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diatomPipeline.dms
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diatomPipeline.dms
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#!/bin/bash
echo " Pipeline stated: $(date)"
makeblastdb -in diatoms.sequences.FINAL2017.fasta -out diatoms -dbtype nucl
echo " QC started: $(date)"
python ./ampliconQC.py --data $1 --forward ATGCGTTGGAGAGARCGTTTC --reverse GATCACCTTCTAATTTACCWACAACTG --threads 130 --histograms --qiime
echo " QIIME Pipeline: $(date)"
for file in $1/*.passedQC.fastq; do awk 'NR%4==2{sum+=1}END{print FILENAME,sum}' $file >> $1/diatomSequenceCounts.txt; done
echo $(date)
pick_otus.py -i $1/readyForQiime.allsamples.fasta -o $1/picked_otus_97
echo $(date)
pick_rep_set.py -i $1/picked_otus_97/readyForQiime.allsamples_otus.txt -f $1/readyForQiime.allsamples.fasta -o $1/repset.fasta
echo $(date)
blastn -db diatoms -query $1/repset.fasta -out $1/repset.diatoms.blastn -task blastn -max_target_seqs 1 -num_threads 130 -outfmt 6 -evalue 0.01
echo $(date)
mkdir $1/assigned_taxonomy
echo $(date)
python ./create_taxonomy_assignments_from_blast.py --taxonomy diatoms.taxonomy.FINAL2017.txt --percid 95.0 --blast $1/repset.diatoms.blastn --output $1/assigned_taxonomy/repset.taxonomy.txt
echo $(date)
make_otu_table.py -i $1/picked_otus_97/readyForQiime.allsamples_otus.txt -t $1/assigned_taxonomy/repset.taxonomy.txt -o $1/otu_table.biom
echo " Lookup taxa from OTU table: $(date)"
filter_taxa_from_otu_table.py -i $1/otu_table.biom -o $1/otu_table.diatomsonly.biom -n MARINE,NOT_DIATOM,Yellow_green_Algae,None
echo " Sort OTU table: $(date)"
sort_otu_table.py -i $1/otu_table.diatomsonly.biom -o $1/otu_table.diatomsonly.biom
echo " Summerise taxa: $(date)"
summarize_taxa.py -L 1 -i $1/otu_table.diatomsonly.biom -o $1/visualised_taxonomy -a
echo " Produce Diatom reports: $(date)"
python ./produceDiatomReports.py --folder $1 --lookup $2
echo "Pipeline finished: $(date)"