Commit 4818a4ba authored by peguerin's avatar peguerin
Browse files

debug update

parent cd999371
......@@ -35,4 +35,4 @@ echo "bash pipeline_single.sh "$var" "$DATA_PATH" "$BDR_PATH
done < liste_fq_dat > fq_dat_cmd.sh
###############################################################################
## run in parallel each command
parallel < fq_data_cmd.sh
parallel < fq_dat_cmd.sh
......@@ -11,6 +11,10 @@ R2_fastq="$DATA_PATH"/"$pref"_R2.fastq.gz
sample_description_file=$2
### absolute path to the folder which contains reference database files
base_dir=$4
### [very important and tricky !!! ]
### prefix of the reference database files after "embl_"
### the prefix must contain no "." or "_" characters
base_pref=`ls $base_dir/embl_* | sed 's/embl_/|/g' | cut -d "|" -f 2 | cut -d "." -f 1 | cut -d "_" -f 1 | uniq`
### path to the folder which stores intermediate and temporary results
main_dir=$(pwd)/main
### path to the folder which contains final results tables for this run
......@@ -53,7 +57,7 @@ all_sample_sequences_uniq="${all_sample_sequences_clean/.fasta/.uniq.fasta}"
obiuniq -m sample $all_sample_sequences_clean > $all_sample_sequences_uniq
##Assign each sequence to a taxon
all_sample_sequences_tag="${all_sample_sequences_uniq/.fasta/.tag.fasta}"
ecotag -d "$base_dir"/embl_* -R $base_dir/db_*.fasta $all_sample_sequences_uniq > $all_sample_sequences_tag
ecotag -d "$base_dir"/embl_"$base_pref" -R $base_dir/db_"$base_pref".fasta $all_sample_sequences_uniq > $all_sample_sequences_tag
##Some unuseful attributes can be removed at this stage
all_sample_sequences_ann="${all_sample_sequences_tag/.fasta/.ann.fasta}"
obiannotate --delete-tag=scientific_name_by_db --delete-tag=obiclean_samplecount \
......@@ -70,6 +74,3 @@ all_sample_sequences_sort="${all_sample_sequences_ann/.fasta/.sort.fasta}"
obisort -k count -r $all_sample_sequences_ann > $all_sample_sequences_sort
##generate a table final results
obitab -o $all_sample_sequences_sort > $fin_dir/"$pref".csv
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment