gsMap 1.60__tar.gz → 1.61a0__tar.gz

{gsmap-1.60 → gsmap-1.61a0}/.github/workflows/publish-to-pypi.yml

@@ -38,7 +38,7 @@ jobs:
     runs-on: ubuntu-latest
     environment:
       name: pypi
-      url: https://pypi.org/p/<package-name>  # Replace <package-name> with your PyPI project name
+      url: https://pypi.org/p/gsMap
     permissions:
       id-token: write  # IMPORTANT: mandatory for trusted publishing
 
@@ -103,7 +103,7 @@ jobs:
 
     environment:
       name: testpypi
-      url: https://test.pypi.org/p/<package-name>
+      url: https://test.pypi.org/p/gsMap
 
     permissions:
       id-token: write  # IMPORTANT: mandatory for trusted publishing

{gsmap-1.60 → gsmap-1.61a0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: gsMap
-Version: 1.60
+Version: 1.61a0
 Summary: Genetics-informed pathogenic spatial mapping
 Author-email: liyang <songliyang@westlake.edu.cn>, wenhao <chenwenhao@westlake.edu.cn>
 Requires-Python: >=3.8
@@ -65,14 +65,14 @@ Provides-Extra: doc
 install use pip:
 
 ```bash
-pip install gsMap-mapping
+pip install gsMap
 ```
 
 install from source:
 
 ```bash
 git clone
-cd gsMap-mapping
+cd gsMap
 pip install -e .
 ```
 
@@ -83,7 +83,7 @@ To use gsMap, navigate to the command line and enter `gsMap` followed by the sub
 ### Basic Command Structure
 
 ```bash
-gsMap subcommand [arguments...]
+gsmap subcommand [arguments...]
 ```
 
 - `subcommand`: The specific operation you wish to perform.
@@ -107,7 +107,7 @@ To run a specific functionality, you need to provide the appropriate subcommand
 
 
 ```bash
-gsMap run_find_latent_representations --input_hdf5_path <path> --output_hdf5_path <path> --sample_name <name>
+gsmap run_find_latent_representations --input_hdf5_path <path> --output_hdf5_path <path> --sample_name <name>
 ```
 
 This command initiates the process of finding latent representations based on the given HDF5 input and output paths and sample name.

{gsmap-1.60 → gsmap-1.61a0}/README.md

@@ -12,14 +12,14 @@
 install use pip:
 
 ```bash
-pip install gsMap-mapping
+pip install gsMap
 ```
 
 install from source:
 
 ```bash
 git clone
-cd gsMap-mapping
+cd gsMap
 pip install -e .
 ```
 
@@ -30,7 +30,7 @@ To use gsMap, navigate to the command line and enter `gsMap` followed by the sub
 ### Basic Command Structure
 
 ```bash
-gsMap subcommand [arguments...]
+gsmap subcommand [arguments...]
 ```
 
 - `subcommand`: The specific operation you wish to perform.
@@ -54,7 +54,7 @@ To run a specific functionality, you need to provide the appropriate subcommand
 
 
 ```bash
-gsMap run_find_latent_representations --input_hdf5_path <path> --output_hdf5_path <path> --sample_name <name>
+gsmap run_find_latent_representations --input_hdf5_path <path> --output_hdf5_path <path> --sample_name <name>
 ```
 
 This command initiates the process of finding latent representations based on the given HDF5 input and output paths and sample name.

{gsmap-1.60 → gsmap-1.61a0}/docs/source/api/cauchy_combination.rst

@@ -4,5 +4,5 @@ Step 5: cauchy_combination (optional)
 .. argparse::
    :module: gsMap.main
    :func: create_parser
-   :prog: gsMap
-   :path: run_cauchy_combination
+   :prog: gsmap
+   :path: run_cauchy_combination

{gsmap-1.60 → gsmap-1.61a0}/docs/source/api/find_latent_representations.rst

@@ -4,5 +4,5 @@ Step 1: find_latent_representation
 .. argparse::
    :module: gsMap.main
    :func: create_parser
-   :prog: gsMap
-   :path: run_find_latent_representations
+   :prog: gsmap
+   :path: run_find_latent_representations

