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Solver_develop.ini
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[DM0Solver_Parameters]
Absolute_Error = 0.015 # Absolute error
PeakAssignation_Column_name = New_PeakAssignation
Sequence_column_name = SiteSequence # Sequence with DM column name
DM0Sequence_output_column_name = DM0Sequence_2 # Column name of the output where the chosen sequence is annotated
DM0Label_output_column_name = DM0Label_2 # Column name of the output where the chosen label is annotated
DM0Label_error_output_column_name = DM0Label_error_2 # Column name of the output where the calulated error in ppm is annotated
output_file_suffix = _DM0S_V2 # Chosen suffix for output file
PeakNaming = PEAK # Parameter that indicates how peaks are named
DM_column_name =New_Assigned_deltaMass # Peak DM
[DM0Solver_DM0List]
DM0 = 0
DM0;C13 = 1.003355
DM0;2C13 = 2.00671
DM0;3C13 = 3.010065
DM0;IAM = 57.020828
DM0;IAM_C13 = 58.023869
DM0;IAM_2C13 = 59.021204
NA_ADDUCT = 21.981943
NA_ADDUCT_C13 = 22.982571
AMMONIUM_ADDUCT = 17.026549
AMMONIUM_ADDUCT_LOSS = -17.026549
H20_LOSS = -18.010565
DM0;-TMT_C13 = -303.205256
DM0;TMT_2C13= 306.193987
DM0;TMT_3C13= 307.194834
DM0;TMT_C13= 305.209106
DM0;TMT= 304.20714
[TrunkSolver_Parameters]
Relative_Error = 10 # Relative error (ppm)
Exp_mh_column_name = RECOMfiltered_MH # Calibrated experimental mh column name
Theo_mh_column_name = theo_mh # Theoretical mh column name
Sequence_column_name = DM0Sequence # Sequence with DM column name
Calibrated_Delta_MH_column_name = Assigned_deltaMass # Calibrated deltamass mh column name
MasterProtein_column_name = PA_accession # Master Protein accesion code column name
decnum=6 # Decimals points required in TrunkSequence column
static_modifications_column_name = modifications # Static modifications column name
New_Deltamass_output_column_name = New_DM # New DM column name
New_Theo_mh_output_column_name = New_Theo_mh # New theoretical mh column name
x = 6 # Number of positions to the right and left, that the TrunkSolver is allowed to extend from the original DM site
TrunkSequence_output_column_name = TrunkSequence # Column name of the output where the chosen sequence is annotated
TrunkPlainPeptide_output_column_name = TrunkPlainPeptide # Column name of the output where the chosen Trunk clean pepetide is annotated
TrunkDM_output_column_name = TrunkDM # Column name of the output where the recaulcutaed DM is annotated, taking in to account the label
TrunkLabel_output_column_name = TrunkLabel # Column name of the output where the chosen label is annotated
TrunkLabel_ppm_output_column_name = TrunkLabel_ppm # Column name of the output where the calulated error in ppm is annotated
Static_modifications_position_output_column_name = Static_modifications_position # Column name of the output where the new fix modifications positions are annotated
Matchnumber_output_column_name = Match_number # Column name of the output where the number of possible options is annotated
Possible_option_output_column_name = Possible_option # Column name of the output where all possible options
output_file_suffix = _TS # Chosen suffix for output file
Missing_cleavages_output_column_name = Missing_cleavages # Output column name for the number of missing cleavages
Truncation_output_column_name = Truncated # Output column name for Truncation. 0;No-truncation , 1; Truncation
[TrunkSolver_CombList]
DM0=0
(+)TMT=304.207146
(+)2TMT=608.414292
(-)TMT=-304.207146
(-)2TMT=-608.414292
[SiteListMaker_Parameters]
Sequence_column_name = New_Assing_Sequence # Sequence column nam
x = 5 # Parameter that indicates the extension (left and right) of the aminoacids wanted to be analyzed
Calibrated_Delta_MH_column_name = New_Assigned_deltaMass #DM column name
PeakAssignation_column_name = New_PeakAssignation #Name of column that contains peak assignation
