organized prep_LINE1_db.sh related scripts and the result

resource/LINE1_db/prep_line.sh → resource/LINE1_db/prep_LINE1_db.sh

@@ -37,14 +37,18 @@ then
 	aws s3 cp s3://human-pangenomics/T2T/CHM13/assemblies/annotation/chm13v2.0_RepeatMasker_4.1.2p1.2022Apr14.bed ./
 fi
 
-python proc_rmsk.py rmsk.txt.gz > rmsk.line1.hg38.bed
+sort -k1,1 -k2,2n -k3,3n chm13v2.0_RepeatMasker_4.1.2p1.2022Apr14.bed | bgzip -c > chm13v2.0_RepeatMasker_4.1.2p1.2022Apr14.bed.gz
+
+tabix -p bed chm13v2.0_RepeatMasker_4.1.2p1.2022Apr14.bed.gz
+
+python subscript/proc_rmsk.py rmsk.txt.gz > rmsk.line1.hg38.bed
 
 liftOver rmsk.line1.hg38.bed hg38ToHg19.over.chain.gz rmsk.line1.hg19.bed.tmp rmsk.line1.unmapped
 
-python mod_label.py rmsk.line1.hg19.bed.tmp > rmsk.line1.hg19.bed
+python subscript/mod_label.py rmsk.line1.hg19.bed.tmp > rmsk.line1.hg19.bed
 
 
-python proc_rmsk_chm13.py chm13v2.0_RepeatMasker_4.1.2p1.2022Apr14.bed.gz > rmsk.line1.chm13v2.0.bed 
+python subscript/proc_rmsk_chm13.py chm13v2.0_RepeatMasker_4.1.2p1.2022Apr14.bed.gz > rmsk.line1.chm13v2.0.bed 
 
 #########
 
@@ -63,13 +67,13 @@ fi
 
 bcftools filter -i 'INFO/SVLEN > 5800 && INFO/SVTYPE == "LINE1"' ALL.wgs.mergedSV.v8.20130502.svs.genotypes.vcf.gz | cut -f 1-8 > 1000genomes.line1.hg19.vcf
 
-python proc_1000genomes.py 1000genomes.line1.hg19.vcf > 1000genomes.line1.hg19.bed
+python subscript/proc_1000genomes.py 1000genomes.line1.hg19.vcf > 1000genomes.line1.hg19.bed
 
 liftOver 1000genomes.line1.hg19.bed hg19ToHg38.over.chain.gz 1000genomes.line1.hg38.bed.tmp 1000genomes.line1.hg38.unmapped
 liftOver 1000genomes.line1.hg19.bed hg19-chm13v2.over.chain.gz 1000genomes.line1.chm13v2.0.bed.tmp 1000genomes.line1.chm13v2.0.unmapped
 
-python mod_label.py 1000genomes.line1.hg38.bed.tmp > 1000genomes.line1.hg38.bed
-python mod_label.py 1000genomes.line1.chm13v2.0.bed.tmp > 1000genomes.line1.chm13v2.0.bed
+python subscript/mod_label.py 1000genomes.line1.hg38.bed.tmp > 1000genomes.line1.hg38.bed
+python subscript/mod_label.py 1000genomes.line1.chm13v2.0.bed.tmp > 1000genomes.line1.chm13v2.0.bed
 
 ##########
 
@@ -89,13 +93,13 @@ fi
 
 bcftools filter -i 'ALT == "<INS:ME:LINE1>" && INFO/SVLEN >= 5800' gnomad_v2.1_sv.controls_only.sites.vcf.gz | cut -f 1-8 > gnomad.line1.hg19.vcf
 
-python proc_gnomad.py gnomad.line1.hg19.vcf > gnomad.line1.hg19.bed
+python subscript/proc_gnomad.py gnomad.line1.hg19.vcf > gnomad.line1.hg19.bed
 
 liftOver gnomad.line1.hg19.bed hg19ToHg38.over.chain.gz gnomad.line1.hg38.bed.tmp gnomad.line1.hg38.unmapped
 liftOver gnomad.line1.hg19.bed hg19-chm13v2.over.chain.gz gnomad.line1.chm13v2.0.bed.tmp gnomad.line1.chm13v2.0.unmapped
 
-python mod_label.py gnomad.line1.hg38.bed.tmp > gnomad.line1.hg38.bed
-python mod_label.py gnomad.line1.chm13v2.0.bed.tmp > gnomad.line1.chm13v2.0.bed
+python subscript/mod_label.py gnomad.line1.hg38.bed.tmp > gnomad.line1.hg38.bed
+python subscript/mod_label.py gnomad.line1.chm13v2.0.bed.tmp > gnomad.line1.chm13v2.0.bed
 
 ##########
 
@@ -120,14 +124,14 @@ bgzip -c LINE1.chm13v2.0.bed > LINE1.chm13v2.0.bed.gz
 tabix -p bed LINE1.chm13v2.0.bed.gz
 
 
-mv LINE1.hg38.bed.gz ../nanomonsv/data/
-mv LINE1.hg38.bed.gz.tbi ../nanomonsv/data/
+# mv LINE1.hg38.bed.gz ../nanomonsv/data/
+# mv LINE1.hg38.bed.gz.tbi ../nanomonsv/data/
 
-mv LINE1.hg19.bed.gz ../nanomonsv/data/
-mv LINE1.hg19.bed.gz.tbi ../nanomonsv/data/
+# mv LINE1.hg19.bed.gz ../nanomonsv/data/
+# mv LINE1.hg19.bed.gz.tbi ../nanomonsv/data/
 
-mv LINE1.chm13v2.0.bed.gz ../nanomonsv/data/
-mv LINE1.chm13v2.0.bed.gz.tbi ../nanomonsv/data/
+# mv LINE1.chm13v2.0.bed.gz ../nanomonsv/data/
+# mv LINE1.chm13v2.0.bed.gz.tbi ../nanomonsv/data/
 
 ##########