Skip to content

Sample mass on prep 20260223 #11

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
AmandaBirmingham merged 3 commits into from
Feb 25, 2026
Merged

Sample mass on prep 20260223 #11

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
4fd7192
refactor, deprecate funcs with sample_df arg
AmandaBirmingham Feb 24, 2026
b088f12
rename 2-df functionality calls, update tests, add tests for 1-df fun…
AmandaBirmingham Feb 25, 2026
cdaf436
restore missing __init__ addition
AmandaBirmingham Feb 25, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions pysyndna/__init__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
FIT_SYNDNA_MODELS_LOG_KEY
from pysyndna.src.calc_cell_counts import calc_ogu_cell_counts_biom, \
calc_ogu_cell_counts_per_g_of_sample_for_qiita, \
calc_ogu_cell_counts_per_g_of_sample_for_qiita_split_input, \
calc_ogu_cell_counts_per_cm2_of_sample_for_qiita, \
calc_ogu_cell_counts_per_ul_of_sample_for_qiita, \
SAMPLE_IN_ALIQUOT_MASS_G_KEY, SAMPLE_SURFACE_AREA_CM2_KEY, \
Expand All @@ -21,6 +22,7 @@
'fit_linear_regression_models_for_qiita',
'calc_ogu_cell_counts_biom',
'calc_ogu_cell_counts_per_g_of_sample_for_qiita',
'calc_ogu_cell_counts_per_g_of_sample_for_qiita_split_input',
'calc_ogu_cell_counts_per_cm2_of_sample_for_qiita',
'calc_ogu_cell_counts_per_ul_of_sample_for_qiita',
'read_ogu_orf_coords_to_df',
Expand Down
250 changes: 234 additions & 16 deletions pysyndna/src/calc_cell_counts.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
import biom
import numpy as np
import pandas as pd
from warnings import deprecated
import yaml
from typing import Optional, Union, Dict, List
from pysyndna.src.util import calc_copies_genomic_element_per_g_series, \
Expand Down Expand Up @@ -218,7 +219,10 @@ def _validate_ogu_ids_in_inputs(
# lengths because we don't really care about any of them that aren't *also*
# in the reads data, and we've already checked those for consistency.

def _calc_ogu_cell_counts_per_x_of_sample_for_qiita(

@deprecated("This function has been deprecated; "
"please use _calc_ogu_cell_counts_per_x_of_sample_for_qiita instead.")
def _calc_ogu_cell_counts_per_x_of_sample_for_qiita_split_input(
sample_info_df: pd.DataFrame,
prep_info_df: pd.DataFrame,
linregress_by_sample_id_fp: str,
Expand Down Expand Up @@ -261,6 +265,12 @@ def _calc_ogu_cell_counts_per_x_of_sample_for_qiita(
String containing the filepath to a tab-separated, two-column,
no-header file in which the first column is the OGU id and the
second is the OGU length in basepairs
output_cell_counts_metric: str
String indicating the metric to use for the output cell counts. Must
be one of OGU_CELLS_PER_G_OF_SAMPLE_KEY, OGU_CELLS_PER_UL_OF_SAMPLE_KEY,
or OGU_CELLS_PER_CM2_OF_SAMPLE_KEY. This determines the units of the
output cell counts and also which column in the sample info is used for
the per-sample calculation.
min_coverage : float
Minimum allowable coverage of an OGU in a sample needed to include
that OGU/sample in the output, expressed in the same units
Expand Down Expand Up @@ -295,6 +305,93 @@ def _calc_ogu_cell_counts_per_x_of_sample_for_qiita(
_ = validate_id_consistency_between_datasets(
sample_info_df, prep_info_df, "sample info", "prep info", True)