PeakNaming = PEAK #Parameter that indicates how peaks are named
Clean_Frequency_Table= Clean_Frequency_Table #Name of the Clean Frequency Table ouput file
Clean_P0_Frequency_Table = Clean_P0_Frequency_Table #Name of the lean P0 Frequency Table ouput file
Frequency_Table = Frequency_Table #Name of the Frequency Table ouput file
[PDMTableMaker_Parameters]
Sequence_column_name = DM0Sequence_2 # Sequence with DM column name
DM_column_name = New_Assigned_deltaMass # DM column name
Theo_mh_column_name = New_Theo_mh # Theoretical mh column name
Outfile_suffix = _PDMTable # Chosen suffix for output file
MasterProtein_column_name = PA_accession_2 # Master Protein accesion code column name
Missing_Cleavage_column_name = Missing_cleavages # Missing cleavage number column name
Truncated_column_name = Truncated # Truncated column name
Score_column_name = Closest_Xcorr_corr #Column in which scores are annotated
Score_parameter = 1 # 1; if the best score is the highest 0; if the best score is the lowest
ScanID_column_name = ScanID #Column name in which SCanID is annotated
[PDMTableMaker_Conditions] # Condition i == value i
number_of_conditions = 0 # Number of conditions
Condition1= New_PeakAssignation # Column name of condition i
Value1 = PEAK # chosen value for condition i
[QDNATableMaker_Parameters]
Output_file_name = QDNATable # Chosen name for output file
[SiteSolver_Parameters]
Relative_Error_ppm = 10 # Relative error (ppm)
Theo_mh_column_name = New_Theo_mh # Theoretical mh column name
Sequence_column_name = New_Assign_Sequence # Sequence with DM column name
cal_Dm_mh_column_name = New_Assigned_deltaMass # Calibrated DM MH name
SiteSequence_column_name = SiteSequence # Column name of the output where the sequence is annotated
SiteCorrection_column_name = SiteCorrection # Column name of the output where correction site is annotated
SiteDM_column_name = SiteDM # Column name of the output where selected DM is annotated
SiteDMError_ppm_column_name = SiteDMError_ppm # Column name of the output where the error of the selected DM is annotated
Output_file_suffix = _SS # Chosen suffix for output file
x = 3 # Number of positions to the right and left, that the TrunkSolver is allowed to extend from the original DM site
[Sticker_Parameters]
Relative_Error_ppm = 10 # Relative error (ppm)
Theo_mh_column_name = Theo_mh # Theoretical mh column name
Sequence_column_name = pdm # Sequence with DM column name
Selected_DM_column_name = d
StickerLabel_User_output_column_name = StickerLabel # Column name of the output where the chosen label is annotated
StickerLabel_ppm_User_output_column_name = StickerLabel_ppm # Column name of the output where the calculated error in ppm for the selected label is annotated
output_file_suffix = _Sticker # Chosen suffix for output file
[GroupMaker_Parameters]
Relative_Error_ppm = 10 # Relative error (ppm)
Theo_mh_column_name = Theo_mh # Theoretical mh column name
DM_PDM_column_name = d # DM of the PDMTable file column name
output_file_suffix = _GM # Chosen suffix for output file
decnum=6 # Decimals points required if deltamass is annotated as a group
[Joiner_Parameters]
Output_column_name= pgm # Output column name in which all labels are joined
Output_file_suffix= _J # Chosen suffix for output file
decnum=6 # Decimals points required if deltamass is
group_column_name = g # Column name that contains the group name
Non_modified_name = NM # Parameter that indicates how Non modified pdms are named
[Joiner_Columns] # Columns to join. Use ";" to select the column Joiner must join if the first column is empty
1=p
2=g;d
3=m
[PTMap_Parameters]
pgm_column_name = pgm
pgm_second_header_column_name = LEVEL
g_column_name = g
g_second_header_column_name = REL
a_column_name = a
a_second_header_column_name = REL
n_column_name = n
n_second_header_column_name = REL
e_column_name = e
e_second_header_column_name = REL
p_column_name = p