{gsmap-1.60 → gsmap-1.61a0}/docs/source/api/format_sumstats.rst

@@ -3,5 +3,5 @@ format_sumstats (optional)
 .. argparse::
    :module: gsMap.main
    :func: create_parser
-   :prog: gsMap
-   :path: format_sumstats
+   :prog: gsmap
+   :path: format_sumstats

{gsmap-1.60 → gsmap-1.61a0}/docs/source/api/generate_ldscore.rst

@@ -4,5 +4,5 @@ Step 3: generate_ldscore
 .. argparse::
    :module: gsMap.main
    :func: create_parser
-   :prog: gsMap
+   :prog: gsmap
    :path: run_generate_ldscore

{gsmap-1.60 → gsmap-1.61a0}/docs/source/api/latent_to_gene.rst

@@ -4,5 +4,5 @@ Step 2: latent_to_gene
 .. argparse::
    :module: gsMap.main
    :func: create_parser
-   :prog: gsMap
+   :prog: gsmap
    :path: run_latent_to_gene

{gsmap-1.60 → gsmap-1.61a0}/docs/source/api/spatial_ldsc.rst

@@ -4,5 +4,5 @@ Step 4: spatial_ldsc
 .. argparse::
    :module: gsMap.main
    :func: create_parser
-   :prog: gsMap
+   :prog: gsmap
    :path: run_spatial_ldsc

{gsmap-1.60 → gsmap-1.61a0}/docs/source/api/visualization.rst

@@ -4,5 +4,5 @@ Step 6: visualization (optional)
 .. argparse::
    :module: gsMap.main
    :func: create_parser
-   :prog: gsMap
-   :path: run_visualize
+   :prog: gsmap
+   :path: run_visualize

{gsmap-1.60 → gsmap-1.61a0}/docs/source/api.rst

@@ -4,19 +4,19 @@ gsMap Command Line Alphabets
 ===========================
 
 
-.. program:: gsMap
+.. program:: gsmap
 
 Synopsis
 --------
 
 .. code-block:: shell
 
-    usage: gsMap [-h] [--version] {run_find_latent_representations,run_latent_to_gene,run_generate_ldscore,run_spatial_ldsc,run_cauchy_combination,run_visualize,run_all_mode} ...
+    usage: gsmap [-h] [--version] {run_find_latent_representations,run_latent_to_gene,run_generate_ldscore,run_spatial_ldsc,run_cauchy_combination,run_visualize,run_all_mode} ...
 
 Description
 -----------
 
-gsMap: Genetics-informed pathogenic spatial mapping.
+gsmap: genetically informed spatial mapping of cells for complex traits.
 
