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Commit 6f140af3 authored by Vishruth Mullapudi's avatar Vishruth Mullapudi
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added fragment modification analysis and output 

added test for multiple abundance columns
removed printing for debugging
parent 6ba13dac
1 merge request!1Fix unlocalized peptide mods not adding
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config.toml
+ 16
− 19
View file @ 6f140af3
......@@ -13,10 +13,9 @@ title="Abundance Parser Configuration"
#input_files=[ "/input/file1",
# path to file2
# ]
input_files="/input/test.csv"
input_files=[]
#fasta file(s) containing the protein sequence(s) to align against
prot_seq_fasta=["/data/1N4RP301STau.fasta","/data/2N4R_wt_tau.fasta"]
prot_seq_fasta=[]
[output]
......@@ -24,33 +23,31 @@ title="Abundance Parser Configuration"
output_directory="output/"
#this stub is prepended by the file name of the input file
output_name_stub="residueModificationAnalysis"
residue_output_name_stub="residueModificationAnalysis"
peptide_output_name_stub='peptideModificationAnalysis'
#Configuration of parser settings[regex]
regex_file="data/parser_regex.toml"
regex_to_use="phosphoregex"
#Configuration of parser settings
[parser_config]
sequence_column_title="Annotated Sequence"
#If false, files will be specified via abundance column
using_fileID_column=false
#Title of column containing abundance. If using_fileID_column is set to
#true, only the first Abundance column specified below will be used
abundance_col_titles=["Abundance","Abundance: F1"]
#true, only the first entry will be used
abundance_col_titles=[]
calculate_peptide_modifications=true
[parser_config.regex]
regex_file="data/parser_regex.toml"
mod_parsing_regex="phosphoregex"
pos_master_regex="pos_master_regex"
[parser_config.master]
#Configs for use of pre-localized modification in master protein in
#parsing
use=false
#the name in the data of the master protein
master_protein_name= 'P10636-8'
#The id of the master protein as it appears in the fasta data
master_protein_fasta_ID='sp|P10636-8|TAU_HUMAN'
#Column header containing the title of the column containing the
#localized modifications
modification_header="Modifications in Master Proteins"
[regex]
regex_file="data/parser_regex.toml"
regex_to_use="phosphoregex"
modification_header="Modifications in Master Proteins"
\ No newline at end of file
main.py
+ 76
− 47
View file @ 6f140af3
......@@ -43,10 +43,10 @@ def main():
# todo implement fileID splitting (pre-processing step?)
# if the file_id column is used we expect to see only one column of abundances
using_file_id_column = configuration['parser_config']['using_fileID_column']
# todo implement
should_calculate_peptide_modifications = True # configuration['parser_config']['calculate_peptide_modifications']
if should_calculate_peptide_modifications:
peptide_outpput_name_stub = configuration['output']['peptide_output_name_stub']
peptide_output_name_stub = configuration['output']['peptide_output_name_stub']
# End of configuration reading--------------------------------------------------------------------------------------
......@@ -74,7 +74,7 @@ def main():
# provided in the configuration
if use_mod_in_master_prot: # localize using the master protein positions and modifications
file_headers_tuple: Tuple[FileTuple, Dict[str, str], Dict[str, str]] = \
parsemasterlocalizations(ftuple, master_protein_fasta_id, mod_regex, master_regex)
parse_masterlocalizations(ftuple, master_protein_fasta_id, mod_regex, master_regex)
else: # localize by aligning the fragment against a protein and looking at the modification index within the
# fragment
file_headers_tuple: Tuple[FileTuple, Dict[str, str], Dict[str, str]] = \
......@@ -90,24 +90,32 @@ def main():
# Calculate the residue and modification abundances of each input against each desired protein----------------------
residue_analysis_all_prot: List[Dict[Dict]] = []
