gsMap 1.64__tar.gz → 1.65__tar.gz

{gsmap-1.64 → gsmap-1.65}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: gsMap
-Version: 1.64
+Version: 1.65
 Summary: Genetics-informed pathogenic spatial mapping
 Author-email: liyang <songliyang@westlake.edu.cn>, wenhao <chenwenhao@westlake.edu.cn>
 Requires-Python: >=3.8

{gsmap-1.64 → gsmap-1.65}/src/gsMap/__init__.py

@@ -2,4 +2,4 @@
 Genetics-informed pathogenic spatial mapping
 '''
 
-__version__ = '1.64'
+__version__ = '1.65'

gsmap-1.65/src/gsMap/setup.py

@@ -0,0 +1,5 @@
+#!/usr/bin/env python
+import setuptools
+
+if __name__ == "__main__":
+    setuptools.setup(name='gsMap')

gsmap-1.64/test/GPS-snakemake-workflow-macaque.smk

@@ -1,268 +0,0 @@
-from pathlib import Path
-
-import numpy as np
-
-workdir: '/storage/yangjianLab/chenwenhao/projects/202312_GPS/data/macaque/processed'
-# workdir: '/storage/yangjianLab/chenwenhao/projects/202312_GPS/data/GPS_test/macaque'
-sample_name = "Cortex_151507"
-chrom = "all"
-QOS = "huge"
-# chrom = range(1,23)
-trait_names = [
-    'PGC3_SCZ_wave3_public_INFO80'
-]
-root = "/storage/yangjianLab/songliyang/SpatialData/Data/Brain/macaque/Cell/processed/h5ad"
-# sample_names = [file.strip().split('.')[0]
-#                 for file in open(f'{root}/representative_slices2').readlines()]
-#
-# sample_names = '''
-# T33_macaque1  T44_macaque1  T82_macaque1  T97_macaque1  T125_macaque1  T127_macaque1  T129_macaque1  T131_macaque1  T135_macaque1  T137_macaque1  T139_macaque1
-# '''.strip().split()
-sample_names=[]
-for file in Path(root).glob('*.h5ad'):
-    sample_names.append(file.stem)
-sample_names.remove('T825_macaque3') # due to 25% of spot don't have spatial coordinates
-
-annotation = "SubClass"
-data_type = "SCT"
-# sample_names = ['T584_macaque2']
-
-rule all:
-    input:
-        expand('{sample_name}/spatial_ldsc/{sample_name}.spatial_ldsc.done',trait_name=trait_names,sample_name=sample_names)
-
-
-# expand('{sample_name}/cauchy_combination/{sample_name}_{trait_name}.Cauchy.csv.gz',trait_name=trait_names,sample_name=sample_names)
-    # expand('{sample_name}/cauchy_combination/{sample_name}_{trait_name}.Cauchy.csv.gz',trait_name=trait_names,sample_name=sample_names)
-
-rule test_run:
-    input:
-        [f'{sample_name}/generate_ldscore/{sample_name}_generate_ldscore_chr{chrom}.done' for sample_name in
-         sample_names]
-
-# localrules: find_latent_representations,latent_to_gene
-def get_annotation(wildcards):
-    if wildcards.sample_name.endswith('3'):
-        print(wildcards.sample_name,'will use None as annotation')
-        return None
-    else:
-        print(wildcards.sample_name,'will use SubClass as annotation')
-        return 'SubClass'
-
-
-rule find_latent_representations:
-    input:
-        hdf5_path=f'{root}/{{sample_name}}.h5ad'
-    output:
-        hdf5_output='{sample_name}/find_latent_representations/{sample_name}_add_latent.h5ad'
-    params:
-        annotation= get_annotation,
-        type=data_type,
-        epochs=300,
-        feat_hidden1=256,
-        feat_hidden2=128,
-        feat_cell=3000,
-        gcn_hidden1=64,
-        gcn_hidden2=30,
-        p_drop=0.1,
-        gcn_lr=0.001,
-        gcn_decay=0.01,
-        n_neighbors=11,
-        label_w=1,
-        rec_w=1,
-        n_comps=300,
-        weighted_adj=False,
-        nheads=3,
-        var=False,
-        convergence_threshold=1e-4,
-        hierarchically=False
-    threads:
-        3
-    benchmark: '{sample_name}/find_latent_representations/{sample_name}_add_latent.h5ad.benchmark'
-    resources:
-        mem_mb_per_cpu=lambda wildcards, threads, attempt: 20_000 * np.log2(attempt + 1),
-        qos=QOS
-    run:
-        command = f"""
-gsmap run_find_latent_representations \
