mh_utils.csv_parser.classes
Classes to model parts of MassHunter CSV files.
New in version 0.2.0.
Classes:
OrderedDict to store a single property of a set of samples. |
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Represents a Result in a MassHunter CSV file. |
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Represents a sample in a MassHunter CSV file. |
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A list of |
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Data:
Invariant |
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Invariant |
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Invariant |
-
class
BaseSamplePropertyDict
[source] Bases:
OrderedDict
OrderedDict to store a single property of a set of samples.
Keys are the sample names and the values are dictionaries mapping compound names to property values.
Attributes:
Returns the number of compounds in the
BaseSamplePropertyDict
.Returns the number of samples in the
BaseSamplePropertyDict
.Returns a list of sample names in the
BaseSamplePropertyDict
.-
property
n_compounds
Returns the number of compounds in the
BaseSamplePropertyDict
.- Return type
-
property
n_samples
Returns the number of samples in the
BaseSamplePropertyDict
.- Return type
-
property
sample_names
Returns a list of sample names in the
BaseSamplePropertyDict
.
-
property
-
class
Result
(cas, name, hits, index=- 1, formula='', score=0.0, abundance=0, height=0, area=0, diff_mDa=0.0, diff_ppm=0.0, rt=0.0, start=0.0, end=0.0, width=0.0, tgt_rt=0.0, rt_diff=0.0, mz=0.0, product_mz=0.0, base_peak=0.0, mass=0.0, average_mass=0.0, tgt_mass=0.0, mining_algorithm='', z_count=0, max_z=0, min_z=0, n_ions=0, polarity='', label='', flags='', flag_severity='', flag_severity_code=0)[source] Bases:
Dictable
Represents a Result in a MassHunter CSV file.
- Parameters
cas
name (
str
)hits
index (
int
) – Default-1
.formula (
str
) – Default''
.score (
float
) – Default0.0
.abundance (
float
) – Default0
.height (
float
) – Default0
.area (
float
) – Default0
.diff_mDa (
float
) – Default0.0
.diff_ppm (
float
) – Default0.0
.rt (
float
) – Default0.0
.start (
float
) – Default0.0
.end (
float
) – Default0.0
.width (
float
) – Default0.0
.tgt_rt (
float
) – Default0.0
.rt_diff (
float
) – Default0.0
.mz (
float
) – Default0.0
.product_mz (
float
) – Default0.0
.base_peak (
float
) – Default0.0
.mass (
float
) – Default0.0
.average_mass (
float
) – Default0.0
.tgt_mass (
float
) – Default0.0
.mining_algorithm (
str
) – Default''
.z_count (
int
) – Default0
.max_z (
int
) – Default0
.min_z (
int
) – Default0
.n_ions (
int
) – Default0
.polarity (
str
) – Default''
.label (
str
) – Default''
.flags (
str
) – Default''
.flag_severity (
str
) – Default''
.flag_severity_code (
int
) – Default0
.
Methods:
from_series
(series)Consruct a
Result
from apandas.Series
.
-
class
Sample
(sample_name, sample_type, instrument_name, position, user, acq_method, da_method, irm_cal_status, filename, results=None)[source] Bases:
Dictable
Represents a sample in a MassHunter CSV file.
- Parameters
sample_name
sample_type
instrument_name
position
user
acq_method
da_method
irm_cal_status
filename
results – Default
None
.
Methods:
add_result
(result)Add a result to the sample.
from_series
(series)Constuct a
Sample
from apandas.Series
.Attributes:
Returns a list of results in the order in which they were identified.
-
classmethod
from_series
(series)[source] Constuct a
Sample
from apandas.Series
.- Parameters
series
- Return type
- Returns
-
class
SampleList
(iterable=(), /)[source] -
A list of
mh_utils.csv_parser.classes.Sample
objects.Methods:
add_new_sample
(*args, **kwargs)Add a new sample to the list and return the
Sample
object representing it.add_sample
(sample)Add a
Sample
object to the list.add_sample_from_series
(series)Create a new sample object from a
pandas.series
and add it to the list.filter
(sample_names[, key, exclude])Filter the list to only contain sample_names whose name is in
sample_names
.from_json_file
(filename, **kwargs)Construct a
SampleList
from JSON file.get_areas_and_scores
(compound_name[, …])Returns two dictionaries: one containing sample names and peak areas for the compound with the given name, the other containing sample names and scores.
