Ecosyste.ms: Issues

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GitHub / levitsky/pyteomics issues and pull requests

#152 - Improve and document modX terminal group support

Pull Request - State: open - Opened by levitsky 16 days ago - 2 comments

#151 - Support for Ion Mobility data from Bruker devices?

Issue - State: open - Opened by LoponteHF about 1 month ago - 5 comments

#150 - question about how cvParams are read

Issue - State: closed - Opened by colin-combe 2 months ago - 2 comments

#149 - question about ms2 reader

Issue - State: closed - Opened by colin-combe 2 months ago - 13 comments

#148 - Add modification caching; Constant terminal mods for ProForma

Pull Request - State: closed - Opened by mobiusklein 2 months ago

#147 - [proforma] Use cache on modification resolvers

Pull Request - State: closed - Opened by RalfG 3 months ago - 8 comments

#145 - question about memory use with mzIdentML reader

Issue - State: open - Opened by colin-combe 3 months ago - 16 comments

#144 - Adjust pickling

Pull Request - State: closed - Opened by mobiusklein 3 months ago

#143 - [proforma] Modifications cannot be pickled after being resolved

Issue - State: closed - Opened by RalfG 3 months ago - 2 comments

#142 - Rename _build_index to build_byte_index

Pull Request - State: closed - Opened by levitsky 5 months ago

#141 - Fix for #136 is unreleased

Issue - State: closed - Opened by sjust-seerbio 5 months ago - 2 comments

#140 - IndexSavingMixin._build_index() is never called by text parsers?

Issue - State: closed - Opened by levitsky 5 months ago - 4 comments

#139 - Failing to parse UniProt description with space in gene symbol

Issue - State: closed - Opened by caetera 5 months ago - 2 comments

#138 - Add a warning when an empty index is created, customize it for mgf

Pull Request - State: closed - Opened by levitsky 6 months ago - 1 comment

#137 - Calculate m/z for proforma in calculate_mass

Pull Request - State: closed - Opened by levitsky 6 months ago - 4 comments

#136 - New problem with parsing FASTA files

Issue - State: closed - Opened by tristanbrown 7 months ago - 3 comments

#135 - Incorrect expasy rule

Issue - State: closed - Opened by Karl-Krauth 7 months ago - 1 comment

#134 - MGF File Loading Error - IndexedMGF Object Empty

Issue - State: closed - Opened by CCranney 7 months ago - 3 comments

#133 - Fix UniMod by ID

Pull Request - State: closed - Opened by mobiusklein 7 months ago - 2 comments

#130 - Mass modification hashing

Pull Request - State: closed - Opened by mobiusklein 8 months ago - 1 comment

#129 - If psims is available, use its Unimod because it caches and vendors

Pull Request - State: closed - Opened by mobiusklein 9 months ago - 3 comments

#128 - Import of Unimod schema crashes when Unimod is down

Issue - State: closed - Opened by jonasscheid 9 months ago - 5 comments

#127 - Deisotoping Methodology - future pyteomics implementation?

Issue - State: closed - Opened by CCranney 9 months ago - 2 comments

#126 - Update imports for sqlalchemy v2.0 changes

Pull Request - State: closed - Opened by RalfG 10 months ago - 4 comments

#125 - Fix levitsky/pyteomics#124

Pull Request - State: closed - Opened by sjust-seerbio 10 months ago

#123 - C-terminal modifications in calculate_mass

Issue - State: closed - Opened by JB91451 10 months ago - 2 comments

#122 - MGF Writing error - `TypeError: 'numpy.int64' object is not iterable`

Issue - State: closed - Opened by CCranney 10 months ago - 3 comments

#121 - Use metaclass to add __init__ to flavored fasta parsers

Pull Request - State: closed - Opened by levitsky 10 months ago

#120 - Add raw fasta file header to parsers

Pull Request - State: closed - Opened by caetera 10 months ago - 7 comments

#119 - Pandas is now a hard requirement

Issue - State: closed - Opened by mobiusklein 10 months ago - 3 comments

#118 - Pandas Version Checking Fails

Issue - State: closed - Opened by jmmitc06 10 months ago - 3 comments

#117 - Add optional quantile regression for get_RCs

Pull Request - State: closed - Opened by markmipt 11 months ago

#116 - Load mzML file with ion mobility

Issue - State: closed - Opened by mobiotwin 11 months ago - 4 comments

#115 - The issue of secondary spectrum

Issue - State: closed - Opened by morestart about 1 year ago - 12 comments

#113 - Polarity missing from mzMLb parser

Issue - State: closed - Opened by sorenwacker about 1 year ago - 2 comments

#112 - Error with version 4.6 when trying to open mzML or mzXML files.