 Options
 -------

{gsmap-1.60 → gsmap-1.61a0}/docs/source/data_format.md

@@ -85,7 +85,7 @@ SNPID	RSID	CHR	POS	EFFECT_ALLELE	OTHER_ALLELE	EFFECT_ALLELE_FREQ	BETA	SE	P	N
 
 To convert the summary statistics, use the commands:
 ```bash
-gsMap format_sumstats \
+gsmap format_sumstats \
 --sumstats GIANT_HEIGHT_YENGO_2022_GWAS_SUMMARY_STATS_ALL 
 --out HEIGHT
 ```
@@ -101,7 +101,7 @@ rs4040617	G	A	-0.463	1602016.000
 ```
 In most cases, this command can automatically recognize different column names of GWAS data, but you can also specify the column names to ensure correctness.
 ```bash
-gsMap format_sumstats \
+gsmap format_sumstats \
 --sumstats GIANT_HEIGHT_YENGO_2022_GWAS_SUMMARY_STATS_ALL 
 --out HEIGHT \
 --a1 EFFECT_ALLELE \
@@ -117,4 +117,4 @@ gsMap format_sumstats \
 For more usage options, please see:
 ```bash
 gsMap format_sumstats -h
-```
+```

{gsmap-1.60 → gsmap-1.61a0}/docs/source/index.rst

@@ -5,7 +5,7 @@ Welcome to gsMap's documentation!
 Introduction
 ------------
 
-``gsMap`` (Genetics-informed Pathogenic Spatial Mapping) is introduced to integrate spatial transcriptomics (ST) data with summary statistics of genome-wide association studies (GWAS), aiming to identify complex trait (disease)-associated cells and map their spatial distributions.
+``gsMap`` (genetically informed spatial mapping of cells for complex traits) is introduced to integrate spatial transcriptomics (ST) data with summary statistics of genome-wide association studies (GWAS), aiming to identify complex trait (disease)-associated cells and map their spatial distributions.
 
 Key Features
 ------------

{gsmap-1.60 → gsmap-1.61a0}/docs/source/mouse_example.md

@@ -94,7 +94,7 @@ W_FILE="gsMap_resource/LDSC_resource/weights_hm3_no_hla/weights." # The SNP regr
 **Execution**:
 ```shell
 HDF5_WITH_LATENT_PATH="$WORKDIR/$SAMPLE_NAME/find_latent_representations/${SAMPLE_NAME}_add_latent.h5ad"
-gsMap run_find_latent_representations \
+gsmap run_find_latent_representations \
     --input_hdf5_path $HDF5_PATH \
     --sample_name $SAMPLE_NAME \
     --output_hdf5_path $HDF5_OUTPUT \
@@ -116,7 +116,7 @@ gsMap run_find_latent_representations \
 **Execution**:
 ```shell
 MKSCORE_FEATHER_PATH="$WORKDIR/$SAMPLE_NAME/latent_to_gene/${SAMPLE_NAME}_gene_marker_score.feather"
-gsMap run_latent_to_gene \
+gsmap run_latent_to_gene \
     --input_hdf5_with_latent_path $HDF5_WITH_LATENT_PATH \
     --sample_name $SAMPLE_NAME \
     --output_feather_path $MKSCORE_FEATHER_PATH \
@@ -160,7 +160,7 @@ If a SNP is within the gene window, it will be assigned the gene specificity sco
 ```shell
 LDScoreDir="$WORKDIR/$SAMPLE_NAME/generate_ldscore"
 for CHROM in {1..22}; do
-    gsMap run_generate_ldscore \
+    gsmap run_generate_ldscore \
         --sample_name $SAMPLE_NAME \
         --chrom $CHROM \
         --ldscore_save_dir $LDScoreDir \
@@ -188,7 +188,7 @@ In this example we choose the all tissue enhancer annotation file (`ENHANCER_ANN
 ```shell
 LDScoreDir="$WORKDIR/$SAMPLE_NAME/generate_ldscore"
 for CHROM in {1..22}; do
-    gsMap run_generate_ldscore \
+    gsmap run_generate_ldscore \
         --sample_name $SAMPLE_NAME \
         --chrom $CHROM \
         --ldscore_save_dir $LDScoreDir \
@@ -218,7 +218,7 @@ This will use both the TSS and enhancer-gene linking to map SNPs to genes. In ca
 ```shell
 LDScoreDir="$WORKDIR/$SAMPLE_NAME/generate_ldscore"
 for CHROM in {1..22}; do
-    gsMap run_generate_ldscore \
+    gsmap run_generate_ldscore \
         --sample_name $SAMPLE_NAME \
         --chrom $CHROM \
         --ldscore_save_dir $LDScoreDir \
@@ -267,7 +267,7 @@ LDSC_DIR="$WORKDIR/$SAMPLE_NAME/spatial_ldsc"
 SUMSTATS_FILE="example_data/GWAS/IQ_NG_2018.sumstats.gz"
 TRAIT_NAME="IQ"
 
