Quick-and-dirty code to generate a shell script to re-organize the directory structure in the short-read-tax-assignment repo.

reorg-dir-structure.py

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#!/usr/bin/env python
# Author: Greg Caporaso

from os.path import join, isdir
from glob import glob

base_in_dir = "/home/caporaso/analysis/short-read-tax-assignment/data/qiime-mock-community/multiple_assign_taxonomy_output/"
base_out_dir = "/home/caporaso/analysis/short-read-tax-assignment/data/eval-pre-computed/"

lines = []
lines.append('#!/usr/bin/env bash')
lines.append('')
lines.append('mkdir %s' % (base_out_dir))
lines.append('')

data_sets = []
for e in glob(join(base_in_dir,'*')):
    id_ = e.split('/')[-1]
    if '_' not in id_:
        data_sets.append(id_)

for data_set in data_sets:
    in_data_set_dir = join(base_in_dir,data_set)
    out_data_set_dir = join(base_out_dir,data_set)
    lines.append('## %s' % data_set)
    lines.append('mkdir %s' % (out_data_set_dir))
    in_methods = [e.split('/')[-1] for e in glob(join(in_data_set_dir,'*')) if isdir(e)]
    out_methods = [e.split('_') for e in in_methods]
    out_ref_tax = 'gg_13_5_otus'

    for i, o in zip(in_methods,out_methods):
        in_method_dir = join(in_data_set_dir,i)
        out_ref_tax_dir = join(out_data_set_dir,o[0])
        out_method_dir = join(out_ref_tax_dir,out_ref_tax)
        try:
            out_param_dir = join(out_method_dir,o[1])
        except IndexError:
            out_param_dir = out_method_dir
        lines.append('mkdir %s' % out_ref_tax_dir)
        lines.append('mkdir %s' % out_method_dir)
        lines.append('mkdir %s' % out_param_dir)
        in_biom_fp = join(in_method_dir,'*w_taxa.biom')
        out_biom_fp = join(out_param_dir,'table.biom')
        lines.append('cp %s %s' % (in_biom_fp,out_biom_fp))
    lines.append('')
    lines.append('')

f = open('reorg.sh','w')
f.write('\n'.join(lines))
f.close()