convert update

scripts/convert_project.sh

@@ -1,47 +1,78 @@
-# create dirs
-dir_list=(logs analysis);\
+# proj info
 project_name="OH-M2941-211115";\
-date_stamp="20211115";\
-final_output="analysis/final_results_$date_stamp.csv";\
-for pd in "${dir_list[@]}"; do if [[ ! -d $pd ]]; then mkdir -p $pd; fi; done;\
+dir_list=(logs analysis);\
+for pd in "${dir_list[@]}"; do if [[ ! -d $project_name/$pd ]]; then mkdir -p $project_name/$pd; fi; done;\
 dir_list=(fasta intermed);\
-for pd in "${dir_list[@]}"; do if [[ ! -d analysis/$pd ]]; then mkdir -p analysis/$pd; fi; done;\
+for pd in "${dir_list[@]}"; do if [[ ! -d $project_name/analysis/$pd ]]; then mkdir -p $project_name/analysis/$pd; fi; done;\
 dir_list=(not_uploaded upload_complete upload_partial upload_failed);\
-for pd in "${dir_list[@]}"; do if [[ ! -d analysis/fasta/$pd ]]; then mkdir -p analysis/fasta/$pd; fi; done;\
-cp /c/Users/33245250/Documents/GitHub/ODH-COVID19/config/* logs;\
-sed -i "s/merged_complete.csv/metadata_${project_name}.csv/" "logs/config_pipeline.yaml";\
-mv GISAID_logs/*/* logs;\
-echo "sample_id,gisaid_status,gisaid_notes,pango_qc,nextclade_clade,pangolin_lineage,pangolin_scorpio,aa_substitutions">$final_output;\
-cat logs/qc_failed.txt>>$final_output;\
-sed -i "s/_consensus.fasta /,qc_fail,qc_/g" $final_output;\
-sed -i "s/%/%_Ns/g" $final_output;\
-aa_file="/l/Micro/Gen Micro/Whole Genome Sequencing/Coronavirus_WGS/COVID-19 Fastas/analysis/mutation_analysis/aa_download_05172022/ohio_aadownload_01012022_to_05172022_sub.csv";\
-IFS=$'\n' read -d '' -r -a sample_list < "logs/qc_passed.txt";\
+for pd in "${dir_list[@]}"; do if [[ ! -d $project_name/analysis/fasta/$pd ]]; then mkdir -p $project_name/analysis/fasta/$pd; fi; done
+
+#copy configs, logs
+project_name="OH-M2941-211115";\
+cp /c/Users/33245250/Documents/GitHub/ODH-COVID19/config/* $project_name/logs;\
+sed -i "s/merged_complete.csv/metadata_${project_name}.csv/" "$project_name/logs/config_pipeline.yaml";\
+mv $project_name/GISAID_logs/*/* $project_name/logs;\
+cat $project_name/"Fastas - GISAID Not Complete"/qc_failed.txt >> logs/qc_failed.txt
+mv $project_name/"fastas_GISAID_errors"/*final* $project_name/logs;\
+mv $project_name/"fastas_GISAID_errors"/*txt $project_name/logs;\
+mv $project_id/"fastas_GISAID_uploaded/"/*sample_log* $project_name/logs;\
+mv project_name/monroe* $project_name/logs
+
+#process passed samples
+project_name="OH-M2941-211115";\
+date_stamp="20211115";\
+final_output="$project_name/analysis/final_results_$date_stamp.csv";\
+aa_file="/c/Users/33245250/Documents/GitHub/ODH-COVID19/scripts/gisaid_hcov-19.tsv";\
+echo "sample_id,gisaid_status,gisaid_notes,pango_status,pangolin_lineage,pangolin_scorpio,pangolin_version,nextclade_clade,aa_substitutions">$final_output;\
+IFS=$'\n' read -d '' -r -a sample_list < "$project_name/logs/qc_passed.txt";\
 for sample_line in "${sample_list[@]}"; do
     sample_id=`echo "${sample_line}" | cut -f10 -d"/" | cut -f1 -d"_"`;\
-    aa_line=`cat "${aa_file}" | grep "${sample_id}"`;\
-    gisaid_id=`echo "${aa_line}" | cut -f2 -d","`;\
-    pangolin_lineage=`echo "${aa_line}" | cut -f3 -d","`;\
-    nextclade_clade=`echo "${aa_line}" | cut -f4 -d","`;\
-    aa_substitutions=`echo "${aa_line}" | cut -f2 -d"(" | sed "s/)//g"`;\