p_second_header_column_name = REL
q_column_name = q
q_second_header_column_name = REL
d_column_name = d
d_second_header_column_name = REL
qf_column_name = qf
qf_second_header_column_name = REL
pFreq_column_name = pFreq
pFreq_second_header_column_name = REL
qfFreq_column_name = qfFreq
qfFreq_second_header_column_name = REL
pgmFreq_column_name = pgmFreq
pgmFreq_second_header_column_name = REL
first_b_column_name = first_b
first_b_second_header_column_name = REL
description_column_name = description
description_second_header_column_name = REL
Missing_Cleavages_column_name = Missing_Cleavage
Missing_Cleavages_second_header_column_name = REL
LPS_p2qf_column_name = Z_p2qf_logLimma_Paciente-Donante #-LPS of p2qf integration
LPS_qf2q_column_name = Z_qf2q_logLimma_Paciente-Donante #-LPS of qf2q integration
LPS_pgm2p_column_name = Z_pgm2p_logLimma_Paciente-Donante #-LPS of pfm2p integration
LPS_pgm2p_NM_column_name = Z_pgm2p_dNM_logLimma_Paciente-Donante #-LPS of pgm2p_MN integration
LPS_p2qf_second_header_column_name = LPS
LPS_qf2q_second_header_column_name = LPS
LPS_pgm2p_second_header_column_name = LPS
LPS_pgm2p_NM_second_header_column_name = LPS
Filter_pgm2p_NM_column_name = Z_pgm2p_dNM_limma_Paciente-Donante #Filtering column( qvalues, pvalue..ect) of pgm2p integration corrected by NMCompare.py
Filter_pgm2p_column_name = Z_pgm2p_limma_NM_ONLY_Paciente-Donante #Filtering column( qvalues, pvalue..ect) of pgm2p integration calculated ONLY with NM
Filter_p2qf_column_name = Z_p2qf_limma_Paciente-Donante #Filtering column( qvalues, pvalue..ect) of p2qf integration
Filter_qf2q_column_name = Z_qf2q_limma_Paciente-Donante #Filtering column( qvalues, pvalue..ect) of qf2q integration
Filter_pgm2p_NM_second_header_column_name = pvalue
Filter_pgm2p_second_header_column_name = pvalue
Filter_p2qf_second_header_column_name = pvalue
Filter_qf2q_second_header_column_name = pvalue
threshold_pgm2p_NM = 0.05 # Threshold of filtering column (pgm2p_NM integration)
threshold_pgm2p = 0.05 # Threshold of filtering column (pgm2p integration)
threshold_p2qf = 0.05 # Threshold of filtering column (p2qf integration)
threshold_qf2q = 0.05 # Threshold of filtering column (qf2q integration)
dX_p2qf_column_name = Z_p2qf_dX_Paciente-Donante #-dX of p2qf integration
dX_qf2q_column_name = Z_qf2q_dX_Paciente-Donante #-dX of qf2q integration
dX_pgm2p_column_name = Z_pgm2p_dX_Paciente-Donante #-dX of pfm2p integration
dX_pgm2p_NM_column_name = Z_pgm2p_dNM_dX_Paciente-Donante #-dX of pgm2p_MN integration
dX_p2qf_second_header_column_name = dX
dX_qf2q_second_header_column_name = dX
dX_pgm2p_second_header_column_name = dX
dX_pgm2p_NM_second_header_column_name = dX
pgmFreqThreshold = 0 # Threhold
NM = NM #How Non modified are named
path_plots_with_threshold = S:\U_Proteomica\UNIDAD\Softwares\dmenas\ucsc_tracker\mods_file\plots_pvalue # Folder in which filtered PTM Maps will be saved
path_plots_Without_threshold = S:\U_Proteomica\UNIDAD\Softwares\dmenas\ucsc_tracker\mods_file\plots #Folder in which completed PTM Maps will be saved
data_filename=fichero_mods.tsv
attributes_list=n_REL,first_b_REL,e_REL,q_REL
[Logging]
create_log = 1 # Create log file, 0=no 1=yes
create_ini = 0 # Create copy of INI file in input directory, 0=no 1=yes (specifying custom parameters in the command line will always create a copy of INI file)
[Gff_creator]
q_column_header= q
missing_cleavages_header= Missing_Cleavages
start_position_in_protein_header = first_b
end_position_in_protein_header = e
mod_position_in_protein_header= n
g_column_header= g
source_comparison= Paciente-Donante
score_qfs= LPS_p2qf
score_pgm= LPS_pgm2p_NM
score_NM= LPS_pgm2p
attributes=a_g_d,n,first_b,e,dX_p2qf,q,dX_pgm2p,dX_pgm2p_NM
NM = NM #How Non modified are named
Mod = Mod #How modifications are named
qf = qf #How qfs are named
dp = DP #How partial digestions are named
dt = DT #How total digestions are named