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adding Woltka v0.1.6, pairends #30

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Sep 12, 2024
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18 changes: 9 additions & 9 deletions .github/workflows/qiita-plugin-ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -76,8 +76,8 @@ jobs:
shell: bash -l {0}
run: |
conda config --add channels bioconda
conda create --yes -n qp-woltka-0.1.4 python=3.9 biom-format bowtie2
conda activate qp-woltka-0.1.4
conda create --yes -n qp-woltka python=3.9 biom-format bowtie2
conda activate qp-woltka
# bowtie2==2.5.0 is what's installed in main qiita so making sure we keep
# using the same version for consistency; note that we will need to force
conda install --yes -c bioconda bowtie2==2.5.0
Expand All @@ -87,7 +87,7 @@ jobs:
pip --quiet install -U pip pip nose flake8
pip --quiet install https://github.com/qiita-spots/qiita_client/archive/master.zip

export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
export QC_WOLTKA_DB_DP=$PWD/qp_woltka/databases/woltka/
export QC_WOLTKA_SYNDNA_DB_DP=$PWD/qp_woltka/databases/synDNA
Expand All @@ -96,12 +96,12 @@ jobs:

woltka_version=`woltka --version`
bowtie2_version=`bowtie2 --version`
if [[ $woltka_version != *"0.1.4"* ]]; then echo "wrong woltka version", $woltka_version; exit 1; fi
if [[ $woltka_version != *"0.1.6"* ]]; then echo "wrong woltka version", $woltka_version; exit 1; fi
if [[ $bowtie2_version != *"2.5.0"* ]]; then echo "wrong bowtie2 version", $bowtie2_version; exit 1; fi

export ENVIRONMENT="source /home/runner/.profile; conda activate qp-woltka; export QC_WOLTKA_DB_DP=$PWD/qp_woltka/databases/woltka/; export QC_WOLTKA_SYNDNA_DB_DP=$PWD/qp_woltka/databases/synDNA"

configure_woltka --env-script 'source /home/runner/.profile; conda activate qp-woltka-0.1.4; export QC_WOLTKA_DB_DP=$PWD/qp_woltka/databases/woltka/; export QC_WOLTKA_SYNDNA_DB_DP=$PWD/qp_woltka/databases/synDNA; export ENVIRONMENT="source /home/runner/.profile; conda activate qp-woltka-0.1.4; export QC_WOLTKA_DB_DP=$PWD/qp_woltka/databases/woltka/; export QC_WOLTKA_SYNDNA_DB_DP=$PWD/qp_woltka/databases/synDNA"' --server-cert $QIITA_SERVER_CERT
configure_woltka --env-script 'source /home/runner/.profile; conda activate qp-woltka; export QC_WOLTKA_DB_DP=$PWD/qp_woltka/databases/woltka/; export QC_WOLTKA_SYNDNA_DB_DP=$PWD/qp_woltka/databases/synDNA; export ENVIRONMENT="source /home/runner/.profile; conda activate qp-woltka; export QC_WOLTKA_DB_DP=$PWD/qp_woltka/databases/woltka/; export QC_WOLTKA_SYNDNA_DB_DP=$PWD/qp_woltka/databases/synDNA"' --ca-cert $QIITA_ROOTCA_CERT

echo "Available Qiita plugins"
ls ~/.qiita_plugins/
Expand All @@ -110,7 +110,7 @@ jobs:
shell: bash -l {0}
run: |
conda activate qiita
export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
sed "s#/home/runner/work/qiita/qiita#${PWD}/qiita-dev/#g" `pwd`/qiita-dev/qiita_core/support_files/config_test.cfg > ${QIITA_CONFIG_FP}

Expand Down Expand Up @@ -141,10 +141,10 @@ jobs:
env:
COVER_PACKAGE: ${{ matrix.cover_package }}
run: |
conda activate qp-woltka-0.1.4
export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
conda activate qp-woltka
export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
export ENVIRONMENT="source /home/runner/.profile; conda activate qp-woltka-0.1.4; export QC_WOLTKA_DB_DP=$PWD/qp_woltka/databases/woltka/; export QC_WOLTKA_SYNDNA_DB_DP=$PWD/qp_woltka/databases/synDNA"
export ENVIRONMENT="source /home/runner/.profile; conda activate qp-woltka; export QC_WOLTKA_DB_DP=$PWD/qp_woltka/databases/woltka/; export QC_WOLTKA_SYNDNA_DB_DP=$PWD/qp_woltka/databases/synDNA"
export QC_WOLTKA_DB_DP=$PWD/qp_woltka/databases/woltka/
export QC_WOLTKA_SYNDNA_DB_DP=$PWD/qp_woltka/databases/synDNA
export PYTHONWARNINGS="ignore:Certificate for localhost has no \`subjectAltName\`"
Expand Down
4 changes: 2 additions & 2 deletions qp_woltka/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,6 @@
}
outputs = {
# taxonomic
'Alignment Profile': 'BIOM',
'Per genome Predictions': 'BIOM',
'Per gene Predictions': 'BIOM',
# functional
Expand All @@ -37,7 +36,8 @@
}
dflt_param_set = generate_woltka_dflt_params()
woltka_cmd = QiitaCommand(
'Woltka v0.1.4', "Functional and Taxonomic Predictions", woltka,
'Woltka v0.1.6, paired-end',
"Functional and Taxonomic Predictions", woltka,
req_params, opt_params, outputs, dflt_param_set)
plugin.register_command(woltka_cmd)

