Skip to content

Commit

Permalink
add merged library
Browse files Browse the repository at this point in the history
  • Loading branch information
@michabirklbauer
michabirklbauer committed Nov 15, 2024
1 parent a2146dc commit 1975fab
Show file tree
Hide file tree
Showing 2 changed files with 147 additions and 11 deletions.
47 changes: 40 additions & 7 deletions create_spectral_library.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
# [email protected]

# version tracking
__version = "1.3.0"
__version = "1.3.1"
__date = "2024-11-14"

# REQUIREMENTS
Expand Down Expand Up @@ -873,6 +873,8 @@ def main(spectra_file: Union[List[str], List[BinaryIO]] = SPECTRA_FILE,
FragmentLossType_s = list()
CLContainingFragment_s = list()
LossyFragment_s = list()
Is_Decoy_s = list()
Decoy_Type_s = list()

# decoy dd columns
linkId_s_decoy = list()
Expand Down Expand Up @@ -903,6 +905,8 @@ def main(spectra_file: Union[List[str], List[BinaryIO]] = SPECTRA_FILE,
FragmentLossType_s_decoy = list()
CLContainingFragment_s_decoy = list()
LossyFragment_s_decoy = list()
Is_Decoy_s_decoy = list()
Decoy_Type_s_decoy = list()

# decoy dt columns
linkId_s_decoy_dt = list()
Expand Down Expand Up @@ -933,6 +937,8 @@ def main(spectra_file: Union[List[str], List[BinaryIO]] = SPECTRA_FILE,
FragmentLossType_s_decoy_dt = list()
CLContainingFragment_s_decoy_dt = list()
LossyFragment_s_decoy_dt = list()
Is_Decoy_s_decoy_dt = list()
Decoy_Type_s_decoy_dt = list()

# decoy td columns
linkId_s_decoy_td = list()
Expand Down Expand Up @@ -963,6 +969,8 @@ def main(spectra_file: Union[List[str], List[BinaryIO]] = SPECTRA_FILE,
FragmentLossType_s_decoy_td = list()
CLContainingFragment_s_decoy_td = list()
LossyFragment_s_decoy_td = list()
Is_Decoy_s_decoy_td = list()
Decoy_Type_s_decoy_td = list()

# process CSMs
for i, row in csms.iterrows():
Expand Down Expand Up @@ -1019,6 +1027,8 @@ def main(spectra_file: Union[List[str], List[BinaryIO]] = SPECTRA_FILE,
FragmentLossType_s.append(frag["FragmentLossType"])
CLContainingFragment_s.append(frag["CLContainingFragment"])
LossyFragment_s.append(frag["LossyFragment"])
Is_Decoy_s.append(False)
Decoy_Type_s.append("TT")

# decoy dd
decoy_csm = generate_decoy_csm_dd(row, crosslinker)
Expand Down Expand Up @@ -1078,6 +1088,8 @@ def main(spectra_file: Union[List[str], List[BinaryIO]] = SPECTRA_FILE,
FragmentLossType_s_decoy.append(decoy_frag["FragmentLossType"])
CLContainingFragment_s_decoy.append(decoy_frag["CLContainingFragment"])
LossyFragment_s_decoy.append(decoy_frag["LossyFragment"])
Is_Decoy_s_decoy.append(True)
Decoy_Type_s_decoy.append("DD")
decoy_frag_mzs.append(decoy_frag["FragmentMz"])

# decoy dt
Expand Down Expand Up @@ -1138,6 +1150,8 @@ def main(spectra_file: Union[List[str], List[BinaryIO]] = SPECTRA_FILE,
FragmentLossType_s_decoy_dt.append(decoy_frag_dt["FragmentLossType"])
CLContainingFragment_s_decoy_dt.append(decoy_frag_dt["CLContainingFragment"])
LossyFragment_s_decoy_dt.append(decoy_frag_dt["LossyFragment"])
Is_Decoy_s_decoy_dt.append(True)
Decoy_Type_s_decoy_dt.append("DT")
decoy_frag_mzs_dt.append(decoy_frag_dt["FragmentMz"])