peptide_analysis_all_prot: List[Dict[Dict]] = []
for ftuple in localized_data:
# for residue modification analysis, calculate the amount each residue is modified
residue_analysis_all_prot.append(calc_residue_mod_abundances(ftuple, modification_localization_col_titles,
frag_localization_col_titles, abundance_col_titles,
protein_seq_records))
# for peptide modification analysis, calculate the amount each peptide fragment is modified
if should_calculate_peptide_modifications:
calc_peptide_mod_abundances(ftuple, modification_localization_col_titles, frag_localization_col_titles,
abundance_col_titles)
peptide_analysis_all_prot.append(calc_peptide_mod_abundances(ftuple, modification_localization_col_titles,
frag_localization_col_titles,
abundance_col_titles, protein_seq_records))
# End of abundance calculations-------------------------------------------------------------------------------------
# output the abundance data-----------------------------------------------------------------------------------------
# TODO peptide modification output
for prot_residue_analysis in residue_analysis_all_prot:
for protID, sample_analysis in prot_residue_analysis.items():
for fileID, abundance_array in sample_analysis.items():
output_residue_analysis_data(protID, fileID, abundance_array, output_directory,
for prot_id, sample_analysis in prot_residue_analysis.items():
for file_id, abundance_array in sample_analysis.items():
output_residue_analysis_data(prot_id, file_id, abundance_array, output_directory,
residue_output_name_stub)
for prot_peptide_analysis in peptide_analysis_all_prot:
for file_id, prot_analysis in prot_peptide_analysis.items():
for prot_id, fragment_list in prot_analysis.items():
output_peptide_analysis_data(prot_id, file_id, fragment_list, output_directory,
peptide_output_name_stub)
# End of data output------------------------------------------------------------------------------------------------
# End of program
return
......@@ -116,8 +124,8 @@ def main():
def gen_raw_sequences(ftuple: FileTuple) -> FileTuple:
"""
Adds a column to the DataFrame containing a stripped down peptide without the cleavage annotations
:param ftuple: The FileTuple to containing the filedata DataFrame to generate the raw sequence of each fragment
:return: a FileTuple containing the fileID and a filedata DataFrame containing the raw sequence in the
:param ftuple: The FileTuple to containing the FileData DataFrame to generate the raw sequence of each fragment
:return: a FileTuple containing the fileID and a FileData DataFrame containing the raw sequence in the
'stripped_sequence' column
"""
file_data: pd.DataFrame = ftuple.FileData # Extract the DataFrame
......@@ -128,7 +136,7 @@ def gen_raw_sequences(ftuple: FileTuple) -> FileTuple:
return FileTuple(ftuple.FileName, file_data)
def parsemasterlocalizations(ftuple: FileTuple, master_prot_fasta_id, mod_regex, pos_master_regex) -> Tuple[
def parse_masterlocalizations(ftuple: FileTuple, master_prot_fasta_id, mod_regex, pos_master_regex) -> Tuple[
FileTuple, Dict[str, str], Dict[str, str]]:
"""
Parses the modification and fragment localizations from a DataFrame using the positions in master and modifications
......@@ -293,43 +301,53 @@ def calc_residue_mod_abundances(ftuple, localization_col_titles: Dict, frag_loca
for mod in mod_localization:
# add the abundance to each modified residue contained in the fragment
res_abundances[mod][0] += frag_abundance
assert (res_abundances[i][0] <= res_abundances[i][1] for i in range(0, len(res_abundances)))
all_prot_abundances[res_abundance_col_title][abundance_col_title] = res_abundances
return all_prot_abundances
# todo
def calc_peptide_mod_abundances(ftuple, mod_localization_col_titles, frag_localization_col_titles,
abundance_col_titles):
abundance_col_titles, protein_seqrecords):
df = ftuple.FileData
fdata = df.fillna(0)