# merge the sample info and prep info dataframes
absolute_quant_params_per_sample_df = \
sample_info_df.merge(prep_info_df, on=SAMPLE_ID_KEY, how='left')

out_txt_by_out_type = _calc_ogu_cell_counts_per_x_of_sample_for_qiita(
absolute_quant_params_per_sample_df, linregress_by_sample_id_fp,
ogu_counts_per_sample_biom, ogu_coverage_df, ogu_lengths_fp, output_cell_counts_metric,
min_coverage, min_rsquared, syndna_mass_fraction_of_sample
)

return out_txt_by_out_type


def _calc_ogu_cell_counts_per_x_of_sample_for_qiita(
absolute_quant_params_per_sample_df: pd.DataFrame,
linregress_by_sample_id_fp: str,
ogu_counts_per_sample_biom: biom.Table,
ogu_coverage_df: pd.DataFrame,
ogu_lengths_fp: str,
output_cell_counts_metric: str,
min_coverage: float,
min_rsquared: float = DEFAULT_MIN_RSQUARED,
syndna_mass_fraction_of_sample: float =
DEFAULT_SYNDNA_MASS_FRACTION_OF_SAMPLE) \
-> Dict[str, Union[str, biom.Table]]:

"""Gets # of cells of each OGU/g of sample for samples from Qiita.

Parameters
----------
absolute_quant_params_per_sample_df: pd.DataFrame
A Dataframe of at least SAMPLE_ID_KEY, GDNA_CONCENTRATION_NG_UL_KEY,
ELUTE_VOL_UL_KEY, and SEQUENCED_SAMPLE_GDNA_MASS_NG_KEY for each
sample in the prep. It should also have at least one of SAMPLE_VOLUME_UL_KEY,
SAMPLE_SURFACE_AREA_CM2_KEY, and/or SAMPLE_IN_ALIQUOT_MASS_G_KEY.
linregress_by_sample_id_fp: str
String containing the filepath to the yaml file holding the
dictionary keyed by sample id, containing for each sample a dictionary
representation of the sample's LinregressResult.
ogu_counts_per_sample_biom: biom.Table
Biom table holding the read counts aligned to each OGU in each sample.
ogu_coverage_df : pd.DataFrame
A DataFrame containing a column for OGU_ID_KEY and either a column for
OGU_PERCENT_COVERAGE_KEY (indicating the coverage is the same for all
samples) or a column for each sample id, which holds the coverage of
that OGU in that sample, expressed as either a fraction or a percent.
NOTE THAT IT IS UP TO THE USER TO ENSURE THAT THEY KNOW WHICH TYPE OF
VALUE (fraction or percent) IS BEING USED AND THAT THEY PROVIDE THE
APPROPRIATE min_coverage PARAMETER (e.g., 0.01 or 1 to drop <1% coverage).
ogu_lengths_fp : str
String containing the filepath to a tab-separated, two-column,
no-header file in which the first column is the OGU id and the
second is the OGU length in basepairs
output_cell_counts_metric: str
String indicating the metric to use for the output cell counts. Must
be one of OGU_CELLS_PER_G_OF_SAMPLE_KEY, OGU_CELLS_PER_UL_OF_SAMPLE_KEY,
or OGU_CELLS_PER_CM2_OF_SAMPLE_KEY. This determines the units of the
output cell counts and also which column in the sample info is used for
the per-sample calculation.
min_coverage : float
Minimum allowable coverage of an OGU in a sample needed to include
that OGU/sample in the output, expressed in the same units
(fraction or percent) as used in ogu_coverage_df.
min_rsquared: float
Minimum allowable R^2 value for the linear regression model for a
sample; any sample with an R^2 value less than this will be excluded
from the output.
syndna_mass_fraction_of_sample: float
Fraction of the mass of the sample that is added as syndna (usually
0.05, which is to say 5%).