-gsMap run_spatial_ldsc \
+gsmap run_spatial_ldsc \
     --sumstats_file $SUMSTATS_FILE \
     --trait_name $TRAIT_NAME \
     --w_file $W_FILE \
@@ -294,7 +294,7 @@ SCZ: example_data/GWAS/PGC3_SCZ_wave3_public_INFO80.sumstats.gz
 ```shell
 LDSC_DIR="$WORKDIR/$SAMPLE_NAME/spatial_ldsc"
 SUMSTATS_CONFIG_FILE="example_data/GWAS/gwas_config.yaml"
-gsMap run_spatial_ldsc \
+gsmap run_spatial_ldsc \
     --w_file $W_FILE \
     --sample_name $SAMPLE_NAME \
     --num_processes 4 \
@@ -314,7 +314,7 @@ gsMap run_spatial_ldsc \
 ```shell
 CAUCHY_SAVE_DIR="$WORKDIR/$SAMPLE_NAME/cauchy_combination"
 TRAIT_NAME="IQ"
-gsMap run_cauchy_combination \
+gsmap run_cauchy_combination \
     --input_hdf5_path $HDF5_PATH \
     --input_ldsc_dir $LDSC_DIR \
     --sample_name $SAMPLE_NAME \
@@ -376,7 +376,7 @@ You could use below command to visualize the gsMap results. You will get a scatt
 - A html file which could be opened in a web browser to interactively explore the results.
 
 ```shell
-gsMap run_visualize \
+gsmap run_visualize \
     --input_hdf5_path $HDF5_PATH \
     --input_ldsc_dir $LDSC_DIR \
     --output_figure_dir $WORKDIR/$SAMPLE_NAME/figures \

{gsmap-1.60 → gsmap-1.61a0}/pyproject.toml

@@ -67,7 +67,7 @@ Documentation = "https://..."
 Website = "https://..."
 
 [project.scripts]
-gsMap = "gsMap.main:main"
+gsmap = "gsMap.main:main"
 
 [tool.flit.module]
 name = "gsMap"

{gsmap-1.60 → gsmap-1.61a0}/src/gsMap/__init__.py

@@ -2,4 +2,4 @@
 Genetics-informed pathogenic spatial mapping
 '''
 
-__version__ = '1.60'
+__version__ = '1.61a'

{gsmap-1.60 → gsmap-1.61a0}/test/GPS-snakemake-workflow-macaque.smk

@@ -84,7 +84,7 @@ rule find_latent_representations:
         qos=QOS
     run:
         command = f"""
-gsMap run_find_latent_representations \
+gsmap run_find_latent_representations \
     --input_hdf5_path {input.hdf5_path} \
     --sample_name {wildcards.sample_name} \
     --output_hdf5_path {output.hdf5_output} \
@@ -136,7 +136,7 @@ rule latent_to_gene:
     benchmark: '{sample_name}/latent_to_gene/{sample_name}_gene_marker_score.feather.benchmark'
     run:
         command = f"""
-gsMap run_latent_to_gene \
+gsmap run_latent_to_gene \
     --input_hdf5_with_latent_path {input.hdf5_with_latent_path} \
     --sample_name {wildcards.sample_name} \
     --output_feather_path {output.feather_path} \
@@ -181,7 +181,7 @@ rule generate_ldscore:
         qos=QOS
     run:
         command = f"""
-        gsMap run_generate_ldscore \
+        gsmap run_generate_ldscore \
             --sample_name {wildcards.sample_name} \
             --chrom {wildcards.chrom} \
             --ldscore_save_dir {params.ld_score_save_dir} \
@@ -238,7 +238,7 @@ rule spatial_ldsc:
         partition='intel-sc3,amd-ep2'
     run:
        command = f"""
-        gsMap run_spatial_ldsc --w_file {params.w_file} --sample_name {wildcards.sample_name} --num_processes {threads} --ldscore_input_dir {params.ldscore_input_dir} --ldsc_save_dir {params.ldsc_save_dir} --sumstats_config_file {params.sumstats_config_file} {f'--all_chunk {params.all_chunk}' if params.all_chunk else ''}
+        gsmap run_spatial_ldsc --w_file {params.w_file} --sample_name {wildcards.sample_name} --num_processes {threads} --ldscore_input_dir {params.ldscore_input_dir} --ldsc_save_dir {params.ldsc_save_dir} --sumstats_config_file {params.sumstats_config_file} {f'--all_chunk {params.all_chunk}' if params.all_chunk else ''}