# Group all fragments of the same sequence into their own groups.
# group each peptide fragment by the sequence
grouped = fdata.groupby('stripped_sequence')
frag_mods = {}
# Calc the abundances for each protein
for mod_col_title_tuple, frag_col_title_tuple, abundance_col_title in \
zip(mod_localization_col_titles.items(), frag_localization_col_titles.items(), abundance_col_titles):
prot_id = mod_col_title_tuple[0]
mod_col_title = mod_col_title_tuple[1]
abundance_col_title = sanitize_str_for_dataframe_index(abundance_col_title)
frag_abundances = np.zeros((len(grouped), 2),
dtype=float)
frag_mods_per_prot = []
i = 0
for frag_sequence, fragment_group in grouped:
frag_abundances[i][1] = fragment_group[abundance_col_title].sum()
for fragment in fragment_group.iterrows():
fragment = fragment[1]
if fragment[mod_col_title]:
frag_abundances[i][0] += fragment[abundance_col_title]
prot_frag_mod_tuple = (prot_id, abundance_col_title, frag_sequence, fragment_group[frag_col_title_tuple[1]] \
.iloc[0], frag_abundances[0], frag_abundances[1])
print(prot_frag_mod_tuple)
i += 1
return frag_mods
sample_frag_abundances = {}
for abund_col_title in abundance_col_titles:
abund_col_title = sanitize_str_for_dataframe_index(abund_col_title)
sample_prot_frag_abundances = {}
for prot_id in protein_seqrecords:
prot_frag_abundances = []
mod_col_title = mod_localization_col_titles[prot_id]
frag_loc_col_title = frag_localization_col_titles[prot_id]
for frags_same_seq in grouped:
# a dd all the abundances for fragments with the same sequence
frag_abundance = frags_same_seq[1][abund_col_title].sum()
# ID all the fragments with modifications
bools = []
for mods in frags_same_seq[1][mod_col_title]:
if mods:
if -1 not in mods:
bools.append(True)
else:
bools.append(False)
else:
bools.append(False)
# add the abundances for all fragments with modifications
mod_abundance = frags_same_seq[1].loc[bools, abund_col_title].sum()
assert (mod_abundance <= frag_abundance)
frag_localization_tuple = frags_same_seq[1][frag_loc_col_title].iloc[0][0]
if -1 in frag_localization_tuple:
prot_frag_abundances.append((frags_same_seq[0], -1, -1, mod_abundance,
frag_abundance))
else:
prot_frag_abundances.append((frags_same_seq[0], frag_localization_tuple[0],
frag_localization_tuple[1], mod_abundance, frag_abundance))
sample_prot_frag_abundances.update({prot_id: prot_frag_abundances})
sample_frag_abundances.update({abund_col_title: sample_prot_frag_abundances})
return sample_frag_abundances
def ingest_file_data(files: List[str]) -> List[FileTuple]:
......@@ -385,18 +403,29 @@ def output_residue_analysis_data(prot_id, fileid, abundance_array, output_direct
writer = csv.writer(outfile)
writer.writerow(["Residue #:", "Modification Abundance", "Residue Abundance", "Modification Proportion"])
for i, arr in enumerate(abundance_array):
# will throw an Runtime warning-invalid value warning when dividing by 0 and print nan
# this is fine, although you could check if arr[1] is 0 and do something if this is not desired
if arr[0] is not 0 or float('NaN') and arr[1] is not 0 or float('NaN'):
writer.writerow([i, arr[0], arr[1], (arr[0] / arr[1])])
if (arr[0] != float('NaN')) and (arr[1] != 0) and (arr[1] != float('NaN')):
mod_prop = arr[0] / arr[1]
writer.writerow([i, arr[0], arr[1], mod_prop])
else:
writer.writerow([i, arr[0], arr[1], float("nan")])
return
# todo implement
def output_peptide_analysis_data():
pass
def output_peptide_analysis_data(prot_id, file_id, fragment_list, output_directory, peptide_output_name_stub):
filename = output_directory + file_id + prot_id + peptide_output_name_stub + ".csv"
with open(filename, 'w') as outfile:
writer = csv.writer(outfile)
writer.writerow(["Fragment", "Start Position", "End Position", "Length", "Phosphorylation Abundance",
"Fragment Abundance", "Modification Proportion"])
for i in fragment_list:
phos_abundance = i[3]
frag_abundance = i[4]
if (phos_abundance != float('NaN')) and (frag_abundance != 0) and (frag_abundance != float('NaN')):
mod_prop = phos_abundance / frag_abundance
writer.writerow([i[0], i[1], i[2], i[3], i[4], mod_prop])
else:
writer.writerow([i[0], i[1], i[2], i[3], i[4], float("nan")])
return
if __name__ == '__main__':
......
