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Commit 70a4b2d6 authored by Vishruth Mullapudi's avatar Vishruth Mullapudi Committed by Vishruth Mullapudi
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fixed unlocalized modifications not being counted in fragment modification... 

fixed unlocalized modifications not being counted in fragment modification analysis by adding a field in the data indicating that the fragment posesses a modification
parent 28505a8f
1 merge request!1Fix unlocalized peptide mods not adding
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.idea/abundanceparser.iml
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− 2
View file @ 70a4b2d6
......@@ -4,11 +4,10 @@
<content url="file://$MODULE_DIR$">
<excludeFolder url="file://$MODULE_DIR$/venv" />
</content>
<orderEntry type="jdk" jdkName="Python 3.7 (venv)" jdkType="Python SDK" />
<orderEntry type="jdk" jdkName="Python 3.7 (abundanceparser)" jdkType="Python SDK" />
<orderEntry type="sourceFolder" forTests="false" />
</component>
<component name="TestRunnerService">
<option name="projectConfiguration" value="Twisted Trial" />
<option name="PROJECT_TEST_RUNNER" value="Twisted Trial" />
</component>
</module>
\ No newline at end of file
.idea/misc.xml
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<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="ProjectRootManager" version="2" project-jdk-name="Python 3.7 (venv)" project-jdk-type="Python SDK" />
<component name="ProjectRootManager" version="2" project-jdk-name="Python 3.7 (abundanceparser)" project-jdk-type="Python SDK" />
</project>
\ No newline at end of file
config.toml
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View file @ 70a4b2d6
#This is a TOML Document
#The TOML specification can be found here: https://github.com/toml-lang/toml
title="Abundance Parser Configuration"
#The input source and parsing parameters
[input]
#The CSV input file(s) to read data from
......@@ -13,14 +11,14 @@ title="Abundance Parser Configuration"
#input_files=[ "/input/file1",
# path to file2
# ]
input_files=["data/input/LUM1_705666-peptide.csv","data/input/LUM1_705666-peptidegroups.csv"]
input_files=["data/input/PCF-DC-1732--12--2019_peptide.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/mouse1yr"
output_directory="output/testfix/dailu122019"
#this stub is prepended by the file name of the input file
residue_output_name_stub="residueModificationAnalysis"
......
main.py
+ 21
− 5
View file @ 70a4b2d6
......@@ -236,11 +236,13 @@ def parse_prot_localizations(ftuple: FileTuple, protein_seq_records: Dict, mod_r
"""
file_data: pd.DataFrame = ftuple.FileData
file_data.insert(file_data.shape[1], "valid_modification", False)
mod_loc_column_titles = dict() # maps Sequence Record ID to modification localization column name in DataFrame
frag_loc_column_titles = dict() # maps Sequence Record ID to fragment localization column name in DataFrame
# iterate through all the input proteins to localize against
for prot_id, protein in protein_seq_records.items():
frag_modification_status = []
prot_mod_localizations = []
positions_in_master = [] # master here is the protein currently being aligned against
# the protein sequence to align against to find the fragment's location in the sequence
......@@ -257,17 +259,29 @@ def parse_prot_localizations(ftuple: FileTuple, protein_seq_records: Dict, mod_r
# PTM modification localization occurs here-------------------------------------------------------------
mod_string = row.modifications
if not str(mod_string) == "nan":
is_validloc = False
matches = re.finditer(mod_regex, mod_string)
prot_mod_localizations.append([int(mod_localization) + frag_index_in_prot for match_obj in matches
for mod_localization in match_obj.groups()
if mod_localization is not ''])
localizations = []
for match_obj in matches:
for mod_localization in match_obj.groups():
is_validloc = True
if mod_localization is not '':
localizations.append((int(mod_localization) + frag_index_in_prot))
prot_mod_localizations.append(localizations)
frag_modification_status.append(is_validloc)
# prot_mod_localizations.append([int(mod_localization) + frag_index_in_prot for match_obj in matches
# for mod_localization in match_obj.groups()
# if mod_localization is not ''])
else:
prot_mod_localizations.append([]) # if no modifications add the list containing no modifications
frag_modification_status.append(False)
# end of PTM/ modification localization-----------------------------------------------------------------
else:
prot_mod_localizations.append([frag_index_in_prot]) # if index is -1 the fragment isn't in this protein
positions_in_master.append([(-1,)]) # indicate that the fragment isn't in this protein
frag_modification_status.append(False)
# clean up the protein ID so we can use it to index things in our DataFrames
sanitized_protein_id = sanitize_str_for_dataframe_index(prot_id)
......@@ -279,6 +293,8 @@ def parse_prot_localizations(ftuple: FileTuple, protein_seq_records: Dict, mod_r
# columns later
file_data.insert(file_data.shape[1], prot_mod_column_title, prot_mod_localizations)
file_data.insert(file_data.shape[1], frag_loc_column_title, positions_in_master)
frag_modification_status = [x or y for x, y in zip(frag_modification_status, file_data['valid_modification'])]
file_data.loc[:, "valid_modification"] = frag_modification_status
mod_loc_column_titles.update({protein.id: prot_mod_column_title})
frag_loc_column_titles.update({protein.id: frag_loc_column_title})
......@@ -355,8 +371,8 @@ def calc_peptide_mod_abundances(ftuple, mod_localization_col_titles, frag_locali
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:
for mods, valid_mod in zip(frags_same_seq[1][mod_col_title], frags_same_seq[1]['valid_modification']):
if mods or valid_mod:
if -1 not in mods:
bools.append(True)
else:
......
tests/sample2.csv deleted 100644 → 0
+ 0
− 71
View file @ 28505a8f
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
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