nau_id = None

from os import chdir, mkdir, rename
from os.path import exists, join
from qiime.test import write_test_data
from IPython.display import FileLinks as ipFileLinks, FileLink as ipFileLink

ipython_nb_base = "/home/ipython-p"
params_fp = join(ipython_nb_base, "qiime_assignment_materials", "params.txt")
reference_seqs = join(ipython_nb_base, "qiime_assignment_materials", "88_otus.fasta")
reference_tree = join(ipython_nb_base, "qiime_assignment_materials", "88_otus.tree")
reference_tax = join(ipython_nb_base, "qiime_assignment_materials", "88_otu_taxonomy.txt")

forensic_seqs = join(ipython_nb_base, "qiime_assignment_materials", "forensic-seqs.fna")
forensic_map = join(ipython_nb_base, "qiime_assignment_materials", "forensic-map.txt")

try:
    personal_dir = join(ipython_nb_base, nau_id)
except AttributeError:
    raise ValueError("Can't create and change to your personal directory. Did you set your NAU ID in the cell above? You must resolve this before you continue.")

if not exists(personal_dir):
    mkdir(personal_dir)
    chdir(personal_dir)
else:
    chdir(personal_dir)

tiny_test_dir = "tiny-test"
tiny_test_path = join(personal_dir, tiny_test_dir)
forensic_dir = "forensic"
forensic_path = join(personal_dir, forensic_dir)

if not exists(tiny_test_path):
    mkdir(tiny_test_path)
    
if not exists(forensic_path):
    mkdir(forensic_path)

# To use FileLink(s), but link to files in the user's working directory
# we wrap the call to FileLink(s) to append the working_dir to the 
# url_prefix. NOTE: This is not something that you'll generally need to
# do - it's only important as we're working with multiple users in the 
# IPython Notebook, which is currently only a single-user environment.
def FileLinks(path):
    return ipFileLinks(path,url_prefix='files/%s/' % nau_id)

def FileLink(path):
    return ipFileLink(path,url_prefix='files/%s/' % nau_id)
    
write_test_data(tiny_test_path)
rename(join(tiny_test_path, "map"), join(tiny_test_path, "map.txt"))
rename(join(tiny_test_path, "seqs"), join(tiny_test_path, "seqs.fna"))

FileLinks(tiny_test_dir)

input_map_fp = join(tiny_test_dir, 'map.txt')
output_dir = join(tiny_test_dir, 'vmf_out')

!validate_mapping_file.py -m $input_map_fp -o $output_dir

FileLinks(output_dir)

FileLinks(output_dir)

input_seqs_fp = join(tiny_test_dir, 'seqs.fna')
output_dir = join(tiny_test_dir, 'or_otus')

!pick_open_reference_otus.py -i $input_seqs_fp -o $output_dir -p $params_fp -r $reference_seqs -s 0.88

FileLinks(output_dir)

otu_table_fp = join(tiny_test_dir, 'or_otus', 'otu_table_mc2_w_tax_no_pynast_failures.biom')
output_fp = join(tiny_test_dir, 'or_otus', 'otu_table_mc2_w_tax_no_pynast_failures_summ.txt')
tree_fp = join(tiny_test_dir, 'or_otus', 'rep_set.tre')

!biom summarize-table -i $otu_table_fp -o $output_fp

FileLink(output_fp)

even_sampling_depth = 17
output_dir = join(tiny_test_dir, "cd_even%d" % even_sampling_depth)

!core_diversity_analyses.py -i $otu_table_fp -o $output_dir -t $tree_fp -e $even_sampling_depth -c "SampleType,days_since_epoch" -m $input_map_fp

cd_index = join(output_dir, "index.html")
FileLink(cd_index)

input_map_fp = forensic_map
output_dir = join(forensic_dir, 'vmf_out')
!validate_mapping_file.py -m $input_map_fp -o $output_dir

FileLinks(output_dir)











even_sampling_depth = None