tests/sample2.csv 0 → 100644
+ 71
− 0
View file @ 6f140af3
Confidence,Annotated Sequence ,Modifications ,Modifications in Master Proteins,# Protein Groups,# PSMs,Master Protein Accessions,Positions in Master Proteins ,# Missed Cleavages,Abundance :F1,Abundance:F2
High ,[R].HLSNVSSTGSIDMVDSPQLATLADEVSASLAK.[Q] ,2xPhospho [S6; S] ,P10636-8 2xPhospho [S383; S] ,1 ,2 ,P10636-8 ,P10636-8 [378-409] ,0 ,3770206.25 ,84602312
High ,[K].TDHGAEIVYKSPVVSGDTSPR.[H] ,2xPhospho [S11; S15] ,P10636-8 2xPhospho [S367; S371] ,1 ,2 ,P10636-8 ,P10636-8 [357-377] ,1 ,490543.4063 ,85879545
High ,[K].AKTDHGAEIVYKSPVVSGDTSPR.[H] ,2xPhospho [S13; S17] ,P10636-8 2xPhospho [S367; S371] ,1 ,1 ,P10636-8 ,P10636-8 [355-377] ,2 , ,92741293
High ,[R].SGYSSPGSPGTPGSR.[S] ,2xPhospho [S] ,P10636-8 2xPhospho [S] ,1 ,5 ,P10636-8 ,P10636-8 [166-180] ,0 ,1425691.75 ,98087441
High ,[K].VAVVRTPPKSPSSAK.[S] ,1xPhospho [T6] ,P10636-8 1xPhospho [T202] ,1 ,4 ,P10636-8 ,P10636-8 [197-211] ,2 ,35290570.5 ,36243518
High ,[K].KVAVVRTPPKSPSSAK.[S] ,1xPhospho [T7] ,P10636-8 1xPhospho [T202] ,1 ,1 ,P10636-8 ,P10636-8 [196-211] ,3 ,97352696 ,43770115
High ,[K].KVAVVRTPPK.[S] ,1xPhospho [T7] ,P10636-8 1xPhospho [T202] ,1 ,1 ,P10636-8 ,P10636-8 [196-205] ,2 ,1866753.375 ,84341486
High ,[R].TPSLPTPPTR.[E] ,1xPhospho [T6] ,P10636-8 1xPhospho [T188] ,1 ,1 ,P10636-8 ,P10636-8 [183-192] ,0 ,5528542 ,93835341
High ,[R].TPSLPTPPTREPK.[K] ,1xPhospho [T6] ,P10636-8 1xPhospho [T188] ,1 ,2 ,P10636-8 ,P10636-8 [183-195] ,1 ,22805599.5 ,67613272
High ,[K].TPPAPKTPPSSGEPPKSGDR.[S] ,1xPhospho [T7] ,P10636-8 1xPhospho [T152] ,1 ,4 ,P10636-8 ,P10636-8 [146-165] ,2 ,35066952 ,12591257
High ,[K].TPPAPKTPPSSGEPPK.[S] ,1xPhospho [T7] ,P10636-8 1xPhospho [T152] ,1 ,4 ,P10636-8 ,P10636-8 [146-161] ,1 ,147009880 ,94815625
High ,[K].TPPSSGEPPK.[S] ,1xPhospho [T1] ,P10636-8 1xPhospho [T152] ,1 ,1 ,P10636-8 ,P10636-8 [152-161] ,0 ,1141578.25 ,72979440
High ,[K].SPVVSGDTSPR.[H] ,1xPhospho [T/S] ,P10636-8 1xPhospho [T/S] ,1 ,5 ,P10636-8 ,P10636-8 [367-377] ,0 ,291275882 ,76313867
High ,[K].TDHGAEIVYKSPVVSGDTSPR.[H] ,1xPhospho [S11] ,P10636-8 1xPhospho [S367] ,1 ,1 ,P10636-8 ,P10636-8 [357-377] ,1 ,3844751.25 ,90047135
High ,[K].IGSLDNITHVPGGGNK.[K] ,1xPhospho [S3] ,P10636-8 1xPhospho [S327] ,1 ,1 ,P10636-8 ,P10636-8 [325-340] ,0 ,3098245 ,5332778
High ,[R].SRTPSLPTPPTR.[E] ,1xPhospho [S5] ,P10636-8 1xPhospho [S185] ,1 ,1 ,P10636-8 ,P10636-8 [181-192] ,1 ,6525094.5 ,17852668
