attach estimate biomass to api

q2_katharoseq/_format.py

@@ -0,0 +1,22 @@
+import qiime2.plugin.model as model
+
+
+STATS_HEADER = ['sample-id',
+                'log_total_reads',
+                'estimated_biomass_per_pcrrxn',
+                'estimated_biomass_per_dnarxn',
+                'extraction_mass_g',
+                'estimated_cells_per_g',
+                'log_estimated_cells_per_g']
+
+
+class EstimatedBiomassFmt(model.TextFileFormat):
+    def sniff(self):
+        line = open(str(self)).readline()
+        hdr = line.strip().split(',')
+
+        return hdr == STATS_HEADER
+
+
+EstimatedBiomassDirFmt = model.SingleFileDirectoryFormat(
+    'EstimatedBiomassDirFmt', 'est_biomass.csv', EstimatedBiomassFmt)

q2_katharoseq/_transformer.py

@@ -0,0 +1,16 @@
+import pandas as pd
+
+from .plugin_setup import plugin
+from ._format import EstimatedBiomassFmt
+
+
+@plugin.register_transformer
+def _1(data: pd.DataFrame) -> EstimatedBiomassFmt:
+    ff = EstimatedBiomassFmt()
+    data.to_csv(str(ff))
+    return ff
+
+
+@plugin.register_transformer
+def _2(ff: EstimatedBiomassFmt) -> pd.DataFrame:
+    return pd.read_csv(str(ff), index_col='sample-id')

q2_katharoseq/_type.py

@@ -0,0 +1,3 @@
+from qiime2.plugin import SemanticType
+
+EstimatedBiomass = SemanticType('EstimatedBiomass')

q2_katharoseq/plugin_setup.py

@@ -1,8 +1,11 @@
+import importlib
 from qiime2.plugin import (Plugin, Citations, Str, Int,
                            MetadataColumn, Categorical, Numeric, Choices)
 from q2_types.feature_table import (FeatureTable, Frequency)
-from . import read_count_threshold
+from . import read_count_threshold, estimating_biomass
 import q2_katharoseq
+from q2_katharoseq._type import EstimatedBiomass
+from q2_katharoseq._format import EstimatedBiomassFmt, EstimatedBiomassDirFmt
 
 
 citations = Citations.load('citations.bib', package='q2_katharoseq')
@@ -19,6 +22,12 @@
 )
 
 
+plugin.register_formats(EstimatedBiomassFmt, EstimatedBiomassDirFmt)
+plugin.register_semantic_types(EstimatedBiomass)
+plugin.register_semantic_type_to_format(EstimatedBiomass,
+                                        artifact_format=EstimatedBiomassDirFmt)
+
+
 plugin.visualizers.register_function(
     function=read_count_threshold,
     inputs={
@@ -60,3 +69,44 @@
                 'positive signal in samples with as few as 50 to 500 cells.',
     citations=[citations['minich2018']]
 )
+
+
+plugin.methods.register_function(
+    function=estimating_biomass,
+    inputs={},
+    parameters={'total_reads': MetadataColumn[Numeric],
+                'control_cell_extraction': MetadataColumn[Numeric],
+                'positive_control_column': MetadataColumn[Categorical],
+                'positive_control_value': Str,
+                'extraction_mass_g': MetadataColumn[Categorical],
+                'min_total_reads': Int,
+                'pcr_template_vol': Int,
+                'dna_extract_vol': Int},
+    outputs=[('estimated_biomass', EstimatedBiomass)],
+    input_descriptions={},
+    parameter_descriptions={
+        'total_reads': 'The total reads present in each sample.',
+        'control_cell_extraction': 'The number of cells in the controls.',
+        'positive_control_column': (
+            'The column in the sample metadata that describes which samples '
+            'are and are not controls.'),
+        'positive_control_value': (
+            'The value in the control column that demarks which samples are '
+            'the positive controls.'),
+        'extraction_mass_g': (
+            'The column in the sample metadata that describes the extraction '
+            'mass for the controls'),
+        'min_total_reads': 'The minimum threshold to apply.',
+        'pcr_template_vol': 'The PCR template volume.',
+        'dna_extract_vol': 'The DNA extraction volume.'},
+    output_descriptions={
+        'estimated_biomass': (
+            'A dataframe containing the details on estimated biomass')
+        },
+    name='Estimate the biomass of samples using KatharoSeq controls.',
+    description='Estimate the biomass of samples using KatharoSeq controls.',
+    citations=[]
+)
+
+
+importlib.import_module('q2_katharoseq._transformer')