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caporaso-lab / cloaked-octo-ninja

Comparative analysis of high-level OTU picking protocols

Home Page:www.caporasolab.us

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Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences: data files

This repository contains commands, shell scripts, processed data files, and IPython Notebooks for:

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences. Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons SM, Chase J, McDonald D, Gonzalez A, Robbins-Pianka A, Clemente JC, Gilbert JA, Huse SM, Zhou H, Knight R, Caporaso JG. (2014) PeerJ 2:e545. http://dx.doi.org/10.7717/peerj.545

IF YOU HAVE DOWNLOADED A STATIC VERSION OF THIS REPOSITORY, WE HIGHLY RECOMMEND THAT YOU DOWNLOAD THE LATEST FROM OUR GITHUB REPOSITORY AS UPDATES AND BUG FIXES WILL BE POSTED THERE.

The raw sequence data analyzed in this study is available in the QIIME Database under study ids 103 (88-soils), 449 (whole-body), and 550 (moving-pictures).

All analyses were run on RHEL using QIIME 1.8.0-dev (specific configuration details below).

An IPython Notebook illustrating how to load and access all data in the tables presented in the paper is available for static viewing on nbviewer or can be run from this repository (depends on pandas, numpy, and the files contained in this repository).

The following sections illustrate how to generate the data that was not included in this repository (due to size).

Configuring the environment

To run the analyses presented in this section, you'll need to following:

  1. QIIME 1.8.0 (base installation is sufficient)
  2. Greengenes (13_8)
  3. Post-split-libraries sequence data for QIIME Database study ids 103 (88-soils), 449 (whole-body, and 550 (moving-pictures.

To configure the environment, you should first clone the GitHub repository (this will required that you have git installed) and change to that directory. From here, we will call that your project directory:

git clone git@github.com:gregcaporaso/cloaked-octo-ninja.git
cd cloaked-octo-ninja

You should next edit config-env.sh to:

  1. define the PROJECT_DIR environment variable as the absolute path to your project directory, and
  2. define the REF_DIR environment variable as the absolute path to your Greengenes reference sequences directory, and
  3. define the MOVING_PICTURES_SEQS, SOILS_SEQS, and WHOLE_BODY_SEQS environment variables as the absolute paths to the post-split-libraries sequence files that you downloaded from the QIIME DB.

Testing the environment

All commands below assume that you are working from your project directory. To configure your environment, run:

source config-env.sh

The OTU picking commands that we're interested in are as follows:

De novo OTU picking (canonically abbreviated uc)

pick_de_novo_otus.py -i <in> -o <out>/uc -p $PROJECT_DIR/parameters/uc.txt -aO 10

"Legacy" open reference OTU picking (canonically abbreviated ucr)

pick_de_novo_otus.py -i <in> -o <out>/ucr -p $PROJECT_DIR/parameters/ucr.txt -aO 10

Closed reference OTU picking (canonically abbreviated ucrC)

pick_closed_reference_otus.py -i <in> -o <out>/ucrC -p $PROJECT_DIR/parameters/ucrC.txt -r $REF_SEQS -aO 10

Subsampled open reference OTU picking (canonically abbreviated ucrss)

pick_open_reference_otus.py -i <in> -o <out>/ucrss -p $PROJECT_DIR/parameters/ucrss.txt -r $REF_SEQS -aO 10 --min_otu_size 1 --prefilter_percent_id 0.0

Subsampled open reference OTU picking (canonically abbreviated ucrss_w_filter)

pick_open_reference_otus.py -i <in> -o <out>/ucrss -p $PROJECT_DIR/parameters/ucrss.txt -r $REF_SEQS -aO 10 --min_otu_size 1

We also run these with the "fast uclust" settings, which are provided in a parameters file as:

pick_otus:max_accepts 1
pick_otus:max_rejects 8
pick_otus:stepwords 8
pick_otus:word_length 8

To obtain the "tiny test" data set, which is useful for sanity checking commands, run:

python -c "from qiime.test import write_test_data; write_test_data('tiny-test')"

