From 5334ce4c53de1bc9c20e42c7f959362613384e05 Mon Sep 17 00:00:00 2001
From: oboulle <olivier.boulle@inria.fr>
Date: Fri, 4 Oct 2024 17:30:58 +0200
Subject: [PATCH] init

---
 consensus_on_all_clusters.sh | 49 ++++++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)
 create mode 100755 consensus_on_all_clusters.sh

diff --git a/consensus_on_all_clusters.sh b/consensus_on_all_clusters.sh
new file mode 100755
index 0000000..b03fb93
--- /dev/null
+++ b/consensus_on_all_clusters.sh
@@ -0,0 +1,49 @@
+#!/bin/bash
+
+
+
+echo "______________ consensus on all clusters ______________"
+
+tests_dir="partitioning/new_tests/100k/"
+
+ref_file=$tests_dir/references_100k.fasta
+clusters_dir=$tests_dir/clusters_100k
+consensus_dir=$tests_dir/consensus_100k
+
+consensus_script="reads_consensus_class.py"
+start_primer="GTTCTACAGTCCGACGATCC"
+stop_primer="TTGGCACCCGAGAATTCCAC"
+kmer_size="21"
+
+#for file in "$clusters_dir"/*.fasta; do
+#    cluster_name=$(basename -- "$file")
+#    python3 "$consensus_script" -i "$file" -o "$consensus_dir"/$cluster_name --start $start_primer --stop $stop_primer --kmer_size $kmer_size --min_occ 2 --seq_size 200
+#
+#done
+
+cat $consensus_dir/*.fasta > $consensus_dir/0_full_consensus.fasta
+
+grep -v "^>" $ref_file > $tests_dir/ref_sequences.txt # get seqs from referrences
+grep -v "^>" $consensus_dir/0_full_consensus.fasta > $tests_dir/consensus_sequences.txt # get seqs from consensuses
+
+# sort the sequences for the comm command
+sort $tests_dir/ref_sequences.txt > $tests_dir/sorted_ref_sequences.txt
+sort $tests_dir/consensus_sequences.txt > $tests_dir/sorted_consensus_sequences.txt
+
+
+comm -12 $tests_dir/sorted_ref_sequences.txt $tests_dir/sorted_consensus_sequences.txt > $consensus_dir/correct_consensus.txt
+
+num_common_sequences=$(wc -l < $consensus_dir/correct_consensus.txt)
+num_total_ref=$(wc -l < $tests_dir/ref_sequences.txt)
+
+rm $tests_dir/ref_sequences.txt $tests_dir/consensus_sequences.txt $tests_dir/sorted_ref_sequences.txt $tests_dir/sorted_consensus_sequences.txt
+
+
+echo "number of correct consensuses found : $num_common_sequences out of a total of $num_total_ref referrences"
+
+#-------------- Exit --------------#
+echo "___END !___"
+
+exit 0
+
+# scp -r oboulle@dnarxiv.irisa.fr:~/Documents/result_analysis/fragment_assembly_analysis/results/demultiplexed_v2 ~/Documents/result_analysis/fragment_assembly_analysis/results
-- 
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