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remove bold2amptk and update tabs in taxonomy doc
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Jon Palmer committed Feb 20, 2019
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80 changes: 40 additions & 40 deletions docs/taxonomy.rst
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Expand Up @@ -91,22 +91,22 @@ These databases were created from Unite v8.0, first downloading two databases fr
.. code-block:: none
#Create full length ITS USEARCH Database, convert taxonomy, and create USEARCH database
amptk database -i UNITE_public_all_02.02.2019.fasta -f ITS1-F -r ITS4 \
--primer_required none -o ITS --create_db usearch --install --source UNITE:8.0
#create SINTAX database
amptk database -i UNITE_public_all_02.02.2019.fasta -f ITS1-F -r ITS4 \
--primer_required none -o ITS --create_db usearch --install --source UNITE:8.0
#create SINTAX database
amptk database -i sh_general_release_dynamic_all_02.02.2019_dev.fasta \
-o ITS_SINTAX --create_db utax -f ITS1-F -r ITS4 --derep_fulllength \
--install --source UNITE:8.0 --primer_required none
--install --source UNITE:8.0 --primer_required none
#Create UTAX Databases
amptk database -i sh_general_release_dynamic_all_02.02.2019_dev.fasta \
-o ITS_UTAX --create_db utax -f ITS1-F -r ITS4 \
--derep_fulllength --install --source UNITE:8.0 --primer_required none
amptk database -i sh_general_release_dynamic_all_02.02.2019_dev.fasta \
-o ITS1_UTAX -f ITS1-F -r ITS2 --primer_required rev --derep_fulllength \
--create_db utax --install --subsample 65000 --source UNITE:8.0
amptk database -i sh_general_release_dynamic_all_02.02.2019_dev.fasta \
-o ITS1_UTAX -f ITS1-F -r ITS2 --primer_required rev --derep_fulllength \
--create_db utax --install --subsample 65000 --source UNITE:8.0
amptk database -i sh_general_release_dynamic_all_02.02.2019_dev.fasta \
-o ITS2_UTAX --create_db utax -f fITS7 -r ITS4 --derep_fulllength \
Expand All @@ -130,63 +130,63 @@ Since it can literally take days to download the arthropod dataset, if you'd lik
cat arthropods.bold-reformated.fa chordates.bold-reformated.fa > arth-chord.bold-reformated.fasta
#generate global alignment database
amptk database -i arth-chord.bold.reformated.fasta -f LCO1490 -r mlCOIintR --primer_required none \
--derep_fulllength --format off --primer_mismatch 4 -o COI --min_len 200 --create_db usearch \
--install --source BOLD:20190219
amptk database -i arth-chord.bold.reformated.fasta -f LCO1490 -r mlCOIintR --primer_required none \
--derep_fulllength --format off --primer_mismatch 4 -o COI --min_len 200 --create_db usearch \
--install --source BOLD:20190219
The second set of output files from `bold2utax.py` are named with `.BIN-consensus.fa` which are the result of 99% clustering for each BIN. We will combine those for the two datasets and then use those data to generate the SINTAX and UTAX databases.

.. code-block:: none
#combine datasets
cat arthropods.BIN-consensus.fa chordates.BIN-consensus.fa > arth-chord.bold.BIN-consensus.fasta
#combine datasets
cat arthropods.BIN-consensus.fa chordates.BIN-consensus.fa > arth-chord.bold.BIN-consensus.fasta
#generate SINTAX database
amptk database -i arth-chord.bold.BIN-consensus.fasta -f LCO1490 -r mlCOIintR --primer_required none \
--derep_fulllength --format off --primer_mismatch 4 -o COI_SINTAX --min_len 200 --create_db sintax \
--install --source BOLD:20190219
#generate UTAX database, need to subsample for memory issues with 32 bit usearch and we require rev primer match here
amptk database -i arth-chord.bold.BIN-consensus.fasta -f LCO1490 -r mlCOIintR --primer_required rev \
--derep_fulllength --format off --subsample 30000 --primer_mismatch 4 -o COI_UTAX --min_len 200 \
--create_db utax --install --source BOLD:20190219
#generate SINTAX database
amptk database -i arth-chord.bold.BIN-consensus.fasta -f LCO1490 -r mlCOIintR --primer_required none \
--derep_fulllength --format off --primer_mismatch 4 -o COI_SINTAX --min_len 200 --create_db sintax \
--install --source BOLD:20190219
#generate UTAX database, need to subsample for memory issues with 32 bit usearch and we require rev primer match here
amptk database -i arth-chord.bold.BIN-consensus.fasta -f LCO1490 -r mlCOIintR --primer_required rev \
--derep_fulllength --format off --subsample 00000 --primer_mismatch 4 -o COI_UTAX --min_len 200 \
--create_db utax --install --source BOLD:20190219
**LSU database**