Returns
-------
output_by_out_type : dict of str or biom.Table
Dictionary of outputs keyed by their type Currently, the following keys
are defined:
CELL_COUNT_RESULT_KEY: biom.Table holding the calculated number of
cells per gram of sample material for each OGU in each sample.
CELL_COUNT_LOG_KEY: log of messages from the cell count calc process.
"""

required_prep_cols = list(
{INPUT_SYNDNA_POOL_MASS_NG_KEY} | set(REQUIRED_DNA_PREP_INFO_KEYS))
validate_required_columns_exist(
absolute_quant_params_per_sample_df, required_prep_cols,
"absolute quant params per sample is missing required column(s)")

# cast in case the input comes in as string or something
syndna_mass_fraction_of_sample = float(syndna_mass_fraction_of_sample)

Expand All @@ -306,16 +403,12 @@ def _calc_ogu_cell_counts_per_x_of_sample_for_qiita(
# the sample (added into the library prep in addition to the sample mass).
# Therefore, if the syndna fraction is 0.05 or 5%, the mass of the sample
# gDNA put into sequencing is 1/0.05 = 20x the mass of syndna pool added.
prep_info_df = cast_cols(
prep_info_df, [INPUT_SYNDNA_POOL_MASS_NG_KEY], True)
prep_info_df[SEQUENCED_SAMPLE_GDNA_MASS_NG_KEY] = \
prep_info_df[INPUT_SYNDNA_POOL_MASS_NG_KEY] * \
absolute_quant_params_per_sample_df = cast_cols(
absolute_quant_params_per_sample_df, [INPUT_SYNDNA_POOL_MASS_NG_KEY], True)
absolute_quant_params_per_sample_df[SEQUENCED_SAMPLE_GDNA_MASS_NG_KEY] = \
absolute_quant_params_per_sample_df[INPUT_SYNDNA_POOL_MASS_NG_KEY] * \
(1 / syndna_mass_fraction_of_sample)

# merge the sample info and prep info dataframes
absolute_quant_params_per_sample_df = \
sample_info_df.merge(prep_info_df, on=SAMPLE_ID_KEY, how='left')

# read in the linregress_by_sample_id yaml file
with open(linregress_by_sample_id_fp) as f:
linregress_by_sample_id = yaml.load(f, Loader=yaml.FullLoader)
Expand Down Expand Up @@ -961,8 +1054,9 @@ def calc_ogu_cell_counts_biom(

return ogu_cell_counts_biom, log_msgs_list


def calc_ogu_cell_counts_per_g_of_sample_for_qiita(
@deprecated("This function has been deprecated; "
"please use calc_ogu_cell_counts_per_g_of_sample_for_qiita instead.")
def calc_ogu_cell_counts_per_g_of_sample_for_qiita_split_input(
sample_info_df: pd.DataFrame,
prep_info_df: pd.DataFrame,
linregress_by_sample_id_fp: str,
Expand Down Expand Up @@ -1030,14 +1124,88 @@ def calc_ogu_cell_counts_per_g_of_sample_for_qiita(
sample_info_df, [SAMPLE_ID_KEY, SAMPLE_IN_ALIQUOT_MASS_G_KEY],
"sample info is missing required column(s)")

return _calc_ogu_cell_counts_per_x_of_sample_for_qiita(
return _calc_ogu_cell_counts_per_x_of_sample_for_qiita_split_input(
sample_info_df, prep_info_df, linregress_by_sample_id_fp,
ogu_counts_per_sample_biom, ogu_coverage_df, ogu_lengths_fp,
OGU_CELLS_PER_G_OF_SAMPLE_KEY, min_coverage, min_rsquared,
syndna_mass_fraction_of_sample)


def calc_ogu_cell_counts_per_cm2_of_sample_for_qiita(
def calc_ogu_cell_counts_per_g_of_sample_for_qiita(
prep_info_df: pd.DataFrame,
linregress_by_sample_id_fp: str,
ogu_counts_per_sample_biom: biom.Table,
ogu_coverage_df: pd.DataFrame,
ogu_lengths_fp: str,
min_coverage: float,
min_rsquared: float = DEFAULT_MIN_RSQUARED,
syndna_mass_fraction_of_sample: float =
DEFAULT_SYNDNA_MASS_FRACTION_OF_SAMPLE) \
-> Dict[str, Union[str, biom.Table]]:
"""Calculates the number of cells per gram of sample material.

