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replace space with _ in NC-term PTMs #180

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18 changes: 9 additions & 9 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -381,12 +381,12 @@ common:
user_defined_modifications: {}
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# For example,
# user_defined_modifications:
# "Dimethyl2@Any N-term":
# "Dimethyl2@Any_N-term":
# composition: "H(2)2H(2)C(2)"
# modloss_composition: "H(0)" # can be without if no modloss
# "Dimethyl2@K":
# composition: "H(2)2H(2)C(2)"
# "Dimethyl6@Any N-term":
# "Dimethyl6@Any_N-term":
# composition: "2H(4)13C(2)"
# "Dimethyl6@K":
# composition: "2H(4)13C(2)"
Expand Down Expand Up @@ -496,16 +496,16 @@ library:
fix_mods:
- Carbamidomethyl@C
var_mods:
- Acetyl@Protein N-term
- Acetyl@Protein_N-term
- Oxidation@M
special_mods: [] # normally for Phospho or GlyGly@K
special_mods_cannot_modify_pep_n_term: False
special_mods_cannot_modify_pep_c_term: False
labeling_channels: {}
# For example,
# labeling_channels:
# 0: ['Dimethyl@Any N-term','Dimethyl@K']
# 4: ['Dimethyl:2H(2)@Any N-term','Dimethyl:2H(2)@K']
# 0: ['Dimethyl@Any_N-term','Dimethyl@K']
# 4: ['Dimethyl:2H(2)@Any_N-term','Dimethyl:2H(2)@K']
# 8: [...]
min_var_mod_num: 0
max_var_mod_num: 2
Expand Down Expand Up @@ -565,7 +565,7 @@ See examples:
import pandas as pd
df = pd.DataFrame({
'sequence': ['ACDEFGHIK','LMNPQRSTVK','WYVSTR'],
'mods': ['Carbamidomethyl@C','Acetyl@Protein N-term;Phospho@S',''],
'mods': ['Carbamidomethyl@C','Acetyl@Protein_N-term;Phospho@S',''],
'mod_sites': ['2','0;7',''],
'charge': [2,3,1],
})
Expand Down Expand Up @@ -593,7 +593,7 @@ df[['sequence','mods','mod_sites']]
| | sequence | mods | mod_sites |
| --- | --- | --- | --- |
| 0 | ACDEFGHIK | Carbamidomethyl@C | 2 |
| 1 | LMNPQRSTVK | Acetyl@Protein N-term;Phospho@S | 0;7 |
| 1 | LMNPQRSTVK | Acetyl@Protein_N-term;Phospho@S | 0;7 |
| 2 | WYVSTR | | |

##### precursor_table
Expand All @@ -605,7 +605,7 @@ df
| | sequence | mods | mod_sites | charge |
| --- | --- | --- | --- | --- |
| 0 | ACDEFGHIK | Carbamidomethyl@C | 2 | 2 |
| 1 | LMNPQRSTVK | Acetyl@Protein N-term;Phospho@S | 0;7 | 3 |
| 1 | LMNPQRSTVK | Acetyl@Protein_N-term;Phospho@S | 0;7 | 3 |
| 2 | WYVSTR | | | 1 |

> Columns of `proteins` and `genes` are optional for these txt/tsv/csv
Expand Down Expand Up @@ -686,7 +686,7 @@ model_mgr:
# alphabase modification to modifications of other search engines
# For example,
# psm_modification_mapping:
# Dimethyl@Any N-term:
# Dimethyl@Any_N-term:
# - _(Dimethyl-n-0)
# - _(Dimethyl)
# Dimethyl:2H(2)@K:
Expand Down
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