The fungal 28S database (LSU) was downloaded from `RDP <http://rdp.cme.msu.edu/download/current_Fungi_unaligned.fa.gz>`_. The sequences were then converted into AMPtk databases as follows:

.. code-block:: none
amptk database -i RDP_v8.0_fungi.fa -o LSU --format rdp2utax --primer_required none \
--skip_trimming --create_db usearch --derep_fulllength --install --source RDP:8
amptk database -i RDP_v8.0_fungi.fa -o LSU --format rdp2utax --primer_required none \
--skip_trimming --create_db usearch --derep_fulllength --install --source RDP:8
amptk database -i RDP_v8.0_fungi.fa -o LSU_SINTAX --format rdp2utax --primer_required none \
--skip_trimming --create_db sintax --derep_fulllength --install --source RDP:8
amptk database -i RDP_v8.0_fungi.fa -o LSU_SINTAX --format rdp2utax --primer_required none \
--skip_trimming --create_db sintax --derep_fulllength --install --source RDP:8
amptk database -i RDP_v8.0_fungi.fa -o LSU_UTAX --format rdp2utax --primer_required none \
--skip_trimming --create_db utax --derep_fulllength --install --source RDP:8 --subsample 4500
amptk database -i RDP_v8.0_fungi.fa -o LSU_UTAX --format rdp2utax --primer_required none \
--skip_trimming --create_db utax --derep_fulllength --install --source RDP:8 --subsample 45000
To generate a training set for UTAX, the sequences were first dereplicated, and clustered at 97% to get representative sequences for training. This training set was then converted to a UTAX database:

.. code-block:: none
amptk database -i fungi.trimmed.fa -o LSU_UTAX --format off \
--skip_trimming --create_db utax --keep_all --install
amptk database -i fungi.trimmed.fa -o LSU_UTAX --format off \
--skip_trimming --create_db utax --keep_all --install
**16S database**
This is downloaded from `R. Edgar's website <http://drive5.com/utax/data/rdp_v16.tar.gz>`_ and then formatted for AMPtk. Note there is room for substantial improvement here, I just don't typically work on 16S - so please let me know if you want some suggestions on what to do here. Here I reformatted the "domain" taxonomy level to "kingdom" for simplicity (even though I know it is taxonomically incorrect).

.. code-block:: none
amptk database -i rdp_16s_v16_sp.kingdom.fa -o 16S --format off --create_db usearch \
--skip_trimming --install --primer_required none --derep_fulllength
amptk database -i rdp_16s_v16_sp.kingdom.fa -o 16S --format off --create_db sintax \
-f 515FB -r 806RB --install --primer_required for --derep_fulllength
amptk database -i rdp_16s_v16_sp.kingdom.fa -o 16S --format off --create_db usearch \
--skip_trimming --install --primer_required none --derep_fulllength
amptk database -i rdp_16s_v16_sp.kingdom.fa -o 16S_SINTAX --format off --create_db sintax \
-f 515FB -r 806RB --install --primer_required for --derep_fulllength
amptk database -i rdp_16s_v16_sp.kingdom.fa -o 16S_UTAX --format off --create_db sintax \
-f 515FB -r 806RB --install --primer_required for --derep_fulllength
Checking Installed Databases
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2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -117,7 +117,7 @@ def run(self):
extras_require=EXTRAS,
include_package_data=True,
license='BSD-2',
scripts=['scripts/amptk', 'scripts/bold2amptk.py', 'scripts/bold2utax.py', 'scripts/amptk_synthetic_mock.py'],
scripts=['scripts/amptk', 'scripts/bold2utax.py', 'scripts/amptk_synthetic_mock.py'],
classifiers=[
# Trove classifiers
# Full list: https://pypi.python.org/pypi?%3Aaction=list_classifiers
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