Returns two dictionaries: one containing sample names and peak areas for the compounds with the given names, the other containing sample names and scores.
get_areas_for_compounds
(compound_names[, …])Returns a dictionary containing sample names and peak areas for the compounds with the given names.
Returns a list containing the names of the compounds present in the samples in alphabetical order.
get_peak_areas
(compound_name[, include_none])Returns a dictionary containing sample names and peak areas for the compound with the given name.
get_retention_times
(compound_name[, …])Returns a dictionary containing sample names and retention times for the compound with the given name.
get_scores
(compound_name[, include_none])Returns a dictionary containing sample names and scores for the compound with the given name.
rename_samples
(rename_mapping[, key])Rename the samples in the list.
reorder_samples
(order_mapping[, key])Reorder the list of
Samples
in place.sort_samples
(key[, reverse])Sort the list of
Samples
in place.Attributes:
Returns a list of sample names in the
SampleList
.-
add_new_sample
(*args, **kwargs)[source] Add a new sample to the list and return the
Sample
object representing it.
-
add_sample_from_series
(series)[source] Create a new sample object from a
pandas.series
and add it to the list.
-
filter
(sample_names, key='sample_name', exclude=False)[source] Filter the list to only contain sample_names whose name is in
sample_names
.- Parameters
- Return type
-
classmethod
from_json_file
(filename, **kwargs)[source] Construct a
SampleList
from JSON file.
-
get_areas_and_scores
(compound_name, include_none=False)[source] Returns two dictionaries: one containing sample names and peak areas for the compound with the given name, the other containing sample names and scores.
- Parameters
- Return type
-
get_areas_and_scores_for_compounds
(compound_names, include_none=False)[source] Returns two dictionaries: one containing sample names and peak areas for the compounds with the given names, the other containing sample names and scores.
- Parameters
- Return type
-
get_areas_for_compounds
(compound_names, include_none=False)[source] Returns a dictionary containing sample names and peak areas for the compounds with the given names.
- Parameters
- Return type
-
get_compounds
()[source] Returns a list containing the names of the compounds present in the samples in alphabetical order.
-
get_peak_areas
(compound_name, include_none=False)[source] Returns a dictionary containing sample names and peak areas for the compound with the given name.
- Parameters
- Return type
-
get_retention_times
(compound_name, include_none=False)[source] Returns a dictionary containing sample names and retention times for the compound with the given name.
- Parameters
- Return type
-
get_scores
(compound_name, include_none=False)[source] Returns a dictionary containing sample names and scores for the compound with the given name.
- Parameters
- Return type
-
rename_samples
(rename_mapping, key='sample_name')[source] Rename the samples in the list.
- Parameters
Use
rename_mapping=
:py:obj:None or omit the sample from therename_mapping
entirely to leave the name unchanged.For example:
rename_mapping = { "Propellant 1ug +ve": "Alliant Unique 1µg/L +ESI", "Propellant 1mg +ve": "Alliant Unique 1mg/L +ESI", "Propellant 1mg -ve": None, }
-
reorder_samples
(order_mapping, key='sample_name')[source] Reorder the list of
Samples
in place.- Parameters
order_mapping (
Dict
) –A mapping between sample names and their new position in the list. For example:
order_mapping = { "Propellant 1ug +ve": 0, "Propellant 1mg +ve": 1, "Propellant 1ug -ve": 2, "Propellant 1mg -ve": 3, }
key (
str
) – The name of the property in the sample to sort by. Default'sample_name'
.
-
property
sample_names
Returns a list of sample names in the
SampleList
.
-
-
class
SamplesAreaDict
[source] Bases:
BaseSamplePropertyDict
collections.OrderedDict
to store area information parsed from MassHunter results CSV files.Methods:
get_compound_areas
(compound_name)Get the peak areas for the given compound in every sample.
-
class
SamplesScoresDict
[source] Bases:
BaseSamplePropertyDict
collections.OrderedDict
to store score information parsed from MassHunter results CSV files.Methods:
get_compound_scores
(compound_name)Get the peak scores for the given compound in every sample.
-
_R
= TypeVar(_R, bound=Result) Type:
TypeVar
Invariant
TypeVar
bound tomh_utils.csv_parser.classes.Result
.
-
_S
= TypeVar(_S, bound=Sample) Type:
TypeVar
Invariant
TypeVar
bound tomh_utils.csv_parser.classes.Sample
.
-
_SL
= TypeVar(_SL, bound=SampleList) Type:
TypeVar
Invariant
TypeVar
bound tomh_utils.csv_parser.classes.SampleList
.