To run four OTU picking protocols on the tiny-test data set, run:

source /home/caporaso/analysis/2014.04.16-ss-otus/config-env.sh; pick_de_novo_otus.py -i $TINY_TEST_SEQS -o $PROJECT_DIR/tiny-test-otus/uc -p $PROJECT_DIR/parameters/uc.txt -aO 10; pick_de_novo_otus.py -i $TINY_TEST_SEQS -o $PROJECT_DIR/tiny-test-otus/ucr -p $PROJECT_DIR/parameters/ucr.txt -aO 10; pick_closed_reference_otus.py -i $TINY_TEST_SEQS -o $PROJECT_DIR/tiny-test-otus/ucrC -p $PROJECT_DIR/parameters/ucrC.txt -r $REF_SEQS -aO 10; pick_open_reference_otus.py -i $TINY_TEST_SEQS -o $PROJECT_DIR/tiny-test-otus/ucrss -p $PROJECT_DIR/parameters/ucrss.txt -r $REF_SEQS -aO 10 --min_otu_size 1 --prefilter_percent_id 0.0

We can then obtain run-time information as follows:

$ cd $PROJECT_DIR
$ grep "^Logging" tiny-test-otus/*/log*txt
tiny-test-otus/uc/log_20140416144749.txt:Logging started at 14:47:49 on 16 Apr 2014
tiny-test-otus/uc/log_20140416144749.txt:Logging stopped at 14:48:25 on 16 Apr 2014
tiny-test-otus/ucrC/log_20140416144900.txt:Logging started at 14:49:00 on 16 Apr 2014
tiny-test-otus/ucrC/log_20140416144900.txt:Logging stopped at 14:50:14 on 16 Apr 2014
tiny-test-otus/ucr/log_20140416144825.txt:Logging started at 14:48:25 on 16 Apr 2014
tiny-test-otus/ucr/log_20140416144825.txt:Logging stopped at 14:49:00 on 16 Apr 2014
tiny-test-otus/ucrss/log_20140416145014.txt:Logging started at 14:50:14 on 16 Apr 2014
tiny-test-otus/ucrss/log_20140416145014.txt:Logging stopped at 14:52:01 on 16 Apr 2014

Input data sets details

88 soils

count_seqs.py -i $SOILS_SEQS

151387  : /home/caporaso/analysis/88-soils/study_103_split_library_seqs.fna (Sequence lengths (mean +/- std): 230.7818 +/- 11.4761)

Moving Pictures

count_seqs.py -i $MOVING_PICTURES_SEQS

68666081  : /home/caporaso/analysis/moving-pictures/study_550_split_library_seqs.fna (Sequence lengths (mean +/- std): 123.2359 +/- 17.4283)

Whole body

count_seqs.py -i $WHOLE_BODY_SEQS

792831  : /home/caporaso/analysis/whole-body/study_449_split_library_seqs.fna (Sequence lengths (mean +/- std): 228.5124 +/- 16.0318)

Commands for data preparation

Define paths to required data files (relative to $PROJECT_DIR) and other per-run information. Each entry in this list contains the following values:

  1. OTU table path
  2. OTU tree path
  3. QIIME 1.8.0-dev OTU picking command
  4. Even sampling depth

l = [("moving-pictures-otus/uc/otu_table.biom", "moving-pictures-otus/uc/rep_set.tre", "pick_de_novo_otus.py -i $MOVING_PICTURES_SEQS -o $PROJECT_DIR/moving-pictures-otus/uc -p $PROJECT_DIR/parameters/uc.txt -aO 10", 5000),
("moving-pictures-otus/ucr/otu_table.biom", "moving-pictures-otus/ucr/rep_set.tre", "pick_de_novo_otus.py -i $MOVING_PICTURES_SEQS -o $PROJECT_DIR/moving-pictures-otus/ucr -p $PROJECT_DIR/parameters/ucr.txt -aO 10", 5000),
("moving-pictures-otus/ucrC/otu_table.biom", "$REF_TREE", "pick_closed_reference_otus.py -i $MOVING_PICTURES_SEQS -o $PROJECT_DIR/moving-pictures-otus/ucrC -p $PROJECT_DIR/parameters/ucrC.txt -r $REF_SEQS -aO 10 -t $REF_TAX", 5000),
("moving-pictures-otus/ucrss/otu_table_mc1_w_tax.biom", "moving-pictures-otus/ucrss/rep_set.tre", "pick_open_reference_otus.py -i $MOVING_PICTURES_SEQS -o $PROJECT_DIR/moving-pictures-otus/ucrss -p $PROJECT_DIR/parameters/ucrss.txt -r $REF_SEQS -aO 10 --min_otu_size 1 --prefilter_percent_id 0.0", 5000),
("moving-pictures-otus/ucrss_wfilter/otu_table_mc1_w_tax.biom", "moving-pictures-otus/ucrss_wfilter/rep_set.tre", "pick_open_reference_otus.py -i $MOVING_PICTURES_SEQS -o $PROJECT_DIR/moving-pictures-otus/ucrss_wfilter -p $PROJECT_DIR/parameters/ucrss.txt -r $REF_SEQS -aO 10 --min_otu_size 1", 5000),

("moving-pictures-otus/uc_fast/otu_table.biom", "moving-pictures-otus/uc_fast/rep_set.tre", "pick_de_novo_otus.py -i $MOVING_PICTURES_SEQS -o $PROJECT_DIR/moving-pictures-otus/uc_fast -p $PROJECT_DIR/parameters/uc_fast.txt -aO 10", 5000),
("moving-pictures-otus/ucr_fast/otu_table.biom", "moving-pictures-otus/ucr_fast/rep_set.tre", "pick_de_novo_otus.py -i $MOVING_PICTURES_SEQS -o $PROJECT_DIR/moving-pictures-otus/ucr_fast -p $PROJECT_DIR/parameters/ucr_fast.txt -aO 10", 5000),
("moving-pictures-otus/ucrC_fast/otu_table.biom", "$REF_TREE", "pick_closed_reference_otus.py -i $MOVING_PICTURES_SEQS -o $PROJECT_DIR/moving-pictures-otus/ucrC_fast -p $PROJECT_DIR/parameters/ucrC_fast.txt -r $REF_SEQS -aO 10 -t $REF_TAX", 5000),
("moving-pictures-otus/ucrss_fast/otu_table_mc1_w_tax.biom", "moving-pictures-otus/ucrss_fast/rep_set.tre", "pick_open_reference_otus.py -i $MOVING_PICTURES_SEQS -o $PROJECT_DIR/moving-pictures-otus/ucrss_fast -p $PROJECT_DIR/parameters/ucrss_fast.txt -r $REF_SEQS -aO 10 --min_otu_size 1 --prefilter_percent_id 0.0", 5000),
("moving-pictures-otus/ucrss_fast_wfilter/otu_table_mc1_w_tax.biom", "moving-pictures-otus/ucrss_fast_wfilter/rep_set.tre", "pick_open_reference_otus.py -i $MOVING_PICTURES_SEQS -o $PROJECT_DIR/moving-pictures-otus/ucrss_fast_wfilter -p $PROJECT_DIR/parameters/ucrss_fast.txt -r $REF_SEQS -aO 10 --min_otu_size 1", 5000),

