From cc6497621281f177e2e9f1a09b521b0bfeb4fe8c Mon Sep 17 00:00:00 2001
From: jplantad <julie.plantade@ens-lyon.fr>
Date: Tue, 25 May 2021 15:07:01 +0200
Subject: [PATCH] compress, index and merge
---
compress_vcf_to_gz.sh | 36 ++++++++++++++++++++++++++++++++++++
generate_index.sh | 17 +++++++++++++++++
merge_fastafiles.sh | 14 ++++++++++++++
3 files changed, 67 insertions(+)
create mode 100755 compress_vcf_to_gz.sh
create mode 100755 generate_index.sh
create mode 100755 merge_fastafiles.sh
diff --git a/compress_vcf_to_gz.sh b/compress_vcf_to_gz.sh
new file mode 100755
index 0000000..1462df2
--- /dev/null
+++ b/compress_vcf_to_gz.sh
@@ -0,0 +1,36 @@
+#!/bin/bash
+
+# set home directory
+home="/home/stagiaire/Bureau/phylogenetics/"
+cd ${home}
+
+# list the vcf that need to be compressed
+data_999_folder="/home/stagiaire/Bureau/gitlab/data_fixed_999/"
+vcf_list=$(ls ${data_999_folder})
+# check the list
+echo ${vcf_list}
+
+# create a new folder that will contain the gz files, and get into it
+mkdir -p data_999_gz
+cd data_999_gz/
+# check working directory
+pwd
+
+for vcf in ${vcf_list}
+do
+ echo -e "#####\nProcessing "${vcf}
+ # suppress the GL line in the VCF file header and save the output into a temporary VCF file
+ sed '/^##FORMAT=<ID=GL/d' ${data_999_folder}${vcf} > ${vcf}_tmp.vcf
+ echo "temporary VCF file created"
+ # compress the temporary VCF file
+ bcftools view ${vcf}_tmp.vcf -Oz -o ${vcf}.gz
+ echo "compressed file computed"
+ # remove the temporary VCF file
+ rm ${vcf}_tmp.vcf
+ echo "temporary VCF file deleted"
+ echo -e ${vcf}" processed.\n#####"
+done
+
+# check that the compressed files are in the folder
+ls -l
+
diff --git a/generate_index.sh b/generate_index.sh
new file mode 100755
index 0000000..6284763
--- /dev/null
+++ b/generate_index.sh
@@ -0,0 +1,17 @@
+#!/bin/bash
+
+# generate an index for a VCF file
+
+# set home directory
+home="/home/stagiaire/Bureau/phylogenetics/data_999_gz/"
+cd ${home}
+
+# list VCF files
+vcf_list=$(ls )
+
+for vcf in ${vcf_list}
+do
+ # index the VCF file
+ bcftools index -f ${vcf} -o ${vcf}.csi
+ echo "##### "${vcf}" done."
+done
diff --git a/merge_fastafiles.sh b/merge_fastafiles.sh
new file mode 100755
index 0000000..993eb1a
--- /dev/null
+++ b/merge_fastafiles.sh
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+# merging fasta files of all individuals for each gene
+
+# set home directory
+home="/home/stagiaire/Bureau/phylogenetics/data_sequences/pon/"
+cd ${home}
+
+indiv_list=$(ls *renamed_AB.fa)
+
+for indiv in ${indiv_list}
+do
+ cat ${indiv} >> "BST2_ponAbe2_all.fa"
+done
--
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