Commit 7f2d7bd3 authored by psimion's avatar psimion
Browse files

various small changes: trying to make conf.file work

parent e3d7f3bd
......@@ -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 [ $CLEANING == "no" ] ; then
echo -e "\nNo reads cleaning will be done (parameter value set to 'no')"
fi
### miscellaneous
mkdir network_info
mv LINKS_* NODES_* nodes_detailed*.csv network_info
......
......@@ -131,7 +131,7 @@ echo
done
# regroup all samples
refseqALL=$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
......
### Cleaning reads if they map onto contaminant transcripts
### Cleaning reads if they map onto contaminant transcripts
......@@ -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
......
......@@ -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
......
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