Bins from reclustering are aggreagted from samples, adapted scripts

RasmussenLab · Jul 17, 2023 · 8be8368 · 8be8368
1 parent 2a08c95
commit 8be8368
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Showing 3 changed files with 10 additions and 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
@@ -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
@@ -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
@@ -10,28 +10,20 @@ 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  
 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