various small changes: trying to make conf.file work

src/CroCo_v1.2.sh

@@ -131,7 +131,7 @@ echo
  done
  # regroup all samples
  refseqALL=$out/ALL_transcripts.ctgs
- cat $out/*.ctgs > $refseqALL
+ cat $out/.ctgs > $refseqALL
  
  # mapping successively every read sets on all transcripts.
  #for (( k=0; k <i; k++ ))
@@ -382,6 +382,14 @@ source "$my_dir/output_network_LINKS_simplified_files.sh"
 #echo -e "\tNODES_gephi_absolute.csv\n\tNODES_gephi_norm.csv\n\tNODES_diagrammer.tsv\n\tNODES_gephi_dubious_absolute.csv\n\tNODES_gephi_dubious_norm.csv\n\tNODES_diagrammer_dubious.tsv"
 source "$my_dir/output_network_NODES_files.sh"
 
+### CLEANING READS
+if [ $CLEANING == "yes" ]; then
+	echo -e "\nCleaning fastq files (reads mapping onto contaminant transcripts will be removed)"
+	source "$my_dir/output_cleaned_read_files.sh"
+elif [ $CLEANING == "no" ] ; then
+	echo -e "\nNo reads cleaning will be done (parameter value set to 'no')"
+fi
+
 ### miscellaneous
 mkdir network_info
 mv LINKS_* NODES_* nodes_detailed*.csv network_info

src/CroCo_v1.2.sh~

@@ -131,7 +131,7 @@ echo
  done
  # regroup all samples
  refseqALL=$out/ALL_transcripts.ctgs
- cat $out/*.ctgs > $refseqALL
+ cat $out/$ref.ctgs > $refseqALL
  
  # mapping successively every read sets on all transcripts.
  #for (( k=0; k <i; k++ ))
@@ -382,6 +382,14 @@ source "$my_dir/output_network_LINKS_simplified_files.sh"
 #echo -e "\tNODES_gephi_absolute.csv\n\tNODES_gephi_norm.csv\n\tNODES_diagrammer.tsv\n\tNODES_gephi_dubious_absolute.csv\n\tNODES_gephi_dubious_norm.csv\n\tNODES_diagrammer_dubious.tsv"
 source "$my_dir/output_network_NODES_files.sh"
 
+### CLEANING READS
+if [ $CLEANING == "yes" ]; then
+	echo -e "\nCleaning fastq files (reads mapping onto contaminant transcripts will be removed)"
+	source "$my_dir/output_cleaned_read_files.sh"
+elif [ $CLEANING == "no" ] ; then
+	echo -e "\nNo reads cleaning will be done (parameter value set to 'no')"
+fi
+
 ### miscellaneous
 mkdir network_info
 mv LINKS_* NODES_* nodes_detailed*.csv network_info

src/output_cleaned_read_files.sh

+### Cleaning reads if they map onto contaminant transcripts
+
+
+
+

src/output_cleaned_read_files.sh~

+### Cleaning reads if they map onto contaminant transcripts
+
+
+
+

src/output_fasta.sh

@@ -4,8 +4,10 @@ if [ $OUTPUTLEVEL == "1" ]; then
 
 elif [ $OUTPUTLEVEL == "2" ]; then
 	echo -e "\nWriting categorized transcriptomes - all categories (it might take some time)"
-	for fasta in $out/*.fasta_mod; do
-		ref=`basename $fasta .fasta_mod`
+	#for fasta in $out/*.fasta_mod; do
+		#ref=`basename $fasta .fasta_mod`
+	for ref in "${orders[@]}"
+		fasta=$out/$ref".fasta_mod"
 		echo -e "\t$ref"
 
 		# version awk

src/output_fasta.sh~

@@ -4,8 +4,10 @@ if [ $OUTPUTLEVEL == "1" ]; then
 
 elif [ $OUTPUTLEVEL == "2" ]; then
 	echo -e "\nWriting categorized transcriptomes - all categories (it might take some time)"
-	for fasta in $out/*.fasta_mod; do
-		ref=`basename $fasta .fasta_mod`
+	#for fasta in $out/*.fasta_mod; do
+		#ref=`basename $fasta .fasta_mod`
+	for ref in "${orders[@]}"
+		fasta=$out/$ref".fasta_mod"
 		echo -e "\t$ref"
 
 		# version awk