Expand Down
3 changes: 3 additions & 0 deletions qp_woltka/support_files/files_list.tsv
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
filename_1 filename_2 record_count
/tmp/folder/S22205_S104_L001_R1_001.fastq.gz /tmp/folder/S22205_S104_L001_R2_001.fastq.gz 1000000
/tmp/folder/S22282_S102_L001_R1_001.fastq.gz /tmp/folder/S22282_S102_L001_R2_001.fastq.gz 1000000
Binary file removed qp_woltka/support_files/free.biom
Binary file not shown.
36 changes: 36 additions & 0 deletions qp_woltka/support_files/summary.html
Original file line number Diff line number Diff line change
@@ -0,0 +1,36 @@
<table border="1" class="dataframe">
<thead>
<tr style="text-align: right;">
<th>filename</th>
<th>md5</th>
<th>file_type</th>
<th>reads</th>
</tr>
</thead>
<tbody>
<tr>
<td>S22205_S104_L001_R1_001.fastq.gz</td>
<td>9dcfb0c77674fdada176262963196db0</td>
<td>raw_forward_seqs</td>
<td>1000000</td>
</tr>
<tr>
<td>S22282_S102_L001_R1_001.fastq.gz</td>
<td>9dcfb0c77674fdada176262963196db0</td>
<td>raw_forward_seqs</td>
<td>1000000</td>
</tr>
<tr>
<td>S22205_S104_L001_R2_001.fastq.gz</td>
<td>9dcfb0c77674fdada176262963196db0</td>
<td>raw_reverse_seqs</td>
<td>1000000</td>
</tr>
<tr>
<td>S22282_S102_L001_R2_001.fastq.gz</td>
<td>9dcfb0c77674fdada176262963196db0</td>
<td>raw_reverse_seqs</td>
<td>1000000</td>
</tr>
</tbody>
</table>
41 changes: 1 addition & 40 deletions qp_woltka/tests/test_util.py
Original file line number Diff line number Diff line change
Expand Up @@ -9,13 +9,9 @@
from unittest import main, TestCase
from os import environ
from os.path import join
from tempfile import TemporaryDirectory
import gzip
import io
import pandas as pd

from qp_woltka.util import (
get_dbs, generate_woltka_dflt_params, mux, demux, search_by_filename,
get_dbs, generate_woltka_dflt_params, search_by_filename,
merge_ranges, coverage_percentage)


Expand All @@ -38,41 +34,6 @@ def test_generate_woltka_dflt_params(self):

self.assertDictEqual(obs, exp)

def test_mux(self):
f1 = b"@foo\nATGC\n+\nIIII\n"
f2 = b"@bar\nAAAA\n+\nIIII\n"
exp = b"@foo@@@foofile\nATGC\n+\nIIII\n@bar@@@barfile\nAAAA\n+\nIIII\n"
with TemporaryDirectory() as d:
f1fp = join(d, 'foofile.fastq')
f2fp = join(d, 'barfile.fastq')
ofp = join(d, 'output')
with gzip.open(f1fp, 'wb') as fp:
fp.write(f1)
with gzip.open(f2fp, 'wb') as fp:
fp.write(f2)
with open(ofp, 'wb') as output:
mux([f1fp, f2fp], output)
with open(ofp, 'rb') as result:
obs = result.read()

self.assertEqual(obs, exp)

def test_demux(self):
prep = pd.DataFrame([['sample_foo', 'foofile'],
['sample_bar', 'barfile']],
columns=['sample_name', 'run_prefix'])
input_ = io.BytesIO(b"foo@@@foofile_R1\tATGC\t+\tIIII\nbar@@@"
b"barfile_R2\tAAAA\t+\tIIII\n")
expfoo = b"foo\tATGC\t+\tIIII\n"
expbar = b"bar\tAAAA\t+\tIIII\n"
with TemporaryDirectory() as d:
demux(input_, d.encode('ascii'), prep)
foo = open(join(d, 'sample_foo.sam'), 'rb').read()
bar = open(join(d, 'sample_bar.sam'), 'rb').read()

self.assertEqual(foo, expfoo)
self.assertEqual(bar, expbar)

def test_search_by_filename(self):
lookup = {'foo_bar': 'baz',
'foo': 'bar'}
Expand Down
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