various minor changes

src/CroCo_v1.1.sh

@@ -55,7 +55,6 @@ START_TIME=$SECONDS
 if [ $RECAT == "no" ]; then
 
 ### setting sample names
-<<<<<<< HEAD
 
 if [ -f $CONFFILE ]; then 
  declare -A fasta_array
@@ -94,7 +93,6 @@ echo "${orders[@]}"
 echo
 ###
 
-=======
 # i=0
 #for fasta in $INDIR/*.fasta ; do
 #   fasta_array[$i]=`basename $fasta .fasta`
@@ -124,7 +122,6 @@ do
   #for i in "${InfosCtg[@]}";   do   echo $i; done;
   
 done < $CONFFILE
->>>>>>> d595607cd6e1098d1b1a5075ed876f52e30e8f4c
 
 ### detecting suspect transcripts with BLAST
  #source "$my_dir/detect_suspect_trans_with_blast.sh"
@@ -148,10 +145,7 @@ done < $CONFFILE
  echo -e "\nIndex built : $out/$toolidx\n"
 
  #for (( j=0; j <i; j++ ))
-<<<<<<< HEAD
-=======
  #for ref in "${!fasta_array[@]}"
->>>>>>> d595607cd6e1098d1b1a5075ed876f52e30e8f4c
  for ref in "${orders[@]}"
  do
    refseqs=$out/$ref".ctgs"
@@ -171,10 +165,7 @@ done < $CONFFILE
  
  # mapping successively every read sets on all transcripts.
  #for (( k=0; k <i; k++ ))
-<<<<<<< HEAD
-=======
  #for ref in "${!fasta_array[@]}"
->>>>>>> d595607cd6e1098d1b1a5075ed876f52e30e8f4c
  for ref in "${orders[@]}"
  do
    InfosCtg=${fasta_array[$ref]}
@@ -256,10 +247,7 @@ done < $CONFFILE
  # splitting "All_transcript.all" file into files corresponding to samples
 
  #for (( j=0; j <i; j++ ))
-<<<<<<< HEAD
-=======
  #for ref in "${!fasta_array[@]}"
->>>>>>> d595607cd6e1098d1b1a5075ed876f52e30e8f4c
  for ref in "${orders[@]}"
  do
    #ref=${fasta_array[$j]}

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++ ))

src/def_values.sh

@@ -15,3 +15,4 @@ SUSPID=95   # blast minimum id% for being a potential suspect of cross contamina
 SUSPLEN=40   # blast minimum id% for being a potential suspect of cross contamination
 OVEREXP=300   # expression level (TPM) above which a transcript might be considered "overexpressed"
 RECAT=no   # previous CroCo output directory to be used to re-categorize transcripts
+CLEANING=no	# cleaning reads from fastq files if they correspond to cross contaminant transcripts

src/def_values.sh~

@@ -15,3 +15,4 @@ SUSPID=95   # blast minimum id% for being a potential suspect of cross contamina
 SUSPLEN=40   # blast minimum id% for being a potential suspect of cross contamination
 OVEREXP=300   # expression level (TPM) above which a transcript might be considered "overexpressed"
 RECAT=no   # previous CroCo output directory to be used to re-categorize transcripts
+CLEANING=no	# cleaning reads from fastq files if they correspond to cross contaminant transcripts

src/detect_suspect_trans_with_blast.sh

@@ -42,7 +42,12 @@ done
 
 
  # regroup all samples
- cat $out/*.fasta_mod > $out/ALL_transcripts.fasta
- cat $out/*.suspects > $out/ALL_transcripts.suspects
- cat $out/*.fasta_suspect > $out/ALL_transcripts.fasta_suspects
+echo '' > $out/ALL_transcripts.fasta
+echo '' > $out/ALL_transcripts.suspects
+echo '' > $out/ALL_transcripts.fasta_suspects
 
+for ref in "${orders[@]}"; do 
+ cat $out/$ref.fasta_mod >> $out/ALL_transcripts.fasta
+ cat $out/$ref.suspects >> $out/ALL_transcripts.suspects
+ cat $out/$ref.fasta_suspect >> $out/ALL_transcripts.fasta_suspects
+done

src/detect_suspect_trans_with_blast.sh~

@@ -42,7 +42,12 @@ done
 
 
  # regroup all samples
- cat $out/*.fasta_mod > $out/ALL_transcripts.fasta
- cat $out/*.suspects > $out/ALL_transcripts.suspects
- cat $out/*.fasta_suspect > $out/ALL_transcripts.fasta_suspects
+echo '' > $out/ALL_transcripts.fasta
+echo '' > $out/ALL_transcripts.suspects
+echo '' > $out/ALL_transcripts.fasta_suspects
 
+for ref in "${orders[@]}"; do 
+ cat $out/$ref.fasta_mod >> $out/ALL_transcripts.fasta
+ cat $out/$ref.suspects >> $out/ALL_transcripts.suspects
+ cat $out/$ref.fasta_suspect >> $out/ALL_transcripts.fasta_suspects
+done