Issue - State: closed - Opened by sorenwacker about 1 year ago - 1 comment

#111 - file_mode keyword only param to write mgf function breaks linters

Issue - State: closed - Opened by hechth about 1 year ago - 2 comments

#110 - Unable to use map() method in PepXML class

Issue - State: closed - Opened by freejstone about 1 year ago - 2 comments

#108 - unable to extract "charge array" with pyteomics.ms2.IndexedMS2

Issue - State: closed - Opened by irleader over 1 year ago - 7 comments

#107 - C-terminal modification parsing in ProForma

Issue - State: closed - Opened by caetera over 1 year ago - 2 comments

#106 - Fix iteration in example for calculating theoretical fragment m/z

Pull Request - State: closed - Opened by michabirklbauer over 1 year ago - 1 comment

#105 - Pass through the decode_binary parameter in read for mzml and mzxml

Pull Request - State: closed - Opened by mobiusklein over 1 year ago - 1 comment

#104 - [mzml] `decode_binary` argument documented but not implemented

Issue - State: closed - Opened by RalfG over 1 year ago - 1 comment

#102 - Hard-code UniRef keys, remove extra fields created by str.split()

Pull Request - State: closed - Opened by levitsky over 1 year ago

#101 - Address broader ProForma colon ambiguity

Pull Request - State: closed - Opened by mobiusklein over 1 year ago

#100 - Incorrect resolving of modification names with semicolon by UnimodModification

Issue - State: closed - Opened by caetera over 1 year ago - 2 comments

#99 - Fix issue #98 for colon-containing mods

Pull Request - State: closed - Opened by mobiusklein over 1 year ago - 1 comment

#97 - Extract date stamp of data acquisition?

Issue - State: closed - Opened by sorenwacker over 1 year ago - 2 comments

#96 - Module 'pyteomics.proforma' has no attribute 'Proforma'

Issue - State: closed - Opened by alessandro-vai over 1 year ago - 1 comment

#95 - Resolve `referenceableParamGroupRef`

Pull Request - State: closed - Opened by mobiusklein over 1 year ago - 4 comments

#94 - RE

Issue - State: closed - Opened by mafreitas over 1 year ago - 6 comments

#93 - Hard-code key=value pairs in Uniprot headers as described in the spec

Pull Request - State: closed - Opened by levitsky over 1 year ago - 4 comments

#92 - Support slicing ProForma

Pull Request - State: closed - Opened by mobiusklein over 1 year ago

#91 - [BUG (??)] Terminal modifications are kept regardless of slicing

Issue - State: closed - Opened by jspaezp over 1 year ago - 2 comments

#90 - Cannot reproduce Example 4: Spectrum Annotation

Issue - State: closed - Opened by alessandro-vai over 1 year ago - 6 comments

#89 - Link to https instead of http

Pull Request - State: closed - Opened by fabianegli over 1 year ago

#88 - Add installatoin instructions for pyteomics for conda from the bioconda channel

Issue - State: closed - Opened by fabianegli over 1 year ago - 7 comments
Labels: documentation

#87 - FDR calculate

Issue - State: closed - Opened by KKKKK-tech over 1 year ago - 2 comments

#85 - Improve documentation of Unimod loading and highlight in ProForma

Pull Request - State: closed - Opened by mobiusklein over 1 year ago - 5 comments

