Clarified BCF filenames

Makefile

@@ -1,5 +1,6 @@
 DEST_DIR=~/lustre2/CTTV24/databases_test
 
+
 default: download process
 download: create_dir d_GRASP d_Phewas_Catalog d_GWAS_DB d_Fantom5 d_DHS d_Regulome d_1000Genomes
 process: GRASP Phewas_Catalog GWAS_DB Fantom5 DHS Regulome tabix 1000Genomes
@@ -73,13 +74,13 @@ define process_1000Genomes_file
 gzip -dc $(1) \
 | vcfkeepsamples - `cat ./scripts/preprocessing/CEPH_samples.txt`\
 | bcftools convert -Ob \
-> ${DEST_DIR}/1000Genomes/CEPH/`basename $(1) | sed -e 's/vcf.gz/bcf.gz/'`;
+> ${DEST_DIR}/1000Genomes/CEPH/`basename $(1) | sed -e 's/vcf.gz/bcf/'`;
 endef
 
 .PHONY: 1000Genomes
 
 1000Genomes:
 	$(eval vcf_files := $(wildcard ${DEST_DIR}/raw/1000Genomes/*.vcf.gz))
 	$(foreach file, $(vcf_files), $(call process_1000Genomes_file, $(file)))
-	$(eval bcf_files := $(wildcard ${DEST_DIR}/1000Genomes/*.bcf.gz))
+	$(eval bcf_files := $(wildcard ${DEST_DIR}/1000Genomes/*.bcf))
 	$(foreach file, $(bcf_files), bcftools index $(file);)

scripts/gwas_to_genes.py

@@ -829,7 +829,7 @@ def calculate_LD_window(snp, window_len=500000,population='CEPH',cutoff=0.5,db=0
     chromosome = snp.chrom
     region = '{}:{}-{}'.format(chromosome,from_pos,to_pos)
 
-    chrom_file = "CEPH.chr%s.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.bcf.gz" % (chromosome)
+    chrom_file = "ALL.chr%s.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.bcf" % (chromosome)
 
     ### Extract this region out from the 1000 genomes BCF
 
@@ -1048,7 +1048,7 @@ def get_lds_from_top_gwas(gwas_snp, ld_snps, population='CEPH', region=None,db=0
 
 
     ### Extract the required region from the VCF
-    chrom_file = '%s.chr%s.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.bcf.gz' % (population, chromosome)
+    chrom_file = 'ALL.chr%s.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.bcf' % (chromosome)
 
     extract_region_comm = "bcftools view -r %s %s -O z -o region.vcf.gz" % (region, os.path.join(DATABASES_DIR, '1000Genomes', population, chrom_file))
     subprocess.call(extract_region_comm.split(" "))