-    --input_hdf5_path {input.hdf5_path} \
-    --sample_name {wildcards.sample_name} \
-    --output_hdf5_path {output.hdf5_output} \
-    { '--annotation ' + params.annotation if params.annotation is not None else ''} \
-    --type {params.type} \
-    --epochs {params.epochs} \
-    --feat_hidden1 {params.feat_hidden1} \
-    --feat_hidden2 {params.feat_hidden2} \
-    --feat_cell {params.feat_cell} \
-    --gcn_hidden1 {params.gcn_hidden1} \
-    --gcn_hidden2 {params.gcn_hidden2} \
-    --p_drop {params.p_drop} \
-    --gcn_lr {params.gcn_lr} \
-    --gcn_decay {params.gcn_decay} \
-    --n_neighbors {params.n_neighbors} \
-    --label_w {params.label_w} \
-    --rec_w {params.rec_w} \
-    --n_comps {params.n_comps} \
-    {'--weighted_adj' if params.weighted_adj else ''} \
-    --nheads {params.nheads} \
-    {'--var' if params.var else ''} \
-    --convergence_threshold {params.convergence_threshold} \
-    {'--hierarchically' if params.hierarchically else ''}
-        """
-        shell(
-            f'{command}'
-        )
-
-
-rule latent_to_gene:
-    input:
-        hdf5_with_latent_path=rules.find_latent_representations.output.hdf5_output
-    output:
-        feather_path='{sample_name}/latent_to_gene/{sample_name}_gene_marker_score.feather'
-    params:
-        latent_representation="latent_GVAE",
-        num_neighbour=51,
-        num_neighbour_spatial=201,
-        species='MACAQUE_GENE_SYM',
-        gs_species='/storage/yangjianLab/songliyang/SpatialData/homologs/macaque_human_homologs.txt',
-        gM_slices=None,
-        annotation=get_annotation,
-        type=data_type
-    threads:
-        1
-    resources:
-        mem_mb_per_cpu=lambda wildcards, threads, attempt: 70_000 * np.log2(attempt + 1),
-        qos=QOS
-    benchmark: '{sample_name}/latent_to_gene/{sample_name}_gene_marker_score.feather.benchmark'
-    run:
-        command = f"""
-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} \
-    { '--annotation ' + params.annotation if params.annotation is not None else ''} \
-    --type {params.type} \
-    --latent_representation {params.latent_representation} \
-    --num_neighbour {params.num_neighbour} \
-    --num_neighbour_spatial {params.num_neighbour_spatial} \
-     {'--species ' + params.species if params.species is not None else ''} \
-     {'--gs_species ' + params.gs_species if params.gs_species is not None else ''} \
-     {'--gM_slices ' + params.gM_slices if params.gM_slices is not None else ''}
-"""
-        shell(
-            f'{command}'
-        )
-
-
-rule generate_ldscore:
-    input:
-        mkscore_feather_file=rules.latent_to_gene.output.feather_path
-    output:
-        done='{sample_name}/generate_ldscore/{sample_name}_generate_ldscore_chr{chrom}.done'
-    params:
-        ld_score_save_dir='{sample_name}/generate_ldscore',
-        gtf_annotation_file="/storage/yangjianLab/songliyang/ReferenceGenome/GRCh37/gencode.v39lift37.annotation.gtf",
-        bfile_root="/storage/yangjianLab/sharedata/LDSC_resource/1000G_EUR_Phase3_plink/1000G.EUR.QC",
-        keep_snp_root="/storage/yangjianLab/sharedata/LDSC_resource/hapmap3_snps/hm",
-        gene_window_size=50000,
-        enhancer_annotation_file=None,
-        snp_multiple_enhancer_strategy='max_mkscore',
-        gene_window_enhancer_priority=None,
-        spots_per_chunk=1000,
-        ld_wind=1,
-        ld_unit="CM",
-        additional_baseline_annotation_dir_path=None
-        # additional_baseline_annotation_dir_path='/storage/yangjianLab/chenwenhao/projects/202312_GPS/data/resource/ldsc/baseline_v1.2/remove_base'
-    benchmark: '{sample_name}/generate_ldscore/{sample_name}_generate_ldscore_chr{chrom}.done.benchmark'
-    threads:
-        3
-    resources:
-        mem_mb_per_cpu=lambda wildcards, threads, attempt: 50_000 / threads * np.log2(attempt + 1),
-        qos=QOS
-    run:
-        command = f"""
-        gsmap run_generate_ldscore \
-            --sample_name {wildcards.sample_name} \
-            --chrom {wildcards.chrom} \
-            --ldscore_save_dir {params.ld_score_save_dir} \
-            --mkscore_feather_file {input.mkscore_feather_file} \
-            --bfile_root {params.bfile_root} \
-            --keep_snp_root {params.keep_snp_root} \
-            --gtf_annotation_file {params.gtf_annotation_file} \
-            --gene_window_size {params.gene_window_size} \
-            {'--enhancer_annotation_file ' + params.enhancer_annotation_file if params.enhancer_annotation_file is not None else ''} \
-            --snp_multiple_enhancer_strategy {params.snp_multiple_enhancer_strategy} \
-            {'--gene_window_enhancer_priority ' + params.gene_window_enhancer_priority if params.gene_window_enhancer_priority is not None else ''} \
-            --spots_per_chunk {params.spots_per_chunk} \
-            --ld_wind {params.ld_wind} \
-            --ld_unit {params.ld_unit} \
-            { '--additional_baseline_annotation_dir_path ' +  params.additional_baseline_annotation_dir_path if params.additional_baseline_annotation_dir_path is not None else '' }
-        """
-        shell(command)
-        shell('touch {output.done}')
-
-
-def get_h2_file(wildcards):
-    gwas_root = "/storage/yangjianLab/songliyang/GWAS_trait/LDSC"
-    return f"{gwas_root}/{wildcards.trait_name}.sumstats.gz",
-
-
-def get_ldscore(wildcards):
-    if chrom == "all":
-        return f"{wildcards.sample_name}/generate_ldscore/{wildcards.sample_name}_generate_ldscore_chr{chrom}.done"
-    else:
-        assert tuple(chrom) == tuple(range(1,23)), "chrom must be all or range(1,23)"
-        return [f"{wildcards.sample_name}/generate_ldscore/{wildcards.sample_name}_generate_ldscore_chr{c}.done" for
-                c in chrom]
-
-
-rule spatial_ldsc:
-    input:
-        # h2_file=get_h2_file,
-        generate_ldscore_done=get_ldscore
-    output:
-        done='{sample_name}/spatial_ldsc/{sample_name}.spatial_ldsc.done'
-    params:
-        ldscore_input_dir=rules.generate_ldscore.params.ld_score_save_dir,
-        ldsc_save_dir='{sample_name}/spatial_ldsc',
-        w_file="/storage/yangjianLab/sharedata/LDSC_resource/LDSC_SEG_ldscores/weights_hm3_no_hla/weights.",
-        sumstats_config_file='/storage/yangjianLab/chenwenhao/projects/202312_GPS/src/gsMap/example/sumstats_config_sub.yaml',
-        all_chunk = None
-    threads:
-        10
-    benchmark:
-        '{sample_name}/spatial_ldsc/{sample_name}.spatial_ldsc.done.benchmark'
-    resources:
-        mem_mb_per_cpu=lambda wildcards, threads, attempt: 40_000 / threads * np.log2(attempt + 1),
-        qos=QOS,
-        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 ''}
-        """
-       shell(
-           f'{command}'
-           'touch {output.done}'
-       )
-
-
-rule cauchy_combination:
-    output:
-        done='{sample_name}/cauchy_combination/{sample_name}_{trait_name}.Cauchy.csv.gz'
-    input:
-        hdf5_path=rules.find_latent_representations.output.hdf5_output,
-        ldsc_done=rules.spatial_ldsc.output.done
-    params:
-        cauchy_save_dir='{sample_name}/cauchy_combination',
-        annotation=annotation,
-        ldsc_dir=rules.spatial_ldsc.params.ldsc_save_dir
-    benchmark:
-        '{sample_name}/cauchy_combination/{sample_name}_{trait_name}.Cauchy.csv.gz.benchmark'
-    threads:
-        2
-    resources:
-        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-1.64/test/GPS-snakemake-workflow.smk