High ,[R].SGYSSPGSPGTPGSR.[S] ,1xPhospho [S/T] ,P10636-8 1xPhospho [S] ,1 ,7 ,P10636-8 ,P10636-8 [166-180] ,0 ,149733789.5 ,22124243
High ,[K].STPTAEAEEAGIGDTPSLEDEAAGHVTQAR.[M] ,1xPhospho [T/S] ,P10636-8 1xPhospho [S/T] ,1 ,3 ,P10636-8 ,P10636-8 [68-97] ,0 ,7920354.125 ,9185267
High ,[R].TPPKSPSSAK.[S] ,1xPhospho [S/T] ,P10636-8 1xPhospho [S/T] ,1 ,3 ,P10636-8 ,P10636-8 [202-211] ,1 ,2525454.594 ,58090514
High ,[R].HLSNVSSTGSIDMVDSPQLATLADEVSASLAK.[Q] ,1xPhospho [T/S]; 1xOxidation [M13],P10636-8 1xPhospho [S/T] ,1 ,4 ,P10636-8 ,P10636-8 [378-409] ,0 ,37349012 ,66648919
High ,[R].HLSNVSSTGSIDMVDSPQLATLADEVSASLAK.[Q] ,1xPhospho [S/T] ,P10636-8 1xPhospho [S/T] ,1 ,5 ,P10636-8 ,P10636-8 [378-409] ,0 ,42549668 ,41174096
High ,[R].KDQGGYTMHQDQEGDTDAGLKESPLQTPTEDGSEEPGSETSDAK.[S],1xPhospho [T/S]; 1xOxidation [M8] ,P10636-8 1xPhospho [S/T] ,1 ,6 ,P10636-8 ,P10636-8 [24-67] ,2 ,2833359 ,90435088
High ,[R].KDQGGYTMHQDQEGDTDAGLKESPLQTPTEDGSEEPGSETSDAK.[S],1xPhospho [S/T] ,P10636-8 1xPhospho [S/T] ,1 ,5 ,P10636-8 ,P10636-8 [24-67] ,2 ,381969 ,33380708
High ,[R].LQTAPVPMPDLKNVK.[S] ,1xOxidation [M8] , ,1 ,2 ,P10636-8 ,P10636-8 [214-228] ,1 ,11043190 ,59925563
High ,[R].LQTAPVPMPDLKNVK.[S] , , ,1 ,2 ,P10636-8 ,P10636-8 [214-228] ,1 ,3375361.5 ,66934687
High ,[R].LQTAPVPMPDLK.[N] ,1xOxidation [M8] , ,1 ,26 ,P10636-8 ,P10636-8 [214-225] ,0 ,2938043353 ,55115903
High ,[R].LQTAPVPMPDLK.[N] , , ,1 ,10 ,P10636-8 ,P10636-8 [214-225] ,0 ,2345507657 ,18349423
High ,[K].LDLSNVQSK.[C] , , ,1 ,9 ,P10636-8 ,P10636-8 [253-261] ,0 ,1056765568 ,24227906
High ,[K].KLDLSNVQSK.[C] , , ,1 ,5 ,P10636-8 ,P10636-8 [252-261] ,1 ,1525892608 ,69084694
High ,[K].IGSLDNITHVPGGGNKK.[I] , , ,1 ,5 ,P10636-8 ,P10636-8 [325-341] ,1 ,963006714.5 ,41478772
High ,[K].IGSLDNITHVPGGGNK.[K] , , ,1 ,16 ,P10636-8 ,P10636-8 [325-340] ,0 ,4624086515 ,19351259
High ,[K].IGSTENLKHQPGGGK.[V] , , ,1 ,1 ,P10636-8 ,P10636-8 [231-245] ,1 ,148045.0938 ,9514705
High ,[R].SRTPSLPTPPTREPK.[K] , , ,1 ,3 ,P10636-8 ,P10636-8 [181-195] ,2 ,698763648 ,36101344
High ,[K].STPTAEAEEAGIGDTPSLEDEAAGHVTQAR.[M] , , ,1 ,12 ,P10636-8 ,P10636-8 [68-97] ,0 ,725873185.9 ,5036078
High ,[K].SPVVSGDTSPR.[H] , , ,1 ,5 ,P10636-8 ,P10636-8 [367-377] ,0 ,1303747568 ,71492316
High ,[R].TPPKSPSSAK.[S] , , ,1 ,5 ,P10636-8 ,P10636-8 [202-211] ,1 ,66745472 ,41408951