("whole-body-otus/uc/otu_table.biom", "whole-body-otus/uc/rep_set.tre", "pick_de_novo_otus.py -i $WHOLE_BODY_SEQS -o $PROJECT_DIR/whole-body-otus/uc -p $PROJECT_DIR/parameters/uc.txt -aO 10", 700),
("whole-body-otus/ucr/otu_table.biom", "whole-body-otus/ucr/rep_set.tre", "pick_de_novo_otus.py -i $WHOLE_BODY_SEQS -o $PROJECT_DIR/whole-body-otus/ucr -p $PROJECT_DIR/parameters/ucr.txt -aO 10", 700),
("whole-body-otus/ucrC/otu_table.biom", "$REF_TREE", "pick_closed_reference_otus.py -i $WHOLE_BODY_SEQS -o $PROJECT_DIR/whole-body-otus/ucrC -p $PROJECT_DIR/parameters/ucrC.txt -r $REF_SEQS -aO 10 -t $REF_TAX", 700),
("whole-body-otus/ucrss/otu_table_mc1_w_tax.biom", "whole-body-otus/ucrss/rep_set.tre", "pick_open_reference_otus.py -i $WHOLE_BODY_SEQS -o $PROJECT_DIR/whole-body-otus/ucrss -p $PROJECT_DIR/parameters/ucrss.txt -r $REF_SEQS -aO 10  --min_otu_size 1 --prefilter_percent_id 0.0", 700),
("whole-body-otus/ucrss_wfilter/otu_table_mc1_w_tax.biom", "whole-body-otus/ucrss_wfilter/rep_set.tre", "pick_open_reference_otus.py -i $WHOLE_BODY_SEQS -o $PROJECT_DIR/whole-body-otus/ucrss_wfilter -p $PROJECT_DIR/parameters/ucrss.txt -r $REF_SEQS -aO 10 --min_otu_size 1", 700),

("whole-body-otus/uc_fast/otu_table.biom", "whole-body-otus/uc_fast/rep_set.tre", "pick_de_novo_otus.py -i $WHOLE_BODY_SEQS -o $PROJECT_DIR/whole-body-otus/uc_fast -p $PROJECT_DIR/parameters/uc_fast.txt -aO 10", 700),
("whole-body-otus/ucr_fast/otu_table.biom", "whole-body-otus/ucr_fast/rep_set.tre", "pick_de_novo_otus.py -i $WHOLE_BODY_SEQS -o $PROJECT_DIR/whole-body-otus/ucr_fast -p $PROJECT_DIR/parameters/ucr_fast.txt -aO 10", 700),
("whole-body-otus/ucrC_fast/otu_table.biom", "$REF_TREE", "pick_closed_reference_otus.py -i $WHOLE_BODY_SEQS -o $PROJECT_DIR/whole-body-otus/ucrC_fast -p $PROJECT_DIR/parameters/ucrC_fast.txt -r $REF_SEQS -aO 10 -t $REF_TAX", 700),
("whole-body-otus/ucrss_fast/otu_table_mc1_w_tax.biom", "whole-body-otus/ucrss_fast/rep_set.tre", "pick_open_reference_otus.py -i $WHOLE_BODY_SEQS -o $PROJECT_DIR/whole-body-otus/ucrss_fast -p $PROJECT_DIR/parameters/ucrss_fast.txt -r $REF_SEQS -aO 10  --min_otu_size 1 --prefilter_percent_id 0.0", 700),
("whole-body-otus/ucrss_fast_wfilter/otu_table_mc1_w_tax.biom", "whole-body-otus/ucrss_fast_wfilter/rep_set.tre", "pick_open_reference_otus.py -i $WHOLE_BODY_SEQS -o $PROJECT_DIR/whole-body-otus/ucrss_fast_wfilter -p $PROJECT_DIR/parameters/ucrss_fast.txt -r $REF_SEQS -aO 10 --min_otu_size 1", 700),

