add scripts

impute_jass/doc/source/index.rst

@@ -79,14 +79,14 @@ RAISS has an interface with the command line (see Command Line Usage bellow).
 
 If you have access to a cluster, an efficient way to use RAISS is to launch
 the imputation of each chromosome on a separate cluster node. The script
-`launch_imputation_all_gwas.sh <https://gitlab.pasteur.fr/statistical-genetics/raiss/blob/master/launch_imputation_all_gwas.sh>`_
+`launch_imputation_all_gwas.sh <https://gitlab.pasteur.fr/statistical-genetics/raiss/blob/master/scripts/launch_imputation_all_gwas.sh>`_
 contain an example of raiss usage with a SLURM scheduler.
 
 Output
 ======
 
 The raiss package outputs imputed GWAS files in the tabular format:
-#TODO suppress complementary columns
+..TODO suppress complementary columns
 
 +------------+---+--+----------------+-----+-----+----------------+------------------+---------+---------+
 |            |A0 |A1| Nsnp_to_impute |Var  |Z    |condition_number|correct_inversion |ld_score |   pos   |
@@ -94,7 +94,6 @@ The raiss package outputs imputed GWAS files in the tabular format:
 | rs11584349 |C  | T|        18	     | 0.85|-0.28|     116.9      |      False       | 1.34    | 1000156 |
 +------------+---+--+----------------+-----+-----+----------------+------------------+---------+---------+
 
-# Keep only useful columns
 
 Command Line Usage
 ==================

scripts/array_args_imputation.txt

+GIANT_HEIGHT chr1
+GIANT_HEIGHT chr2
+GIANT_HEIGHT chr3
+GIANT_HEIGHT chr4
+GIANT_HEIGHT chr5
+GIANT_HEIGHT chr6
+GIANT_HEIGHT chr7
+GIANT_HEIGHT chr8
+GIANT_HEIGHT chr9
+GIANT_HEIGHT chr10
+GIANT_HEIGHT chr11
+GIANT_HEIGHT chr12
+GIANT_HEIGHT chr13
+GIANT_HEIGHT chr14
+GIANT_HEIGHT chr15
+GIANT_HEIGHT chr16
+GIANT_HEIGHT chr17
+GIANT_HEIGHT chr18
+GIANT_HEIGHT chr19
+GIANT_HEIGHT chr20
+GIANT_HEIGHT chr21
+GIANT_HEIGHT chr22
+GIANT_BMI chr1
+GIANT_BMI chr2
+GIANT_BMI chr3
+GIANT_BMI chr4
+GIANT_BMI chr5
+GIANT_BMI chr6
+GIANT_BMI chr7
+GIANT_BMI chr8
+GIANT_BMI chr9
+GIANT_BMI chr10
+GIANT_BMI chr11
+GIANT_BMI chr12
+GIANT_BMI chr13
+GIANT_BMI chr14
+GIANT_BMI chr15
+GIANT_BMI chr16
+GIANT_BMI chr17
+GIANT_BMI chr18
+GIANT_BMI chr19
+GIANT_BMI chr20
+GIANT_BMI chr21
+GIANT_BMI chr22

scripts/launch_imputation_all_gwas.sh

+#!/bin/bash
+#SBATCH --mem=32000
+#SBATCH -o /pasteur/projets/policy01/PCMA/WKD_Hanna/impute_for_jass/genome_imputation_script/imputation_log/IMPFJ_%a.log
+#SBATCH -e /pasteur/projets/policy01/PCMA/WKD_Hanna/impute_for_jass/genome_imputation_script/error_log/error_%a.log
+
+#define data location
+module load Python/3.6.0
+output_folder="/pasteur/projets/policy01/PCMA/1._DATA/ImFJ_imputed_zfiles"
+ref_folder="/pasteur/projets/policy01/PCMA/1._DATA/ImpG_refpanel"
+zscore_folder="/pasteur/projets/policy01/PCMA/1._DATA/ImpG_zfiles"
+ld_folder="/pasteur/projets/policy01/PCMA/WKD_Hanna/impute_for_jass/berisa_ld_block"
+
+
+args=$(head -n ${SLURM_ARRAY_TASK_ID} $1 | tail -n 1)
+study=$(echo $args | cut -d' ' -f1)
+chrom=$(echo $args | cut -d' ' -f2)
+#quick fix to access entry point on tars
+alias impute_jass="python3 /pasteur/homes/hjulienn/.local/lib/python3.6/site-packages/impute_jass/__main__.py"
+#study="GIANT_HEIGHT"
+#chrom="chr22"
+
+echo "Study: ${study}; Chrom: ${chrom}"
+
+#time impute_jass --chrom ${chrom} --gwas ${study} --ref-folder ${ref_folder} --ld-folder ${ld_folder} --zscore-folder ${zscore_folder} --output-folder ${output_folder}
+time python3 /pasteur/homes/hjulienn/.local/lib/python3.6/site-packages/impute_jass/__main__.py --chrom ${chrom} --gwas ${study} --ref-folder ${ref_folder} --ld-folder ${ld_folder} --zscore-folder ${zscore_folder} --output-folder ${output_folder}