@@ -1,229 +0,0 @@
-import numpy as np
-
-workdir: '/storage/yangjianLab/chenwenhao/projects/202312_GPS/data/GPS_test/Nature_Neuroscience_2021/snake_workdir'
-sample_names = ["Cortex_151507"]
-# chrom = "all"
-
-chrom = range(1,23)
-# trait_names=[
-#     'ADULT1_ADULT2_ONSET_ASTHMA'
-# ]
-annotation= "layer_guess"
-data_type = 'count'
-rule all:
-    input:
-        expand('{sample_name}/spatial_ldsc/{sample_name}.spatial_ldsc.done', sample_name=sample_names)
-        # expand('{sample_name}/cauchy_combination/{sample_name}_{trait_name}.Cauchy.csv.gz', trait_name=trait_names, sample_name=sample_names)
-
-rule find_latent_representations:
-    input:
-        hdf5_path = "/storage/yangjianLab/songliyang/SpatialData/Data/Brain/Human/Nature_Neuroscience_2021/processed/h5ad/Cortex_151507.h5ad"
-    output:
-        hdf5_output='{sample_name}/find_latent_representations/{sample_name}_add_latent.h5ad'
-    params:
-        annotation=annotation,
-        type=data_type,
-        epochs=300,
-        feat_hidden1=256,
-        feat_hidden2=128,
-        feat_cell=3000,
-        gcn_hidden1=64,
-        gcn_hidden2=30,
-        p_drop=0.1,
-        gcn_lr=0.001,
-        gcn_decay=0.01,
-        n_neighbors=11,
-        label_w=1,
-        rec_w=1,
-        n_comps=300,
-        weighted_adj=False,
-        nheads=3,
-        var=False,
-        convergence_threshold=1e-4,
-        hierarchically=False
-    threads:
-        1
-    benchmark: '{sample_name}/find_latent_representations/{sample_name}_add_latent.h5ad.benchmark'
-    run:
-        command = f"""
-gsmap run_find_latent_representations \
-    --input_hdf5_path {input.hdf5_path} \
-    --sample_name {wildcards.sample_name} \
-    --output_hdf5_path {output.hdf5_output} \
-    { '--annotation ' + params.annotation if params.annotation is not None else ''} \
-    --type {params.type} \
-    --epochs {params.epochs} \
-    --feat_hidden1 {params.feat_hidden1} \
-    --feat_hidden2 {params.feat_hidden2} \
-    --feat_cell {params.feat_cell} \
-    --gcn_hidden1 {params.gcn_hidden1} \
-    --gcn_hidden2 {params.gcn_hidden2} \
-    --p_drop {params.p_drop} \
-    --gcn_lr {params.gcn_lr} \
-    --gcn_decay {params.gcn_decay} \
-    --n_neighbors {params.n_neighbors} \
-    --label_w {params.label_w} \
-    --rec_w {params.rec_w} \
-    --n_comps {params.n_comps} \
-    {'--weighted_adj' if params.weighted_adj else ''} \
-    --nheads {params.nheads} \
-    {'--var' if params.var else ''} \
-    --convergence_threshold {params.convergence_threshold} \
-    {'--hierarchically' if params.hierarchically else ''}
-        """
-        shell(
-            f'{command}'
-        )
-
-
-rule latent_to_gene:
-    input:
-        hdf5_with_latent_path=rules.find_latent_representations.output.hdf5_output
-    output:
-        feather_path='{sample_name}/latent_to_gene/{sample_name}_gene_marker_score.feather'
-    params:
-        latent_representation="latent_GVAE",
-        num_neighbour=51,
-        num_neighbour_spatial=201,
-        species=None,
-        gs_species=None,
-        gM_slices=None,
-        annotation=annotation,
-        type=data_type
-    threads:
-        1
-    resources:
-        mem_mb_per_cpu=lambda wildcards, threads, attempt: 70_000 * np.log2(attempt + 1),
-        qos='huge'
-    benchmark: '{sample_name}/latent_to_gene/{sample_name}_gene_marker_score.feather.benchmark'
-    run:
-        command = f"""
-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} \
-    { '--annotation ' + params.annotation if params.annotation is not None else ''} \
-    --type {params.type} \
-    --latent_representation {params.latent_representation} \
-    --num_neighbour {params.num_neighbour} \
-    --num_neighbour_spatial {params.num_neighbour_spatial} \
-     {'--species ' + params.species if params.species is not None else ''} \
-     {'--gs_species ' + params.gs_species if params.gs_species is not None else ''} \
-     {'--gM_slices ' + params.gM_slices if params.gM_slices is not None else ''}
-"""
-        shell(
-            f'{command}'
-        )
-
-
-
-rule generate_ldscore:
-    input:
-        mkscore_feather_file=rules.latent_to_gene.output.feather_path
-    output:
-        done='{sample_name}/generate_ldscore/{sample_name}_generate_ldscore_chr{chrom}.done'
-    params:
-        ld_score_save_dir='{sample_name}/generate_ldscore',
-        gtf_annotation_file="/storage/yangjianLab/songliyang/ReferenceGenome/GRCh37/gencode.v39lift37.annotation.gtf",