High ,[K].TPPSSGEPPK.[S] , , ,1 ,5 ,P10636-8 ,P10636-8 [152-161] ,0 ,257468414.4 ,61879916
High ,[K].TPPSSGEPPKSGDR.[S] , , ,1 ,6 ,P10636-8 ,P10636-8 [152-165] ,1 ,103032414.3 ,38342837
High ,[R].TPSLPTPPTREPK.[K] , , ,1 ,8 ,P10636-8 ,P10636-8 [183-195] ,1 ,1604505144 ,80068010
High ,[K].TDHGAEIVYK.[S] , , ,1 ,5 ,P10636-8 ,P10636-8 [357-366] ,0 ,529712534 ,96010574
High ,[K].SKDGTGSDDKK.[A] , , ,1 ,1 ,P10636-8 ,P10636-8 [102-112] ,2 ,1939050.375 ,32759389
High ,[R].QEFEVMEDHAGTYGLGDRK.[D] ,1xOxidation [M6] , ,1 ,16 ,P10636-8 ,P10636-8 [6-24] ,1 ,234584178.3 ,33165088
High ,[R].QEFEVMEDHAGTYGLGDRK.[D] , , ,1 ,8 ,P10636-8 ,P10636-8 [6-24] ,1 ,352983975.5 ,95560066
High ,[R].QEFEVMEDHAGTYGLGDR.[K] ,1xOxidation [M6] , ,1 ,24 ,P10636-8 ,P10636-8 [6-23] ,0 ,541478609 ,5099972
High ,[R].QEFEVMEDHAGTYGLGDR.[K] , , ,1 ,8 ,P10636-8 ,P10636-8 [6-23] ,0 ,663580316 ,57096692
High ,[R].SGYSSPGSPGTPGSR.[S] , , ,1 ,7 ,P10636-8 ,P10636-8 [166-180] ,0 ,1886451761 ,72762532
High ,[K].DQGGYTMHQDQEGDTDAGLKESPLQTPTEDGSEEPGSETSDAK.[S] ,1xOxidation [M7] , ,1 ,8 ,P10636-8 ,P10636-8 [25-67] ,1 ,242811709.3 ,34474881
High ,[K].DQGGYTMHQDQEGDTDAGLKESPLQTPTEDGSEEPGSETSDAK.[S] , , ,1 ,4 ,P10636-8 ,P10636-8 [25-67] ,1 ,263117809.9 ,68130546
High ,[K].DQGGYTMHQDQEGDTDAGLK.[E] ,1xOxidation [M7] , ,1 ,15 ,P10636-8 ,P10636-8 [25-44] ,0 ,148222051.8 ,32337478
High ,[K].DQGGYTMHQDQEGDTDAGLK.[E] , , ,1 ,5 ,P10636-8 ,P10636-8 [25-44] ,0 ,169405957.9 ,92807240
High ,[K].DNIKHVSGGGSVQIVYKPVDLSK.[V] , , ,1 ,1 ,P10636-8 ,P10636-8 [266-288] ,1 , ,38907207
High ,[K].ESPLQTPTEDGSEEPGSETSDAK.[S] , , ,1 ,9 ,P10636-8 ,P10636-8 [45-67] ,0 ,740036840 ,99535953
High ,[K].AKTDHGAEIVYK.[S] , , ,1 ,3 ,P10636-8 ,P10636-8 [355-366] ,1 ,652942514.6 ,84744142
High ,[R].HLSNVSSTGSIDMVDSPQLATLADEVSASLAK.[Q] ,1xOxidation [M13] , ,1 ,17 ,P10636-8 ,P10636-8 [378-409] ,0 ,465597371.5 ,29112938
High ,[K].HVSGGGSVQIVYKPVDLSK.[V] , , ,1 ,56 ,P10636-8 ,P10636-8 [270-288] ,0 ,617176649.5 ,33872557
High ,[R].HLSNVSSTGSIDMVDSPQLATLADEVSASLAK.[Q] , , ,1 ,13 ,P10636-8 ,P10636-8 [378-409] ,0 ,549771859.3 ,44853427
High ,[R].KDQGGYTMHQDQEGDTDAGLKESPLQTPTEDGSEEPGSETSDAK.[S],1xOxidation [M8] , ,1 ,2 ,P10636-8 ,P10636-8 [24-67] ,2 ,132546086.5 ,98766340
High ,[R].KDQGGYTMHQDQEGDTDAGLK.[E] ,1xOxidation [M8] , ,1 ,12 ,P10636-8 ,P10636-8 [24-44] ,1 ,68147217.5 ,6462453
High ,[R].KDQGGYTMHQDQEGDTDAGLK.[E] , , ,1 ,2 ,P10636-8 ,P10636-8 [24-44] ,1 ,47451437.75 ,34182396