("88-soils-otus/uc/otu_table.biom", "88-soils-otus/uc/rep_set.tre", "pick_de_novo_otus.py -i $SOILS_SEQS -o $PROJECT_DIR/88-soils-otus/uc -p $PROJECT_DIR/parameters/uc.txt -aO 10", 400),
("88-soils-otus/ucr/otu_table.biom", "88-soils-otus/ucr/rep_set.tre", "pick_de_novo_otus.py -i $SOILS_SEQS -o $PROJECT_DIR/88-soils-otus/ucr -p $PROJECT_DIR/parameters/ucr.txt -aO 10", 400),
("88-soils-otus/ucrC/otu_table.biom", "$REF_TREE", "pick_closed_reference_otus.py -i $SOILS_SEQS -o $PROJECT_DIR/88-soils-otus/ucrC -p $PROJECT_DIR/parameters/ucrC.txt -r $REF_SEQS -aO 10 -t $REF_TAX", 400),
("88-soils-otus/ucrss/otu_table_mc1_w_tax.biom", "88-soils-otus/ucrss/rep_set.tre", "pick_open_reference_otus.py -i $SOILS_SEQS -o $PROJECT_DIR/88-soils-otus/ucrss -p $PROJECT_DIR/parameters/ucrss.txt -r $REF_SEQS -aO 10 --min_otu_size 1 --prefilter_percent_id 0.0", 400),
("88-soils-otus/ucrss_wfilter/otu_table_mc1_w_tax.biom", "88-soils-otus/ucrss_wfilter/rep_set.tre", "pick_open_reference_otus.py -i $SOILS_SEQS -o $PROJECT_DIR/88-soils-otus/ucrss_wfilter -p $PROJECT_DIR/parameters/ucrss.txt -r $REF_SEQS -aO 10 --min_otu_size 1", 400),

("88-soils-otus/uc_fast/otu_table.biom", "88-soils-otus/uc_fast/rep_set.tre", "pick_de_novo_otus.py -i $SOILS_SEQS -o $PROJECT_DIR/88-soils-otus/uc_fast -p $PROJECT_DIR/parameters/uc_fast.txt -aO 10", 400),
("88-soils-otus/ucr_fast/otu_table.biom", "88-soils-otus/ucr_fast/rep_set.tre", "pick_de_novo_otus.py -i $SOILS_SEQS -o $PROJECT_DIR/88-soils-otus/ucr_fast -p $PROJECT_DIR/parameters/ucr_fast.txt -aO 10", 400),
("88-soils-otus/ucrC_fast/otu_table.biom", "$REF_TREE", "pick_closed_reference_otus.py -i $SOILS_SEQS -o $PROJECT_DIR/88-soils-otus/ucrC_fast -p $PROJECT_DIR/parameters/ucrC_fast.txt -r $REF_SEQS -aO 10 -t $REF_TAX", 400),
("88-soils-otus/ucrss_fast/otu_table_mc1_w_tax.biom", "88-soils-otus/ucrss_fast/rep_set.tre", "pick_open_reference_otus.py -i $SOILS_SEQS -o $PROJECT_DIR/88-soils-otus/ucrss_fast -p $PROJECT_DIR/parameters/ucrss_fast.txt -r $REF_SEQS -aO 10 --min_otu_size 1 --prefilter_percent_id 0.0", 400),
("88-soils-otus/ucrss_fast_wfilter/otu_table_mc1_w_tax.biom", "88-soils-otus/ucrss_fast_wfilter/rep_set.tre", "pick_open_reference_otus.py -i $SOILS_SEQS -o $PROJECT_DIR/88-soils-otus/ucrss_fast_wfilter -p $PROJECT_DIR/parameters/ucrss_fast.txt -r $REF_SEQS -aO 10 --min_otu_size 1", 400)]

Perform analyses:


# generate BIOM table summaries
for e in l:
    biom_fp = e[0]
    summ_fp = biom_fp.replace('.biom', '_summ.txt')
    cmd = "biom summarize-table -i %s -o %s" % (biom_fp, summ_fp)
    !$cmd

# generate rarified otu tables
for e in l:
    in_fp = e[0]
    d = e[3]
    out_fp = e[0].replace('.biom', '_even%d.biom' % d)
    cmd = 'echo "cd /home/caporaso/analysis/2014.04.16-ss-otus ; single_rarefaction.py -i %s -o %s -d %d" | qsub -keo -N sr' % (in_fp, out_fp, d)
    !$cmd

