!wget https://s3.amazonaws.com/qiime-tutorial/moving_pictures_tutorial.tgz

!tar xzf moving_pictures_tutorial.tgz

reference_seqs="/home/ubuntu/qiime_software/gg_otus-12_10-release/rep_set/94_otus.fasta"
reference_tree="/home/ubuntu/qiime_software/gg_otus-12_10-release/trees/94_otus.tree"
reference_tax="/home/ubuntu/qiime_software/gg_otus-12_10-release/taxonomy/94_otu_taxonomy.txt"

!split_libraries_fastq.py -o slout/ -i moving_pictures_tutorial/subsampled_fastq/subsampled_s_1_sequence.fastq,moving_pictures_tutorial/subsampled_fastq/subsampled_s_2_sequence.fastq,moving_pictures_tutorial/subsampled_fastq/subsampled_s_3_sequence.fastq,moving_pictures_tutorial/subsampled_fastq/subsampled_s_4_sequence.fastq,moving_pictures_tutorial/subsampled_fastq/subsampled_s_5_sequence.fastq,moving_pictures_tutorial/subsampled_fastq/subsampled_s_6_sequence.fastq -b moving_pictures_tutorial/subsampled_fastq/subsampled_s_1_sequence_barcodes.fastq,moving_pictures_tutorial/subsampled_fastq/subsampled_s_2_sequence_barcodes.fastq,moving_pictures_tutorial/subsampled_fastq/subsampled_s_3_sequence_barcodes.fastq,moving_pictures_tutorial/subsampled_fastq/subsampled_s_4_sequence_barcodes.fastq,moving_pictures_tutorial/subsampled_fastq/subsampled_s_5_sequence_barcodes.fastq,moving_pictures_tutorial/subsampled_fastq/subsampled_s_6_sequence_barcodes.fastq -m moving_pictures_tutorial/filtered_mapping_l1.txt,moving_pictures_tutorial/filtered_mapping_l2.txt,moving_pictures_tutorial/filtered_mapping_l3.txt,moving_pictures_tutorial/filtered_mapping_l4.txt,moving_pictures_tutorial/filtered_mapping_l5.txt,moving_pictures_tutorial/filtered_mapping_l6.txt


from IPython.display import FileLinks

FileLinks('slout')

!rm -r ucrC_fast
!pick_reference_otus_through_otu_table.py -o ucrC_fast/ -i slout/seqs.fna -r $reference_seqs -t $reference_tax -p moving_pictures_tutorial/ucrC_fast_params.txt

!per_library_stats.py -i ucrC_fast/uclust_ref_picked_otus/otu_table.biom

!merge_mapping_files.py -o combined_mapping_file.txt -m moving_pictures_tutorial/filtered_mapping_l1.txt,moving_pictures_tutorial/filtered_mapping_l2.txt,moving_pictures_tutorial/filtered_mapping_l3.txt,moving_pictures_tutorial/filtered_mapping_l4.txt,moving_pictures_tutorial/filtered_mapping_l5.txt,moving_pictures_tutorial/filtered_mapping_l6.txt


!rm -r bdiv_even121
!beta_diversity_through_plots.py -o bdiv_even121/ -i ucrC_fast/uclust_ref_picked_otus/otu_table.biom -m combined_mapping_file.txt -t $reference_tree -e 258

FileLinks('bdiv_even121')