#84 - use packaging instead of distutils if available

Pull Request - State: closed - Opened by fabianegli over 1 year ago

#82 - [Pitch] Include unimod with the release of pyteomics

Issue - State: closed - Opened by jspaezp over 1 year ago - 8 comments

#81 - Example 4: Spectrum Annotation appears to be broken

Issue - State: closed - Opened by wsnoble over 1 year ago - 3 comments

#79 - [Question] How to get instrument information from mzML

Issue - State: closed - Opened by jspaezp over 1 year ago - 2 comments

#77 - [proforma] Final and C-terminal modifications are parsed as one

Issue - State: closed - Opened by RalfG almost 2 years ago

#76 - fasta .get_by_id method only matching single entry

Issue - State: closed - Opened by radusuciu about 2 years ago - 4 comments

#75 - Update to regex for Uniprot Fasta heade rparser

Issue - State: closed - Opened by hguturu about 2 years ago - 7 comments

#74 - tandem.DataFrame fails when tandem was run on .cmn input

Issue - State: closed - Opened by kesinger about 2 years ago - 2 comments

#73 - Is there an idXML writer anywhere? what about a schema?

Issue - State: closed - Opened by trishorts about 2 years ago - 2 comments

#72 - How to convert the modified scans into an mzXML file?

Issue - State: closed - Opened by Mnago over 2 years ago - 1 comment

#71 - typo?

Pull Request - State: closed - Opened by superrino130 over 2 years ago - 1 comment

#70 - Switch USI test backend

Pull Request - State: closed - Opened by mobiusklein over 2 years ago - 1 comment

#69 - Fix generic modification resolver

Pull Request - State: closed - Opened by mobiusklein over 2 years ago - 1 comment

#67 - Explicitly close the thread pool in PROXIAggregator on GC

Pull Request - State: closed - Opened by mobiusklein over 2 years ago - 1 comment

#66 - ThreadPool in PROXIAggregator not closed

Issue - State: closed - Opened by bittremieux over 2 years ago - 2 comments

#65 - can't get m/z array and intensity array

Issue - State: closed - Opened by morestart over 2 years ago - 5 comments

#64 - Restores IndexedIterfind.map functionality

Pull Request - State: closed - Opened by mobiusklein over 2 years ago

#63 - Proforma modification hashing and other fixes

Pull Request - State: closed - Opened by mobiusklein over 2 years ago - 2 comments

#62 - [proforma] Make modification object hashable

Issue - State: closed - Opened by RalfG over 2 years ago - 6 comments

#61 - Implement `charge_carrier` and `absolute` arguments for m/z calculation

Pull Request - State: closed - Opened by levitsky over 2 years ago - 8 comments

#60 - mass calculation with negative charge

Issue - State: closed - Opened by mgleeming over 2 years ago - 3 comments
Labels: enhancement, good first issue

#58 - DOCFIX Remove trailing "s" from example code

Pull Request - State: closed - Opened by mobiusklein almost 3 years ago

#57 - Document the unit handling and controlled vocabulary string features

Pull Request - State: closed - Opened by mobiusklein almost 3 years ago

#56 - mzML reader for RT ambiguous units

Issue - State: closed - Opened by mwang87 almost 3 years ago - 4 comments

#54 - Shuffling that preserves some amino acids

Pull Request - State: closed - Opened by caetera almost 3 years ago - 2 comments

#53 - Update default featureXML schema_info and version, add overrides

Pull Request - State: closed - Opened by levitsky almost 3 years ago

#52 - Warning is triggered even with `use_index=False`

Issue - State: closed - Opened by hguturu almost 3 years ago - 4 comments

#51 - Fix ProForma Parsing and Update Docs

Pull Request - State: closed - Opened by mobiusklein almost 3 years ago - 1 comment

#50 - `spectrum_reference` should not be a int in `featureXML`

Issue - State: closed - Opened by hguturu almost 3 years ago - 8 comments

#48 - Properly detect non-standard array name when it is a term value

Pull Request - State: closed - Opened by mobiusklein about 3 years ago

#47 - Problems with loading Unimod into PostgreSQL

Issue - State: open - Opened by radusuciu about 3 years ago - 2 comments

#45 - PROXIAggregator may also return tagged responses instead of merging

Pull Request - State: closed - Opened by mobiusklein about 3 years ago

#44 - mzident parser

Issue - State: closed - Opened by jschmacht about 3 years ago - 3 comments