# run alpha diversity and beta diversity
for e in l:
    full_otu_table_fp = e[0]
    tree_fp = e[1]
    d = e[3]
    in_fp = full_otu_table_fp.replace('.biom', '_even%d.biom' % d)
    input_dir = split(full_otu_table_fp)[0]
    alpha_out_fp = join(input_dir,'adiv_even%d.txt' % d)
    beta_out_dir = join(input_dir,'bdiv_even%d' % d)
    alpha_cmd = 'cd /home/caporaso/analysis/2014.04.16-ss-otus; source config-env.sh ; echo "cd /home/caporaso/analysis/2014.04.16-ss-otus ; source config-env.sh ; alpha_diversity.py -i %s -o %s -m observed_species,PD_whole_tree -t %s" | qsub -keo -N adiv' % (in_fp, alpha_out_fp, tree_fp)
    beta_cmd = 'cd /home/caporaso/analysis/2014.04.16-ss-otus; source config-env.sh ; echo "cd /home/caporaso/analysis/2014.04.16-ss-otus ; source config-env.sh ; beta_diversity.py -i %s -o %s -t %s" | qsub -keo -N bdiv' % (in_fp, beta_out_dir, tree_fp)
    !$alpha_cmd
    !$beta_cmd

# compute taxa summary tables and gzip them
for e in l:
    full_otu_table_fp = e[0]
    input_dir = split(full_otu_table_fp)[0]
    cmd = 'echo "cd /home/caporaso/analysis/2014.04.16-ss-otus; summarize_taxa.py -i %s -o %s/taxa_tables -L 2,3,4,5,6,7 --suppress_biom_table_output" | qsub ' % (full_otu_table_fp, input_dir)
    !$cmd

fps = glob('*otus/*/taxa_tables/*txt')
for fp in fps:
    cmd = 'gzip %s' % fp
    !$cmd

# run group significance (moving pictures)
for e in l[:10]:
    full_otu_table_fp = e[0]
    d = e[3]
    in_fp = full_otu_table_fp.replace('.biom', '_even%d.biom' % d)
    input_dir = split(full_otu_table_fp)[0]
    out_fp = join(input_dir,'group_significance_even%d.txt' % d)
    group_sig_cmd = "cd /home/caporaso/analysis/2014.04.16-ss-otus ; source config-env.sh ; group_significance.py -i %s -m %s -o %s -c %s" % (in_fp, "$MOVING_PICTURES_MAP", out_fp, "BODY_SITE")
    cmd = 'cd /home/caporaso/analysis/2014.04.16-ss-otus ; source config-env.sh ; echo "%s" | qsub -keo -N gs' % group_sig_cmd
    !$cmd

# run group significance (whole body)
for e in l[10:20]:
    full_otu_table_fp = e[0]
    d = e[3]
    in_fp = full_otu_table_fp.replace('.biom', '_even%d.biom' % d)
    input_dir = split(full_otu_table_fp)[0]
    out_fp = join(input_dir,'group_significance_even%d.txt' % d)
    group_sig_cmd = "cd /home/caporaso/analysis/2014.04.16-ss-otus ; source config-env.sh ; group_significance.py -i %s -m %s -o %s -c %s" % (in_fp, "$WHOLE_BODY_MAP", out_fp, 'body_habitat_basic')
    cmd = 'cd /home/caporaso/analysis/2014.04.16-ss-otus ; source config-env.sh ; echo "%s" | qsub -keo -N gs' % group_sig_cmd
    !$cmd

# run group significance (88-soils)
for e in l[20:]:
    full_otu_table_fp = e[0]
    d = e[3]
    in_fp = full_otu_table_fp.replace('.biom', '_even%d.biom' % d)
    input_dir = split(full_otu_table_fp)[0]
    out_fp = join(input_dir,'group_significance_even%d.txt' % d)
    group_sig_cmd = "cd /home/caporaso/analysis/2014.04.16-ss-otus ; source config-env.sh ; group_significance.py -i %s -m %s -o %s -c %s" % (in_fp, "$SOILS_MAP", out_fp, "ph_bin")
    cmd = 'cd /home/caporaso/analysis/2014.04.16-ss-otus ; source config-env.sh ; echo "%s" | qsub -keo -N gs' % group_sig_cmd
    !$cmd


