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Merge pull request #97 from bigbio/dev
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first attempt to change from csv to parquet
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ypriverol authored Aug 2, 2024
2 parents 5bce450 + 4d3f509 commit d2965ef
Showing 11 changed files with 255 additions and 220 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/python-package.yml
Original file line number Diff line number Diff line change
@@ -16,7 +16,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: [3.7, 3.8, 3.9, 3.11]
python-version: [3.8, 3.9, 3.11]

steps:
- uses: actions/checkout@v2
1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -133,3 +133,4 @@ dmypy.json
.pyre/

.idea
/quantms.db
15 changes: 15 additions & 0 deletions environment.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
name: pmultiqc
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- multiqc==1.23
- pandas
- pyteomics
- pyopenms
- sdrf-pipelines >= 0.0.28
- lxml
- numpy == 1.24.3
- pyarrow

4 changes: 2 additions & 2 deletions pmultiqc/main.py
Original file line number Diff line number Diff line change
@@ -6,7 +6,7 @@
from __future__ import print_function
from pkg_resources import get_distribution
import logging
from multiqc.utils import config
from multiqc import config

# Initialise the main MultiQC logger
log = logging.getLogger('pmultiqc')
@@ -44,7 +44,7 @@ def pmultiqc_plugin_execution_start():
config.update_dict(config.sp, {'quantms/mzML': {'fn': '*.mzML', 'num_lines': 0}})

if 'quantms/ms_info' not in config.sp:
config.update_dict(config.sp, {'quantms/ms_info': {'fn': '*_ms_info.tsv', 'num_lines': 0}})
config.update_dict(config.sp, {'quantms/ms_info': {'fn': '*_ms_info.parquet', 'num_lines': 0}})

if 'quantms/idXML' not in config.sp:
config.update_dict(config.sp, {'quantms/idXML': {'fn': '*.idXML', 'num_lines': 0}})
7 changes: 0 additions & 7 deletions pmultiqc/modules/quantms/histogram.py
Original file line number Diff line number Diff line change
@@ -155,12 +155,5 @@ def to_dict(self, percentage = False, cats = None):
for i in self.bins:
self.cats[i] = dict()
self.cats[i]['name'] = i
if self.plot_category == 1:
self.cats[i]['description'] = self.description + ' ' + \
(self.bins[-1] if i == self.bins[-1] else 'is ' + i)
elif self.plot_category == 2:
self.cats[i]['description'] = self.description + ' ' + \
(self.bins[-1] if i == self.bins[-1] else 'is between ' + \
i.split(' ~ ')[0] + ' and ' + i.split(' ~ ')[1])

self.dict['cats'] = self.cats
2 changes: 1 addition & 1 deletion pmultiqc/modules/quantms/ms_functions.py
Original file line number Diff line number Diff line change
@@ -20,7 +20,7 @@ def get_ms_qc_info(ms_info: pd.DataFrame):
Note that here I am using min and not mean for purely qc reasons.
Since the diagnostic aspect here is mainly to see major fluctuations
in the intensity, and usually these are scans with very low intensity
due to bubbles or ionization issues, thus the mean would hide that.
due to bubbles or ionization issues; thus the mean would hide that.
@param ms_info:
@return:
213 changes: 114 additions & 99 deletions pmultiqc/modules/quantms/quantms.py

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214 changes: 112 additions & 102 deletions pmultiqc/modules/quantms/sparklines.py

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7 changes: 4 additions & 3 deletions requirements.txt
Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
multiqc==1.19.0
multiqc==1.23
pandas
pyteomics
pyopenms
sdrf-pipelines >= 0.0.18
sdrf-pipelines >= 0.0.28
lxml
numpy
numpy==1.24.3
pyarrow
9 changes: 4 additions & 5 deletions setup.py
Original file line number Diff line number Diff line change
@@ -6,8 +6,7 @@
"""

from setuptools import setup, find_packages

version = '0.0.24'
version = '0.0.25'


def readme():
@@ -31,11 +30,11 @@ def readme():
include_package_data=True,
install_requires=[
'lxml',
'multiqc==1.19.0',
'multiqc==1.23',
'pandas',
'pyteomics',
'sdrf-pipelines >= 0.0.18',
'numpy',
'sdrf-pipelines >= 0.0.28',
'numpy == 1.24.3',
'pyopenms'
],
entry_points={
1 change: 1 addition & 0 deletions tests/test_proteomicslfq.py
Original file line number Diff line number Diff line change
@@ -7,3 +7,4 @@ class TestMultiqcModule(TestCase):
path_mztab1 = 'resources/PXD005942-Sample-25-out.mzTab'
def test_parse_out_mz_tab(self):
print("Improve tests here")

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