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Merge pull request #127 from MannLabs/development
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FIX MannLabs/alphapeptdeep#119; FIX adding fix mods
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@jalew188
jalew188 authored Dec 26, 2023
2 parents 57e9e51 + 1242ee9 commit 3649766
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Showing 3 changed files with 215 additions and 354 deletions.
83 changes: 47 additions & 36 deletions alphabase/protein/fasta.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -488,10 +488,16 @@ def parse_labels(labels:list):
cterm_label_mod = label
return label_aas, label_mod_dict, nterm_label_mod, cterm_label_mod

def create_labeling_peptide_df(peptide_df:pd.DataFrame, labels:list):
def create_labeling_peptide_df(
peptide_df:pd.DataFrame, labels:list,
inplace:bool=False
):
if len(peptide_df) == 0: return peptide_df

df = peptide_df.copy()
if inplace:
df = peptide_df
else:
df = peptide_df.copy()

(
label_aas, label_mod_dict,
Expand Down Expand Up @@ -789,12 +795,12 @@ def __init__(self,
self._parse_fix_and_var_mods()

def _parse_fix_and_var_mods(self):
self.fix_mod_aas = ''
self.fix_mod_prot_nterm_dict = {}
self.fix_mod_prot_cterm_dict = {}
self.fix_mod_pep_nterm_dict = {}
self.fix_mod_pep_cterm_dict = {}
self.fix_mod_dict = {}
# self.fix_mod_aas = ''
# self.fix_mod_prot_nterm_dict = {}
# self.fix_mod_prot_cterm_dict = {}
# self.fix_mod_pep_nterm_dict = {}
# self.fix_mod_pep_cterm_dict = {}
# self.fix_mod_dict = {}

def _set_term_mod(term_mod,
prot_nterm, prot_cterm, pep_nterm, pep_cterm,
Expand Down Expand Up @@ -828,19 +834,19 @@ def _set_dict(term_dict,site,mod,
allow_conflicts
)

for mod in self.fix_mods:
if mod.find('@')+2 == len(mod):
self.fix_mod_aas += mod[-1]
self.fix_mod_dict[mod[-1]] = mod
else:
_set_term_mod(
mod,
self.fix_mod_prot_nterm_dict,
self.fix_mod_prot_cterm_dict,
self.fix_mod_pep_nterm_dict,
self.fix_mod_pep_cterm_dict,
allow_conflicts=False
)
# for mod in self.fix_mods:
# if mod.find('@')+2 == len(mod):
# self.fix_mod_aas += mod[-1]
# self.fix_mod_dict[mod[-1]] = mod
# else:
# _set_term_mod(
# mod,
# self.fix_mod_prot_nterm_dict,
# self.fix_mod_prot_cterm_dict,
# self.fix_mod_pep_nterm_dict,
# self.fix_mod_pep_cterm_dict,
# allow_conflicts=False
# )

self.var_mod_aas = ''
self.var_mod_prot_nterm_dict = {}
Expand All @@ -863,7 +869,7 @@ def _set_dict(term_dict,site,mod,
else:
for mod in self.var_mods:
if mod.find('@')+2 == len(mod):
if mod[-1] in self.fix_mod_dict: continue
# if mod[-1] in self.fix_mod_dict: continue
self.var_mod_aas += mod[-1]
self.var_mod_dict[mod[-1]] = mod
get_var_mods_per_sites = get_var_mods_per_sites_single_mod_on_aa
Expand Down Expand Up @@ -1122,18 +1128,18 @@ def add_mods_for_one_seq(self, sequence:str,
list[str]: list of modification names
list[str]: list of modification sites
"""
fix_mods, fix_mod_sites = get_fix_mods(
sequence, self.fix_mod_aas, self.fix_mod_dict
)
#TODO add prot and pep C-term fix mods
#TODO add prot and pep N-term fix mods

if len(fix_mods) == 0:
fix_mods = ['']
fix_mod_sites = ['']
else:
fix_mods = [fix_mods]
fix_mod_sites = [fix_mod_sites]
# fix_mods, fix_mod_sites = get_fix_mods(
# sequence, self.fix_mod_aas, self.fix_mod_dict
# )
# #TODO add prot and pep C-term fix mods
# #TODO add prot and pep N-term fix mods

# if len(fix_mods) == 0:
# fix_mods = ['']
# fix_mod_sites = ['']
# else:
# fix_mods = [fix_mods]
# fix_mod_sites = [fix_mod_sites]

var_mods_list, var_mod_sites_list = get_var_mods(
sequence, self.var_mod_aas, self.var_mod_dict,
Expand All @@ -1160,12 +1166,12 @@ def add_mods_for_one_seq(self, sequence:str,
return (
list(
';'.join([i for i in items if i]) for items in itertools.product(
fix_mods, nterm_var_mods, var_mods_list
nterm_var_mods, var_mods_list
)
),
list(
';'.join([i for i in items if i]) for items in itertools.product(
fix_mod_sites, nterm_var_mod_sites, var_mod_sites_list
nterm_var_mod_sites, var_mod_sites_list
)
),
)
Expand Down Expand Up @@ -1195,6 +1201,11 @@ def add_modifications(self):
self._precursor_df,
['mods','mod_sites']
)
self._precursor_df.dropna(subset=['mods'], inplace=True)
self._precursor_df = create_labeling_peptide_df(
self._precursor_df, self.fix_mods,
inplace=True
)
self._precursor_df.reset_index(drop=True, inplace=True)

def add_special_modifications(self):
Expand Down
26 changes: 13 additions & 13 deletions nbdev_nbs/constants/aa.ipynb
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -29,7 +29,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -38,7 +38,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -258,7 +258,7 @@
"90 Z C(1000000) 1.200000e+07"
]
},
"execution_count": 3,
"execution_count": null,
"metadata": {},
"output_type": "execute_result"
}
Expand Down Expand Up @@ -293,7 +293,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -314,7 +314,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -339,7 +339,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -359,7 +359,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand All @@ -382,7 +382,7 @@
" 453.26996726, 396.24850354, 259.18959168, 146.1055277 ]])}"
]
},
"execution_count": 7,
"execution_count": null,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -404,7 +404,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand All @@ -424,7 +424,7 @@
" 1.28094963e+02]])"
]
},
"execution_count": 8,
"execution_count": null,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -436,7 +436,7 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -447,7 +447,7 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand Down
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