# decoy td
Expand Down Expand Up @@ -1198,6 +1212,8 @@ def main(spectra_file: Union[List[str], List[BinaryIO]] = SPECTRA_FILE,
FragmentLossType_s_decoy_td.append(decoy_frag_td["FragmentLossType"])
CLContainingFragment_s_decoy_td.append(decoy_frag_td["CLContainingFragment"])
LossyFragment_s_decoy_td.append(decoy_frag_td["LossyFragment"])
Is_Decoy_s_decoy_td.append(True)
Decoy_Type_s_decoy_td.append("TD")
decoy_frag_mzs_td.append(decoy_frag_td["FragmentMz"])

if (i + 1) % 100 == 0:
Expand Down Expand Up @@ -1231,7 +1247,9 @@ def main(spectra_file: Union[List[str], List[BinaryIO]] = SPECTRA_FILE,
"RelativeIntensity": RelativeIntensity_s,
"FragmentLossType": FragmentLossType_s,
"CLContainingFragment": CLContainingFragment_s,
"LossyFragment": LossyFragment_s}
"LossyFragment": LossyFragment_s,
"IsDecoy": Is_Decoy_s,
"DecoyType": Decoy_Type_s}

spectral_library = pd.DataFrame(tt_dict)

Expand Down Expand Up @@ -1262,7 +1280,9 @@ def main(spectra_file: Union[List[str], List[BinaryIO]] = SPECTRA_FILE,
"RelativeIntensity": RelativeIntensity_s_decoy,
"FragmentLossType": FragmentLossType_s_decoy,
"CLContainingFragment": CLContainingFragment_s_decoy,
"LossyFragment": LossyFragment_s_decoy}
"LossyFragment": LossyFragment_s_decoy,
"IsDecoy": Is_Decoy_s_decoy,
"DecoyType": Decoy_Type_s_decoy}

spectral_library_decoy_dd = pd.DataFrame(dd_dict)

Expand Down Expand Up @@ -1293,7 +1313,9 @@ def main(spectra_file: Union[List[str], List[BinaryIO]] = SPECTRA_FILE,
"RelativeIntensity": RelativeIntensity_s_decoy_dt,
"FragmentLossType": FragmentLossType_s_decoy_dt,
"CLContainingFragment": CLContainingFragment_s_decoy_dt,
"LossyFragment": LossyFragment_s_decoy_dt}
"LossyFragment": LossyFragment_s_decoy_dt,
"IsDecoy": Is_Decoy_s_decoy_dt,
"DecoyType": Decoy_Type_s_decoy_dt}

spectral_library_decoy_dt = pd.DataFrame(dt_dict)

Expand Down Expand Up @@ -1324,7 +1346,9 @@ def main(spectra_file: Union[List[str], List[BinaryIO]] = SPECTRA_FILE,
"RelativeIntensity": RelativeIntensity_s_decoy_td,
"FragmentLossType": FragmentLossType_s_decoy_td,
"CLContainingFragment": CLContainingFragment_s_decoy_td,
"LossyFragment": LossyFragment_s_decoy_td}
"LossyFragment": LossyFragment_s_decoy_td,
"IsDecoy": Is_Decoy_s_decoy_td,
"DecoyType": Decoy_Type_s_decoy_td}

spectral_library_decoy_td = pd.DataFrame(td_dict)

Expand All @@ -1341,8 +1365,17 @@ def main(spectra_file: Union[List[str], List[BinaryIO]] = SPECTRA_FILE,
print(".".join(csms_file.split(".")[:-1]) + "_spectralLibraryDECOY_DD.csv")
print(".".join(csms_file.split(".")[:-1]) + "_spectralLibraryDECOY_DT.csv")
print(".".join(csms_file.split(".")[:-1]) + "_spectralLibraryDECOY_TD.csv")

return {"TargetLib": spectral_library, "DecoyLib": spectral_library_decoy_dd, "DecoyLib_DT": spectral_library_decoy_dt, "DecoyLib_TD": spectral_library_decoy_td}

print("Creating merged library...")
merged_spec_lib = pd.concat([spectral_library, spectral_library_decoy_dd, spectral_library_decoy_dt, spectral_library_decoy_td], ignore_index = True)
should_shape = spectral_library.shape[0] + spectral_library_decoy_dd.shape[0] + spectral_library_decoy_dt.shape[0] + spectral_library_decoy_td.shape[0]
if merged_spec_lib.shape[0] != should_shape:
warnings.warn(f"Merged spectral library has {merged_spec_lib.shape[0]} rows, should be {should_shape} rows! Potential loss of data, please consider merging manually!")
merged_spec_lib.to_csv(".".join(csms_file.split(".")[:-1]) + "_spectralLibraryFULL.csv", index = True)
print("SUCCESS: Merged spectral library created with filename:")
print(".".join(csms_file.split(".")[:-1]) + "_spectralLibraryFULL.csv")

return {"TargetLib": spectral_library, "DecoyLib": spectral_library_decoy_dd, "DecoyLib_DT": spectral_library_decoy_dt, "DecoyLib_TD": spectral_library_decoy_td, "FullLib": merged_spec_lib}

##### SCRIPT #####

Expand Down
Loading

0 comments on commit 1975fab

Please sign in to comment.