-        bfile_root="/storage/yangjianLab/sharedata/LDSC_resource/1000G_EUR_Phase3_plink/1000G.EUR.QC",
-        keep_snp_root="/storage/yangjianLab/sharedata/LDSC_resource/hapmap3_snps/hm",
-        gene_window_size=50000,
-        enhancer_annotation_file=None,
-        snp_multiple_enhancer_strategy='max_mkscore',
-        gene_window_enhancer_priority=None,
-        spots_per_chunk=5000,
-        ld_wind=1,
-        ld_unit="CM",
-        additional_baseline_annotation_dir_path='/storage/yangjianLab/chenwenhao/projects/202312_GPS/data/resource/ldsc/baseline_v1.2/remove_base'
-    benchmark: '{sample_name}/generate_ldscore/{sample_name}_generate_ldscore_chr{chrom}.done.benchmark'
-    threads:
-        3
-    resources:
-        mem_mb_per_cpu=lambda wildcards, threads, attempt: 45_000 / threads * np.log2(attempt + 1),
-        qos='huge'
-    run:
-        command = f"""
-        gsmap run_generate_ldscore \
-            --sample_name {wildcards.sample_name} \
-            --chrom {wildcards.chrom} \
-            --ldscore_save_dir {params.ld_score_save_dir} \
-            --mkscore_feather_file {input.mkscore_feather_file} \
-            --bfile_root {params.bfile_root} \
-            --keep_snp_root {params.keep_snp_root} \
-            --gtf_annotation_file {params.gtf_annotation_file} \
-            --gene_window_size {params.gene_window_size} \
-            {'--enhancer_annotation_file ' + params.enhancer_annotation_file if params.enhancer_annotation_file is not None else ''} \
-            --snp_multiple_enhancer_strategy {params.snp_multiple_enhancer_strategy} \
-            {'--gene_window_enhancer_priority ' + params.gene_window_enhancer_priority if params.gene_window_enhancer_priority is not None else ''} \
-            --spots_per_chunk {params.spots_per_chunk} \
-            --ld_wind {params.ld_wind} \
-            --ld_unit {params.ld_unit} \
-            { '--additional_baseline_annotation_dir_path' +  params.additional_baseline_annotation_dir_path if params.additional_baseline_annotation_dir_path is not None else '' }
-        """
-        shell(command)
-        shell('touch {output.done}')
-
-
-def get_h2_file(wildcards):
-    gwas_root = "/storage/yangjianLab/songliyang/GWAS_trait/LDSC"
-    return f"{gwas_root}/{wildcards.trait_name}.sumstats.gz",
-
-
-def get_ldscore(wildcards):
-    if chrom == "all":
-        return f"{wildcards.sample_name}/generate_ldscore/{wildcards.sample_name}_generate_ldscore_chr{chrom}.done"
-    else:
-        assert tuple(chrom) == tuple(range(1,23)), "chrom must be all or range(1,23)"
-        return [f"{wildcards.sample_name}/generate_ldscore/{wildcards.sample_name}_generate_ldscore_chr{c}.done" for
-                c in chrom]
-
-
-rule spatial_ldsc:
-    input:
-        # h2_file=get_h2_file,
-        generate_ldscore_done=get_ldscore
-    output:
-        done='{sample_name}/spatial_ldsc/{sample_name}.spatial_ldsc.done'
-    params:
-        ldscore_input_dir=rules.generate_ldscore.params.ld_score_save_dir,
-        ldsc_save_dir='{sample_name}/spatial_ldsc',
-        w_file="/storage/yangjianLab/sharedata/LDSC_resource/LDSC_SEG_ldscores/weights_hm3_no_hla/weights.",
-        sumstats_config_file='/storage/yangjianLab/chenwenhao/projects/202312_GPS/src/gsMap/example/sumstats_config_sub.yaml',
-        all_chunk = None
-    threads:
-        2
-    benchmark:
-        '{sample_name}/spatial_ldsc/{sample_name}.spatial_ldsc.done.benchmark'
-    resources:
-        mem_mb_per_cpu=lambda wildcards, threads, attempt: 60_000 / threads * np.log2(attempt + 1),
-        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 ''}
-        """
-       shell(
-           f'{command}'
-           'touch {output.done}'
-       )
-
-
-rule cauchy_combination:
-    output:
-        done='{sample_name}/cauchy_combination/{sample_name}_{trait_name}.Cauchy.csv.gz'
-    input:
-        hdf5_path=rules.find_latent_representations.output.hdf5_output,
-        ldsc_done=rules.spatial_ldsc.output.done
-    params:
-        cauchy_save_dir='{sample_name}/cauchy_combination',
-        annotation=annotation,
-        ldsc_dir=rules.spatial_ldsc.params.ldsc_save_dir
-    benchmark:
-        '{sample_name}/cauchy_combination/{sample_name}_{trait_name}.Cauchy.csv.gz.benchmark'
-    threads:
-        2
-    resources:
-        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}
-        """