-    echo "${sample_id},gisaid_pass,${gisaid_id},passed_qc,${nextclade_clade},${pangolin_lineage},,"${aa_substitutions}"">>$final_output;\
-done;\
+    convert_id=`echo ${sample_id} | sed "s/202/SC/g"`;\
+    aa_line=`cat "${aa_file}" | grep "${convert_id}"`;\
+    if [[ $aa_line == "" ]]; then
+        gisaid_status="fail";\
+        gisaid_id="NA";\
+        pangolin_lineage="NA";\
+        aa_substitutions="NA";\
+    else
+        gisaid_status="pass";\
+        gisaid_id=`echo "${aa_line}" | awk -F"\t" '{ print $2 }'`;\
+        pangolin_lineage=`echo "${aa_line}" | awk -F"\t" '{ print $15 }'`;\
+        aa_substitutions=`echo "${aa_line}" | awk -F"\t" '{ print $17 }'`;\
+    fi;\
+    nextclade_clade="NA";\
+    final_line=`echo "${sample_id},gisaid_$gisaid_status,${gisaid_id},$gisaid_status,${pangolin_lineage},NA,MONROE,${nextclade_clade},${aa_substitutions}"`;\
+    echo $final_line | sed "s/(/\"/g" | sed "s/)/\"/g">>$final_output;\
+done
+
+#process failed samples, prep fastas
+project_name="OH-M2941-211115";\
+date_stamp="20211115";\
+final_output="$project_name/analysis/final_results_$date_stamp.csv";\
+cat logs/qc_failed.txt >>$final_output;\
+sed -i "s/_consensus.fasta /,qc_fail,qc_,fail,NA,NA,MONROE,NA,NA/g" $final_output;\
+sed -i "s/%/%_Ns/g" $final_output;\
 error_log="fastas_GISAID_errors/error_log.txt";\
-IFS=$'\n' read -d '' -r -a sample_list < $error_log;\
-for sample_line in "${sample_list[@]}"; do
-    sample_id=`echo "${sample_line}" | cut -f3 -d"/" | cut -f2 -d"-"`;\
-    sed -i "s/$sample_id,gisaid_pass/$sample_id,gisaid_rejected/g" $final_output;\
-done;\
-mv "Fastas - GISAID Not Complete/"*fasta analysis/fasta/not_uploaded;\
-mv fastas_GISAID_errors/*fasta analysis/fasta/upload_failed;\
-mv fastas_GISAID_errors/error_log* analysis/intermed/gisaid_rejected.txt;\
-mv fastas_GISAID_uploaded/*fasta analysis/fasta/upload_partial;\
-mv gisaid_log* logs;\
-mv monroe* analysis;\
-mv fastas_GISAID_errors/metadata* logs/metadata_gisaid_failed.csv;\
-mv logs/qc_passed* analysis/intermed/gisaid_passed.txt;\
-for f in analysis/fasta/*/*; do new_name=`echo $f | sed "s/_consensus//g"`; mv $f $new_name; done;\
-rm -r fastas*;\
-rm -r Fastas*;\
-rm -r GISAID*;\
-rm logs/warning*
+mv $project_name/"Fastas - GISAID Not Complete/*.fa*" $project_name/analysis/fasta/not_uploaded;\
+mv $project_name/"fastas_GISAID_errors/*fa*" $project_name/analysis/fasta/not_uploaded;\
+mv $project_name/"fastas_GISAID_uploaded/*fa*" $project_name/analysis/fasta/not_uploaded
+
+#process fastas
+project_name="OH-M2941-211115";\
+date_stamp="20211115";\
+final_output="$project_name/analysis/final_results_$date_stamp.csv";\
+for fasta_id in `ls $project_name/analysis/fasta/not_uploaded`; do
+    sample_id=`echo $fasta_id | cut -f5 -d"/" | cut -f1 -d"."`;\
+    status=`cat $final_output | grep $sample_id | cut -f2 -d","`;\
+    if [[ $status == "gisaid_pass" ]]; then
+        echo "pass $sample_id"
+        mv $fasta_id $project_name/analysis/fasta/not_uploaded/$sample_id.fa
+    else
+        echo "fail $sample_id"
+        mv $fasta_id $project_name/analysis/fasta/upload_partial/$sample_id.fa
+    fi;\
+done
+# rm -r fastas*;\
+# rm -r Fastas*;\
+# rm -r GISAID*;\
+# rm logs/warning*