# run mantel tests
def get_unifrac_dm_fp(e, metric_name):
    full_otu_table_fp = e[0]
    d = e[3]
    in_fp = full_otu_table_fp.replace('.biom', '_even%d.biom' % d)
    bdiv_dir = join(split(full_otu_table_fp)[0], 'bdiv_even%d' % d)
    dm_fp = ''.join([metric_name, '_',
                     splitext(split(in_fp)[1])[0],
                     '.txt'])
    return join(bdiv_dir,dm_fp)

datasets = [('moving-pictures-otus', range(10)),
            ('whole-body-otus', range(10,20)),
            ('88-soils-otus',range(20,30))]
for metric in ['unweighted_unifrac', 'weighted_unifrac']:
    for otu_dir, data_range in datasets:
        dm_fps = \
            [get_unifrac_dm_fp(l[i], metric) for i in data_range]
        mantel_fp = join(
            otu_dir, '%s_mantel_results.txt' % metric)
        cmp_cmd = 'compare_distance_matrices.py -i %s -o %s --method mantel -n 999' %\
            (','.join(dm_fps), mantel_fp)
        cmd = 'echo "cd /home/caporaso/analysis/2014.04.16-ss-otus ; source config-env.sh ; %s" | qsub -keo -N cmp_dist' % cmp_cmd
        !$cmd

# taxa correlation analysis
for data_set_id in data_set_ids:
    for level in range(2,8):
        for i, method1 in enumerate(order):
            curr_results[method1] = {}
            fp1 = glob("%s-otus/%s/taxa_tables/*L%d.txt.gz" % (data_set_id, method1, level))[0]
            s1 = pd.io.parsers.read_csv(fp1, sep='\t', compression='gzip',index_col=0).stack()
            for method2 in order[:i]:
                fp2 = glob("%s-otus/%s/taxa_tables/*L%d.txt.gz" % (data_set_id, method2, level))[0]
                s2 = pd.io.parsers.read_csv(fp2, sep='\t', compression='gzip',index_col=0).stack()
                curr_results[method1][method2] = s1.corr(s2, method='pearson')
        df = pd.DataFrame(curr_results)
        df = df.reindex_axis(order,axis=0).reindex_axis(order,axis=1)
        df.to_csv("%s-otus/taxa_correlations/level_%d.csv" % (data_set_id, level))

QIIME config information

$ print_qiime_config.py

System information
==================
         Platform:	linux2
   Python version:	2.7.3 (default, May  3 2013, 07:17:12)  [GCC 4.4.7 20120313 (Red Hat 4.4.7-3)]
Python executable:	/data/qiime_software/python-2.7.3-release/bin/python

Dependency versions
===================
                     PyCogent version:	1.5.3
                        NumPy version:	1.7.1
                        SciPy version:	0.13.3
                   matplotlib version:	1.3.1
                  biom-format version:	1.3.1
                         qcli version:	0.1.0
                         pyqi version:	0.3.1
                   scikit-bio version:	0.0.0-dev
                QIIME library version:	1.8.0-dev, master@3a5ac1d
                 QIIME script version:	1.8.0-dev
        PyNAST version (if installed):	1.2.2
                      Emperor version:	0.9.3
RDP Classifier version (if installed):	rdp_classifier-2.2.jar
          Java version (if installed):	1.6.0_24

QIIME config values
===================
                     blastmat_dir:	/data/qiime_software/blast-2.2.22-release/data
                    python_exe_fp:	/data/qiime_software/python-2.7.3-release/bin/python
                         sc_queue:	all.q
   template_alignment_lanemask_fp:	/data/lanemask_in_1s_and_0s
     pynast_template_alignment_fp:	/data/core_set_aligned.fasta.imputed
                      working_dir:	/tmp/
                 seconds_to_sleep:	1
pynast_template_alignment_blastdb:	None
assign_taxonomy_reference_seqs_fp:	/data/gg_13_8_otus/rep_set/97_otus.fasta
                     torque_queue:	friendlyq
      topiaryexplorer_project_dir:	None
                    jobs_to_start:	1
                cloud_environment:	False
                qiime_scripts_dir:	/data/qiime_software/qiime-1.8.0-repository-779803b3/bin
            denoiser_min_per_core:	50
                  cluster_jobs_fp:	start_parallel_jobs_torque.py
assign_taxonomy_id_to_taxonomy_fp:	/data/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
                         temp_dir:	/home/caporaso/temp/
                      blastall_fp:	/data/qiime_software/blast-2.2.22-release/bin/blastall

