Ittw0YT_qdNY,7465
@@ -227,7 +227,7 @@ biopipen/utils/reference.py,sha256=6bPSwQa-GiDfr7xLR9a5T64Ey40y24yn3QfQ5wDFZkU,4
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  biopipen/utils/rnaseq.R,sha256=Ro2B2dG-Z2oVaT5tkwp9RHBz4dp_RF-JcizlM5GYXFs,1298
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  biopipen/utils/single_cell.R,sha256=bKduqOQjSC8BtZJuwfUShR49omoEMbB57n3Gi6dYlqA,4147
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  biopipen/utils/vcf.py,sha256=ajXs0M_QghEctlvUlSRjWQIABVF02wPdYd-0LP4mIsU,9377
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- biopipen-0.25.0.dist-info/METADATA,sha256=LhwQ6Pd8ZTG02hpDd04BK3G2T9uocKMI0Ioa3K4DoI8,932
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- biopipen-0.25.0.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
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- biopipen-0.25.0.dist-info/entry_points.txt,sha256=O7K7PHoJi-4tERYpqmryuTvrFNEsptMpqliZzB2oBQQ,577
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- biopipen-0.25.0.dist-info/RECORD,,
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+ biopipen-0.25.2.dist-info/METADATA,sha256=k3E_YX4GeDSwCwjTh7fyG_UivPes67k5_S_rXqENt50,932
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+ biopipen-0.25.2.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
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+ biopipen-0.25.2.dist-info/entry_points.txt,sha256=O7K7PHoJi-4tERYpqmryuTvrFNEsptMpqliZzB2oBQQ,577
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+ biopipen-0.25.2.dist-info/RECORD,,