Parameters
----------
prep_info_df: pd.DataFrame
A Dataframe containing prep info for all samples in the prep,
including SAMPLE_ID_KEY, GDNA_CONCENTRATION_NG_UL_KEY, and
ELUTE_VOL_UL_KEY, INPUT_SYNDNA_POOL_MASS_NG_KEY, and
SAMPLE_IN_ALIQUOT_MASS_G_KEY.
linregress_by_sample_id_fp: str
String containing the filepath to the yaml file holding the
dictionary keyed by sample id, containing for each sample a dictionary
representation of the sample's LinregressResult.
ogu_counts_per_sample_biom: biom.Table
Biom table holding the read counts aligned to each OGU in each sample.
ogu_coverage_df : pd.DataFrame
A DataFrame containing a column for OGU_ID_KEY and either a column for
OGU_PERCENT_COVERAGE_KEY (indicating the coverage is the same for all
samples) or a column for each sample id, which holds the coverage of
that OGU in that sample, expressed as either a fraction or a percentage.
NOTE THAT IT IS UP TO THE USER TO ENSURE THAT THEY KNOW WHICH TYPE OF
VALUE (fraction or percent) IS BEING USED AND THAT THEY PROVIDE THE
APPROPRIATE min_coverage VALUE ACCORDINGLY.
ogu_lengths_fp : str
String containing the filepath to a tab-separated, two-column,
no-header file in which the first column is the OGU id and the
second is the OGU length in basepairs
min_coverage : float
Minimum allowable coverage of an OGU in a sample needed to include
that OGU/sample in the output, expressed in the same units
(fraction or percent) as used in ogu_coverage_df.
min_rsquared: float
Minimum allowable R^2 value for the linear regression model for a
sample; any sample with an R^2 value less than this will be excluded
from the output.
syndna_mass_fraction_of_sample: float
Fraction of the mass of the sample that is added as syndna (usually
0.05, which is to say 5%).

Returns
-------
output_by_out_type : dict of str or biom.Table
Dictionary of outputs keyed by their type Currently, the following keys
are defined:
CELL_COUNT_RESULT_KEY: biom.Table holding the calculated number of
cells per gram of sample material for each OGU in each sample.
CELL_COUNT_LOG_KEY: log of messages from the cell count calc process.
"""

# check if the input has the specific required columns
validate_required_columns_exist(
prep_info_df, [SAMPLE_ID_KEY, SAMPLE_IN_ALIQUOT_MASS_G_KEY],
"prep info is missing required column(s)")

return _calc_ogu_cell_counts_per_x_of_sample_for_qiita(
prep_info_df, linregress_by_sample_id_fp,
ogu_counts_per_sample_biom, ogu_coverage_df, ogu_lengths_fp,
OGU_CELLS_PER_G_OF_SAMPLE_KEY, min_coverage, min_rsquared,
syndna_mass_fraction_of_sample)


@deprecated("This function has been deprecated; "
"please use calc_ogu_cell_counts_per_cm2_of_sample_for_qiita instead.")
def calc_ogu_cell_counts_per_cm2_of_sample_for_qiita_split_input(
sample_info_df: pd.DataFrame,
prep_info_df: pd.DataFrame,
linregress_by_sample_id_fp: str,
Expand All @@ -1055,14 +1223,40 @@ def calc_ogu_cell_counts_per_cm2_of_sample_for_qiita(
sample_info_df, [SAMPLE_ID_KEY, SAMPLE_SURFACE_AREA_CM2_KEY],
"sample info is missing required column(s)")