Temporary notes

echo "cd /home/caporaso/analysis/2014.04.16-ss-otus; source config-env.sh; pick_open_reference_otus.py -i $MOVING_PICTURES_SEQS -o $PROJECT_DIR/moving-pictures-otus/ucrss_fast_O29_r73 -p $PROJECT_DIR/parameters/ucrss_fast.txt -r $REF_SEQS_73 -aO 29 --min_otu_size 1 --prefilter_percent_id 0.0" | qsub -keo -N mp-73

echo "cd /home/caporaso/analysis/2014.04.16-ss-otus; source config-env.sh; pick_de_novo_otus.py -i $MOVING_PICTURES_SEQS -o $PROJECT_DIR/moving-pictures-otus/ucr_fast_O29_r97 -p $PROJECT_DIR/parameters/ucr_fast.txt -aO 29 ; pick_open_reference_otus.py -i $MOVING_PICTURES_SEQS -o $PROJECT_DIR/moving-pictures-otus/ucrss_fast_O29_r97 -p $PROJECT_DIR/parameters/ucrss_fast.txt -r $REF_SEQS -aO 29 --min_otu_size 1 --prefilter_percent_id 0.0" | qsub -keo -N mp-97

echo "cd /home/caporaso/analysis/2014.04.16-ss-otus; source config-env.sh; pick_open_reference_otus.py -i $MOVING_PICTURES_SEQS -o $PROJECT_DIR/moving-pictures-otus/ucrss_fast_O29_s1 -p $PROJECT_DIR/parameters/ucrss_fast.txt -r $REF_SEQS -aO 29 --min_otu_size 1 -s 0.1 --prefilter_percent_id 0.0" | qsub -keo -N mp-97


echo "cd /home/caporaso/analysis/2014.04.16-ss-otus; source config-env.sh; pick_de_novo_otus.py -i $MOVING_PICTURES_SEQS -o $PROJECT_DIR/moving-pictures-otus/ucr_fast_O29_r73 -p $PROJECT_DIR/parameters/ucr_fast_r73.txt -aO 29 ; pick_open_reference_otus.py -i $MOVING_PICTURES_SEQS -o $PROJECT_DIR/moving-pictures-otus/ucrss_fast_O29_r82 -p $PROJECT_DIR/parameters/ucrss_fast.txt -r $REF_SEQS_82 -aO 29 --min_otu_size 1 --prefilter_percent_id 0.0 ; pick_de_novo_otus.py -i $MOVING_PICTURES_SEQS -o $PROJECT_DIR/moving-pictures-otus/ucr_fast_O29_r82 -p $PROJECT_DIR/parameters/ucr_fast_r82.txt -aO 29 ; pick_open_reference_otus.py -i $MOVING_PICTURES_SEQS -o $PROJECT_DIR/moving-pictures-otus/ucrss_fast_O29_r61 -p $PROJECT_DIR/parameters/ucrss_fast.txt -r $REF_SEQS_61 -aO 29 --min_otu_size 1 --prefilter_percent_id 0.0 ; pick_de_novo_otus.py -i $MOVING_PICTURES_SEQS -o $PROJECT_DIR/moving-pictures-otus/ucr_fast_O29_r61 -p $PROJECT_DIR/parameters/ucr_fast_r61.txt -aO 29" | qsub -keo -N mp-runtime

About

Comparative analysis of high-level OTU picking protocols

www.caporasolab.us

License:BSD 3-Clause "New" or "Revised" License

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