os import error

Author: Ganten-Hornby

src/GPS/spatial_ldsc_multiple_sumstats.py

@@ -1,3 +1,7 @@
+import os
+import numpy as np
+import pandas as pd
+
 import argparse
 import logging
 import multiprocessing
@@ -13,9 +17,6 @@
 
 logger = logging.getLogger(__name__)
 
-import numpy as np
-import pandas as pd
-
 
 # %%
 def _coef_new(jknife):
@@ -262,7 +263,6 @@ def run_spatial_ldsc(config: SpatialLDSCConfig):
         # args = parser.parse_args(args_list)
     else:
         args = parser.parse_args()
-    import os
 
     os.chdir('/storage/yangjianLab/chenwenhao/tmp/GPS_Height_debug')
     TASK_ID = 16

test/GPS-snakemake-workflow-macaque.smk

@@ -24,7 +24,7 @@ sample_names.remove('T825_macaque3') # due to 25% of spot don't have spatial coo
 
 annotation = "SubClass"
 data_type = "SCT"
-# sample_names = ['T584_macaque2']
+sample_names = ['T584_macaque2']
 num_processes = 20
 
 rule all:
@@ -123,8 +123,6 @@ rule latent_to_gene:
         latent_representation="latent_GVAE",
         num_neighbour=51,
         num_neighbour_spatial=201,
-        fold=1.0,
-        pst=0.2,
         species='MACAQUE_GENE_SYM',
         gs_species='/storage/yangjianLab/songliyang/SpatialData/homologs/macaque_human_homologs.txt',
         gM_slices=None,
@@ -148,8 +146,6 @@ GPS run_latent_to_gene \
     --latent_representation {params.latent_representation} \
     --num_neighbour {params.num_neighbour} \
     --num_neighbour_spatial {params.num_neighbour_spatial} \
-    --fold {params.fold} \
-    --pst {params.pst} \
      {'--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 ''}
@@ -166,11 +162,14 @@ rule generate_ldscore:
         done='{sample_name}/generate_ldscore/{sample_name}_generate_ldscore_chr{chrom}.done'
     params:
         ld_score_save_dir='{sample_name}/generate_ldscore',
-        gtf_file="/storage/yangjianLab/songliyang/ReferenceGenome/GRCh37/gencode.v39lift37.annotation.gtf",
+        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",
-        window_size=50000,
-        spots_per_chunk=1000,
+        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"
     benchmark: '{sample_name}/generate_ldscore/{sample_name}_generate_ldscore_chr{chrom}.done.benchmark'
@@ -179,11 +178,25 @@ rule generate_ldscore:
     resources:
         mem_mb_per_cpu=lambda wildcards, threads, attempt: 45_000 / threads * np.log2(attempt + 1),
         qos='huge'
-    shell:
-        """
-        GPS run_generate_ldscore --sample_name {wildcards.sample_name} --chrom {wildcards.chrom} --ldscore_save_dir {params.ld_score_save_dir} --gtf_annotation_file {params.gtf_annotation_file} --mkscore_feather_file {input.mkscore_feather_file} --bfile_root {params.bfile_root} --keep_snp_root {params.keep_snp_root} --window_size {params.window_size} --spots_per_chunk {params.spots_per_chunk} --ld_wind {params.ld_wind} --ld_unit {params.ld_unit}
-        touch {output.done}
+    run:
+        command = f"""
+        GPS 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}
         """
+        shell(command)
 
 
 def get_h2_file(wildcards):
@@ -210,7 +223,7 @@ rule spatial_ldsc:
         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/GPS/example/sumstats_config.yaml',
+        sumstats_config_file='/storage/yangjianLab/chenwenhao/projects/202312_GPS/src/GPS/example/sumstats_config_sub.yaml',
         all_chunk = None
     threads:
         2