High ,[R].KDQGGYTMHQDQEGDTDAGLKESPLQTPTEDGSEEPGSETSDAK.[S], , ,1 ,3 ,P10636-8 ,P10636-8 [24-67] ,2 ,25293893.63 ,63120561
High ,[K].SRLQTAPVPMPDLK.[N] , , ,1 ,1 ,P10636-8 ,P10636-8 [212-225] ,1 ,5722389 ,33652639
High ,[R].IPAKTPPAPK.[T] , , ,1 ,1 ,P10636-8 ,P10636-8 [142-151] ,1 ,2015586.75 ,38656450
High ,[K].CGSLGNIHHKPGGGQVEVK.[S] ,1xCarbamidomethyl [C1] , ,1 ,3 ,P10636-8 ,P10636-8 [293-311] ,0 ,218379137.5 ,63191884
High ,[K].IGSTENLK.[H] , , ,1 ,5 ,P10636-8 ,P10636-8 [231-238] ,0 ,887492361 ,95150178
High ,[R].TPSLPTPPTR.[E] , , ,1 ,4 ,P10636-8 ,P10636-8 [183-192] ,0 ,1085564561 ,84114105
High ,[R].SRTPSLPTPPTR.[E] , , ,1 ,1 ,P10636-8 ,P10636-8 [181-192] ,1 ,308283264 ,78590822
High ,[K].SKIGSTENLKHQPGGGK.[V] , , ,1 ,1 ,P10636-8 ,P10636-8 [229-245] ,2 ,551345.375 ,38888975
High ,[K].GADGKTKIATPR.[G] , , ,1 ,1 ,P10636-8 ,P10636-8 [115-126] ,2 ,593317.6875 ,45036840
High ,[K].SEKLDFKDR.[V] , , ,1 ,2 ,P10636-8 ,P10636-8 [312-320] ,2 ,32312068 ,53312265
High ,[KR].CGSKDNIK.[H] ,1xCarbamidomethyl [C1] , ,2 ,1 ,P10636-8; P27546 ,P10636-8 [262-269]; P27546 [981-988],1 ,4449589 ,82881130
tests/testConfig.toml
+ 5
− 5
View file @ 6f140af3
......@@ -13,18 +13,18 @@ title="Abundance Parser Configuration"
#input_files=[ "/input/file1",
# path to file2
# ]
input_files=["tests/sampleInput.csv"]
input_files=["tests/sample2.csv"]
#fasta file(s) containing the protein sequence(s) to align against
prot_seq_fasta=["data/2N4R_wt_tau.fasta","data/1N4RP301STau.fasta"]
[output]
#Relative or absolute path to desired output directory
output_directory="output/"
output_directory="output/testOutput/"
#this stub is prepended by the file name of the input file
residue_output_name_stub="residueModificationAnalysis"
peptide_output_name_stub='peptideModificationAnalusis'
peptide_output_name_stub='peptideModificationAnalysis'
#Configuration of parser settings
[parser_config]
......@@ -33,8 +33,8 @@ title="Abundance Parser Configuration"
using_fileID_column=false
#Title of column containing abundance. If using_fileID_column is set to
#true, only the first entry will be used
abundance_col_titles=["Abundance :F1"]
calculate_peptide_modifications=false
abundance_col_titles=["Abundance :F1", "Abundance:F2"]
calculate_peptide_modifications=true
[parser_config.regex]
regex_file="data/parser_regex.toml"
......
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