return _calc_ogu_cell_counts_per_x_of_sample_for_qiita(
return _calc_ogu_cell_counts_per_x_of_sample_for_qiita_split_input(
sample_info_df, prep_info_df, linregress_by_sample_id_fp,
ogu_counts_per_sample_biom, ogu_coverage_df, ogu_lengths_fp,
OGU_CELLS_PER_CM2_OF_SAMPLE_KEY, min_coverage, min_rsquared,
syndna_mass_fraction_of_sample)


def calc_ogu_cell_counts_per_ul_of_sample_for_qiita(
def calc_ogu_cell_counts_per_cm2_of_sample_for_qiita(
prep_info_df: pd.DataFrame,
linregress_by_sample_id_fp: str,
ogu_counts_per_sample_biom: biom.Table,
ogu_coverage_df: pd.DataFrame,
ogu_lengths_fp: str,
min_coverage: float,
min_rsquared: float = DEFAULT_MIN_RSQUARED,
syndna_mass_fraction_of_sample: float =
DEFAULT_SYNDNA_MASS_FRACTION_OF_SAMPLE) \
-> Dict[str, Union[str, biom.Table]]:

# check if the input has the specific required columns
validate_required_columns_exist(
prep_info_df, [SAMPLE_ID_KEY, SAMPLE_SURFACE_AREA_CM2_KEY],
"prep info is missing required column(s)")

return _calc_ogu_cell_counts_per_x_of_sample_for_qiita(
prep_info_df, linregress_by_sample_id_fp,
ogu_counts_per_sample_biom, ogu_coverage_df, ogu_lengths_fp,
OGU_CELLS_PER_CM2_OF_SAMPLE_KEY, min_coverage, min_rsquared,
syndna_mass_fraction_of_sample)


@deprecated("This function has been deprecated; "
"please use calc_ogu_cell_counts_per_ul_of_sample_for_qiita instead.")
def calc_ogu_cell_counts_per_ul_of_sample_for_qiita_split_input(
sample_info_df: pd.DataFrame,
prep_info_df: pd.DataFrame,
linregress_by_sample_id_fp: str,
Expand All @@ -1080,8 +1274,32 @@ def calc_ogu_cell_counts_per_ul_of_sample_for_qiita(
sample_info_df, [SAMPLE_ID_KEY, SAMPLE_VOLUME_UL_KEY],
"sample info is missing required column(s)")

return _calc_ogu_cell_counts_per_x_of_sample_for_qiita(
return _calc_ogu_cell_counts_per_x_of_sample_for_qiita_split_input(
sample_info_df, prep_info_df, linregress_by_sample_id_fp,
ogu_counts_per_sample_biom, ogu_coverage_df, ogu_lengths_fp,
OGU_CELLS_PER_UL_OF_SAMPLE_KEY, min_coverage, min_rsquared,
syndna_mass_fraction_of_sample)


def calc_ogu_cell_counts_per_ul_of_sample_for_qiita(
prep_info_df: pd.DataFrame,
linregress_by_sample_id_fp: str,
ogu_counts_per_sample_biom: biom.Table,
ogu_coverage_df: pd.DataFrame,
ogu_lengths_fp: str,
min_coverage: float,
min_rsquared: float = DEFAULT_MIN_RSQUARED,
syndna_mass_fraction_of_sample: float =
DEFAULT_SYNDNA_MASS_FRACTION_OF_SAMPLE) \
-> Dict[str, Union[str, biom.Table]]:

# check if the input has the specific required columns
validate_required_columns_exist(
prep_info_df, [SAMPLE_ID_KEY, SAMPLE_VOLUME_UL_KEY],
"prep info is missing required column(s)")

return _calc_ogu_cell_counts_per_x_of_sample_for_qiita(
prep_info_df, linregress_by_sample_id_fp,
ogu_counts_per_sample_biom, ogu_coverage_df, ogu_lengths_fp,
OGU_CELLS_PER_UL_OF_SAMPLE_KEY, min_coverage, min_rsquared,
syndna_mass_fraction_of_sample)
Loading
Loading