From 19cc1a9b33c536169826013a1636ddd64e22a8a8 Mon Sep 17 00:00:00 2001
From: "hanna.julienne" <hanna.julienne@pasteur.fr>
Date: Mon, 17 May 2021 14:37:48 +0200
Subject: [PATCH] increase allele length
---
jass/models/inittable.py | 2 +-
jass/models/worktable.py | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/jass/models/inittable.py b/jass/models/inittable.py
index c568c8ee..719a9268 100755
--- a/jass/models/inittable.py
+++ b/jass/models/inittable.py
@@ -222,7 +222,7 @@ def create_inittable_file(
which_cols.extend(list(pheno_select))
hdf_init.put("PhenoList", pheno_list, format="table", data_columns=True)
hdf_init.put("Regions", regions, format="table", data_columns=True)
- sum_stat_tab_min_itemsizes = {"snp_ids": 50, "Ref_allele":50,"Alt_allele":50}
+ sum_stat_tab_min_itemsizes = {"snp_ids": 80, "Ref_allele":70,"Alt_allele":70}
regions_bychr = regions.groupby("chr")
diff --git a/jass/models/worktable.py b/jass/models/worktable.py
index c2e287a5..a249eb9b 100755
--- a/jass/models/worktable.py
+++ b/jass/models/worktable.py
@@ -193,9 +193,9 @@ def create_worktable_file(
) # Covariance matrix
regions = read_hdf(init_file_path, "Regions").index.tolist()
- sum_stat_tab_min_itemsizes = {"snp_ids": 50, "Region": 10, "CHR": 5,"Ref_allele" : 50, "Alt_allele":50}
+ sum_stat_tab_min_itemsizes = {"snp_ids": 80, "Region": 10, "CHR": 5,"Ref_allele" : 70, "Alt_allele":70}
#['Region', "MiddlePosition", "snp_ids","CHR", "position", "Ref_allele", "Alt_allele", "JASS_PVAL", "UNIVARIATE_MIN_PVAL", "signif_status"]
- region_sub_table_min_itemsizes = {"Region": 10, "index": 10, "CHR": 5, "snp_ids": 50, "signif_status":20,"Ref_allele" : 50, "Alt_allele":50}
+ region_sub_table_min_itemsizes = {"Region": 10, "index": 10, "CHR": 5, "snp_ids": 80, "signif_status":20,"Ref_allele" : 70, "Alt_allele":70}
smart_na_computation = not (remove_nan)
module_name, function_name = stat.split(":")
--
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