         """
        shell(
            f'{command}'
@@ -264,5 +264,5 @@ rule cauchy_combination:
         mem_mb_per_cpu=25_000
     shell:
         """
-        gsMap run_cauchy_combination --input_hdf5_path {input.hdf5_path} --input_ldsc_dir {params.ldsc_dir} --sample_name {wildcards.sample_name} --output_cauchy_dir {params.cauchy_save_dir} --trait_name {wildcards.trait_name} --annotation {params.annotation}
+        gsmap run_cauchy_combination --input_hdf5_path {input.hdf5_path} --input_ldsc_dir {params.ldsc_dir} --sample_name {wildcards.sample_name} --output_cauchy_dir {params.cauchy_save_dir} --trait_name {wildcards.trait_name} --annotation {params.annotation}
         """

{gsmap-1.60 → gsmap-1.61a0}/test/GPS-snakemake-workflow.smk

@@ -46,7 +46,7 @@ rule find_latent_representations:
     benchmark: '{sample_name}/find_latent_representations/{sample_name}_add_latent.h5ad.benchmark'
     run:
         command = f"""
-gsMap run_find_latent_representations \
+gsmap run_find_latent_representations \
     --input_hdf5_path {input.hdf5_path} \
     --sample_name {wildcards.sample_name} \
     --output_hdf5_path {output.hdf5_output} \
@@ -98,7 +98,7 @@ rule latent_to_gene:
     benchmark: '{sample_name}/latent_to_gene/{sample_name}_gene_marker_score.feather.benchmark'
     run:
         command = f"""
-gsMap run_latent_to_gene \
+gsmap run_latent_to_gene \
     --input_hdf5_with_latent_path {input.hdf5_with_latent_path} \
     --sample_name {wildcards.sample_name} \
     --output_feather_path {output.feather_path} \
@@ -143,7 +143,7 @@ rule generate_ldscore:
         qos='huge'
     run:
         command = f"""
-        gsMap run_generate_ldscore \
+        gsmap run_generate_ldscore \
             --sample_name {wildcards.sample_name} \
             --chrom {wildcards.chrom} \
             --ldscore_save_dir {params.ld_score_save_dir} \
@@ -199,7 +199,7 @@ rule spatial_ldsc:
         qos='huge'
     run:
        command = f"""
-        gsMap run_spatial_ldsc --w_file {params.w_file} --sample_name {wildcards.sample_name} --num_processes {threads} --ldscore_input_dir {params.ldscore_input_dir} --ldsc_save_dir {params.ldsc_save_dir} --sumstats_config_file {params.sumstats_config_file} {f'--all_chunk {params.all_chunk}' if params.all_chunk else ''}
+        gsmap run_spatial_ldsc --w_file {params.w_file} --sample_name {wildcards.sample_name} --num_processes {threads} --ldscore_input_dir {params.ldscore_input_dir} --ldsc_save_dir {params.ldsc_save_dir} --sumstats_config_file {params.sumstats_config_file} {f'--all_chunk {params.all_chunk}' if params.all_chunk else ''}
         """
        shell(
            f'{command}'
@@ -225,5 +225,5 @@ rule cauchy_combination:
         mem_mb_per_cpu=25_000
     shell:
         """
-        gsMap run_cauchy_combination --input_hdf5_path {input.hdf5_path} --input_ldsc_dir {params.ldsc_dir} --sample_name {wildcards.sample_name} --output_cauchy_dir {params.cauchy_save_dir} --trait_name {wildcards.trait_name} --annotation {params.annotation}
+        gsmap run_cauchy_combination --input_hdf5_path {input.hdf5_path} --input_ldsc_dir {params.ldsc_dir} --sample_name {wildcards.sample_name} --output_cauchy_dir {params.cauchy_save_dir} --trait_name {wildcards.trait_name} --annotation {params.annotation}
         """