Commit 18430303 authored by psimion's avatar psimion
Browse files

various minor changes

parents 7f2d7bd3 bd02a2aa
...@@ -55,7 +55,6 @@ START_TIME=$SECONDS ...@@ -55,7 +55,6 @@ START_TIME=$SECONDS
if [ $RECAT == "no" ]; then if [ $RECAT == "no" ]; then
### setting sample names ### setting sample names
<<<<<<< HEAD
if [ -f $CONFFILE ]; then if [ -f $CONFFILE ]; then
declare -A fasta_array declare -A fasta_array
...@@ -94,7 +93,6 @@ echo "${orders[@]}" ...@@ -94,7 +93,6 @@ echo "${orders[@]}"
echo echo
### ###
=======
# i=0 # i=0
#for fasta in $INDIR/*.fasta ; do #for fasta in $INDIR/*.fasta ; do
# fasta_array[$i]=`basename $fasta .fasta` # fasta_array[$i]=`basename $fasta .fasta`
...@@ -124,7 +122,6 @@ do ...@@ -124,7 +122,6 @@ do
#for i in "${InfosCtg[@]}"; do echo $i; done; #for i in "${InfosCtg[@]}"; do echo $i; done;
done < $CONFFILE done < $CONFFILE
>>>>>>> d595607cd6e1098d1b1a5075ed876f52e30e8f4c
### detecting suspect transcripts with BLAST ### detecting suspect transcripts with BLAST
#source "$my_dir/detect_suspect_trans_with_blast.sh" #source "$my_dir/detect_suspect_trans_with_blast.sh"
...@@ -148,10 +145,7 @@ done < $CONFFILE ...@@ -148,10 +145,7 @@ done < $CONFFILE
echo -e "\nIndex built : $out/$toolidx\n" echo -e "\nIndex built : $out/$toolidx\n"
#for (( j=0; j <i; j++ )) #for (( j=0; j <i; j++ ))
<<<<<<< HEAD
=======
#for ref in "${!fasta_array[@]}" #for ref in "${!fasta_array[@]}"
>>>>>>> d595607cd6e1098d1b1a5075ed876f52e30e8f4c
for ref in "${orders[@]}" for ref in "${orders[@]}"
do do
refseqs=$out/$ref".ctgs" refseqs=$out/$ref".ctgs"
...@@ -171,10 +165,7 @@ done < $CONFFILE ...@@ -171,10 +165,7 @@ done < $CONFFILE
# mapping successively every read sets on all transcripts. # mapping successively every read sets on all transcripts.
#for (( k=0; k <i; k++ )) #for (( k=0; k <i; k++ ))
<<<<<<< HEAD
=======
#for ref in "${!fasta_array[@]}" #for ref in "${!fasta_array[@]}"
>>>>>>> d595607cd6e1098d1b1a5075ed876f52e30e8f4c
for ref in "${orders[@]}" for ref in "${orders[@]}"
do do
InfosCtg=${fasta_array[$ref]} InfosCtg=${fasta_array[$ref]}
...@@ -256,10 +247,7 @@ done < $CONFFILE ...@@ -256,10 +247,7 @@ done < $CONFFILE
# splitting "All_transcript.all" file into files corresponding to samples # splitting "All_transcript.all" file into files corresponding to samples
#for (( j=0; j <i; j++ )) #for (( j=0; j <i; j++ ))
<<<<<<< HEAD
=======
#for ref in "${!fasta_array[@]}" #for ref in "${!fasta_array[@]}"
>>>>>>> d595607cd6e1098d1b1a5075ed876f52e30e8f4c
for ref in "${orders[@]}" for ref in "${orders[@]}"
do do
#ref=${fasta_array[$j]} #ref=${fasta_array[$j]}
......
...@@ -131,7 +131,7 @@ echo ...@@ -131,7 +131,7 @@ echo
done done
# regroup all samples # regroup all samples
refseqALL=$out/ALL_transcripts.ctgs refseqALL=$out/ALL_transcripts.ctgs
cat $out/.ctgs > $refseqALL cat $out/$ref.ctgs > $refseqALL
# mapping successively every read sets on all transcripts. # mapping successively every read sets on all transcripts.
#for (( k=0; k <i; k++ )) #for (( k=0; k <i; k++ ))
......
...@@ -15,3 +15,4 @@ SUSPID=95 # blast minimum id% for being a potential suspect of cross contamina ...@@ -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 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" 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 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
...@@ -15,3 +15,4 @@ SUSPID=95 # blast minimum id% for being a potential suspect of cross contamina ...@@ -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 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" 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 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
...@@ -42,7 +42,12 @@ done ...@@ -42,7 +42,12 @@ done
# regroup all samples # regroup all samples
cat $out/*.fasta_mod > $out/ALL_transcripts.fasta echo '' > $out/ALL_transcripts.fasta
cat $out/*.suspects > $out/ALL_transcripts.suspects echo '' > $out/ALL_transcripts.suspects
cat $out/*.fasta_suspect > $out/ALL_transcripts.fasta_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
...@@ -42,7 +42,12 @@ done ...@@ -42,7 +42,12 @@ done
# regroup all samples # regroup all samples
cat $out/*.fasta_mod > $out/ALL_transcripts.fasta echo '' > $out/ALL_transcripts.fasta
cat $out/*.suspects > $out/ALL_transcripts.suspects echo '' > $out/ALL_transcripts.suspects
cat $out/*.fasta_suspect > $out/ALL_transcripts.fasta_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
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