From 8be8368b998e05d0a47d1a7de2b00c26c1bc06bb Mon Sep 17 00:00:00 2001
From: "pau.piera.linde@gmail.com" <paupie@g-12-l0002.cm.cluster>
Date: Mon, 17 Jul 2023 11:03:54 +0200
Subject: [PATCH] Bins from reclustering are aggreagted from samples, adapted
 scripts

---
 .../create_cluster_scores_bin_path_dict.py    |  4 ++--
 workflow_taxVamb/src/symlink_nc_bins.py       |  3 ++-
 .../src/write_clusters_from_final_bins.sh     | 20 ++++++-------------
 3 files changed, 10 insertions(+), 17 deletions(-)

diff --git a/workflow_taxVamb/src/create_cluster_scores_bin_path_dict.py b/workflow_taxVamb/src/create_cluster_scores_bin_path_dict.py
index c4d9023b..5cf5ae98 100644
--- a/workflow_taxVamb/src/create_cluster_scores_bin_path_dict.py
+++ b/workflow_taxVamb/src/create_cluster_scores_bin_path_dict.py
@@ -32,9 +32,9 @@ def get_cluster_score_bin_path(
             bin_name = cluster + ".fna"
             if bin_name in bins:
                 cluster_score[cluster] = (com, con)
-                bin_path[cluster + ".fna"] = os.path.join(
+                bin_path[cluster + ".fna"] = os.path.abspath(os.path.join(
                     path_bins, sample, cluster + ".fna"
-                )
+                ))
     return cluster_score, bin_path
 
 
diff --git a/workflow_taxVamb/src/symlink_nc_bins.py b/workflow_taxVamb/src/symlink_nc_bins.py
index 1568ab85..f68a3a7d 100644
--- a/workflow_taxVamb/src/symlink_nc_bins.py
+++ b/workflow_taxVamb/src/symlink_nc_bins.py
@@ -39,6 +39,7 @@
     comp,cont = comp_cont
     bin_ = cluster+bin_format
     if (comp >= min_comp and cont <= max_cont ):
-        os.symlink(os.path.join(os.getcwd(),bp_d[bin_]),os.path.join(opt.o,bin_))
+        #print(bp_d[bin_])
+        os.symlink(bp_d[bin_],os.path.join(opt.o,bin_))
 
  
diff --git a/workflow_taxVamb/src/write_clusters_from_final_bins.sh b/workflow_taxVamb/src/write_clusters_from_final_bins.sh
index 344c86bb..93ceab42 100644
--- a/workflow_taxVamb/src/write_clusters_from_final_bins.sh
+++ b/workflow_taxVamb/src/write_clusters_from_final_bins.sh
@@ -10,12 +10,7 @@ while getopts "d:o:" opt; do
   esac
 done
 echo 'creating z y v clusters from the final set of bins'
-for s in $(ls $drep_dir)
-do
-s="$drep_dir"/"$s"/
-if [ -d "$s" ]
-then
-cd $s
+cd $drep_dir
 for bin in $(ls . 2> /dev/null)
 
 do  
@@ -23,15 +18,12 @@ if [[ $bin == **".fna" ]]
 then
 
 cluster_name=$(echo $bin | sed 's=.fna==g' | sed 's=.fa==g')
-
-for contig in $(grep '>' $bin | sed 's=>==g') 
-do
-echo -e   "$cluster_name""\t""$contig"  >> $clusters_file
-done
+echo $cluster_name
+#for contig in $(grep '>' $bin | sed 's=>==g') 
+#do
+#echo -e   "$cluster_name""\t""$contig"  >> $clusters_file
+#done
 
 
 fi
 done
-
-fi
-done