-
Notifications
You must be signed in to change notification settings - Fork 8
/
dia_psm_reader.py
191 lines (160 loc) · 5.62 KB
/
dia_psm_reader.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
import pandas as pd
import numpy as np
from alphabase.psm_reader.psm_reader import psm_reader_provider, psm_reader_yaml
from alphabase.psm_reader.maxquant_reader import MaxQuantReader
class SpectronautReader(MaxQuantReader):
"""Reader for Spectronaut's output library TSV/CSV.
Other parameters, please see `MaxQuantReader`
in `alphabase.psm_reader.maxquant_reader`
Parameters
----------
csv_sep : str, optional
Delimiter for TSV/CSV, by default '\t'
"""
def __init__(
self,
*,
column_mapping: dict = None,
modification_mapping: dict = None,
fdr=0.01,
keep_decoy=False,
fixed_C57=False,
mod_seq_columns=psm_reader_yaml["spectronaut"]["mod_seq_columns"],
rt_unit="minute",
**kwargs,
):
super().__init__(
column_mapping=column_mapping,
modification_mapping=modification_mapping,
fdr=fdr,
keep_decoy=keep_decoy,
mod_seq_columns=mod_seq_columns,
fixed_C57=fixed_C57,
rt_unit=rt_unit,
**kwargs,
)
self.mod_seq_column = "ModifiedPeptide"
self._min_max_rt_norm = True
def _init_column_mapping(self):
self.column_mapping = psm_reader_yaml["spectronaut"]["column_mapping"]
def _load_file(self, filename):
self.csv_sep = self._get_table_delimiter(filename)
df = pd.read_csv(filename, sep=self.csv_sep, keep_default_na=False)
self._find_mod_seq_column(df)
if "ReferenceRun" in df.columns:
df.drop_duplicates(
["ReferenceRun", self.mod_seq_column, "PrecursorCharge"], inplace=True
)
else:
df.drop_duplicates([self.mod_seq_column, "PrecursorCharge"], inplace=True)
df.reset_index(drop=True, inplace=True)
return df
class SwathReader(SpectronautReader):
def __init__(
self,
*,
column_mapping: dict = None,
modification_mapping: dict = None,
fdr=0.01,
keep_decoy=False,
fixed_C57=False,
mod_seq_columns=psm_reader_yaml["spectronaut"]["mod_seq_columns"],
**kwargs,
):
"""
SWATH or OpenSWATH library, similar to `SpectronautReader`
"""
super().__init__(
column_mapping=column_mapping,
modification_mapping=modification_mapping,
fdr=fdr,
keep_decoy=keep_decoy,
fixed_C57=fixed_C57,
mod_seq_columns=mod_seq_columns,
**kwargs,
)
class DiannReader(SpectronautReader):
def __init__(
self,
*,
column_mapping: dict = None,
modification_mapping: dict = None,
fdr=0.01,
keep_decoy=False,
fixed_C57=False,
rt_unit="minute",
**kwargs,
):
"""
Also similar to `MaxQuantReader`,
but different in column_mapping and modificatin_mapping
"""
super().__init__(
column_mapping=column_mapping,
modification_mapping=modification_mapping,
fdr=fdr,
keep_decoy=keep_decoy,
fixed_C57=fixed_C57,
rt_unit=rt_unit,
**kwargs,
)
self.mod_seq_column = "Modified.Sequence"
self._min_max_rt_norm = False
def _init_column_mapping(self):
self.column_mapping = psm_reader_yaml["diann"]["column_mapping"]
def _load_file(self, filename):
self.csv_sep = self._get_table_delimiter(filename)
df = pd.read_csv(filename, sep=self.csv_sep, keep_default_na=False)
return df
def _post_process(self, origin_df: pd.DataFrame):
super()._post_process(origin_df)
self._psm_df.rename(columns={"spec_idx": "diann_spec_idx"}, inplace=True)
class SpectronautReportReader(MaxQuantReader):
"""Reader for Spectronaut's report TSV/CSV.
Other parameters, please see `MaxQuantReader`
in `alphabase.psm_reader.maxquant_reader`
Parameters
----------
csv_sep : str, optional
Delimiter for TSV/CSV, by default ','
"""
def __init__(
self,
*,
column_mapping: dict = None,
modification_mapping: dict = None,
fdr=0.01,
keep_decoy=False,
fixed_C57=False,
rt_unit="minute",
**kwargs,
):
super().__init__(
column_mapping=column_mapping,
modification_mapping=modification_mapping,
fdr=fdr,
keep_decoy=keep_decoy,
fixed_C57=fixed_C57,
rt_unit=rt_unit,
**kwargs,
)
self.precursor_column = "EG.PrecursorId"
self._min_max_rt_norm = False
def _init_column_mapping(self):
self.column_mapping = psm_reader_yaml["spectronaut_report"]["column_mapping"]
def _load_file(self, filename):
self.mod_seq_column = "ModifiedSequence"
self.csv_sep = self._get_table_delimiter(filename)
df = pd.read_csv(filename, sep=self.csv_sep, keep_default_na=False)
df[[self.mod_seq_column, "charge"]] = df[self.precursor_column].str.split(
".", expand=True, n=2
)
df["charge"] = df.charge.astype(np.int8)
return df
def register_readers():
psm_reader_provider.register_reader("spectronaut", SpectronautReader)
psm_reader_provider.register_reader("speclib_tsv", SpectronautReader)
psm_reader_provider.register_reader("openswath", SwathReader)
psm_reader_provider.register_reader("swath", SwathReader)
psm_reader_provider.register_reader("diann", DiannReader)
psm_reader_provider.register_reader("spectronaut_report", SpectronautReportReader)