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Compute first two isotopologues intensity from peptide sequence.

Project description

Seq-to-first-iso

Compute first isotopologues intensity from peptide sequence

Installation

pip-based

$ pip install seq-to-first-iso

Developer mode

Install conda.

Clone repo:

$ git clone https://github.com/pierrepo/seq-to-first-iso
$ cd seq-to-first-iso

Create conda environment:

$ conda env create -f environment.yml

Remarque: for a fully reproducible environment, you could also use:

$ conda env create -f environment.lock.yml

Activate conda environment:

$ conda activate seq-to-first-iso

Install local package:

$ pip install -e .

Usage

The script takes a file with one sequence of amino acids per line and returns a tsv of the file with columns:

sequence mass formula formula_X M0_NC  M1_NC  M0_12C  M1_12C 

Once installed, the script can be called with:

$ seq-to-first-iso filename [-o output_name] [-n amino_acids...]

Optional arguments are in square brackets
This will create filename.tsv if filename is a correct file

Options

  • -h, --help:
    Provide a help page

  • -o, --output:
    Change the name of the output file

  • -n, --non-labelled-aa:
    Take 1 or more amino acid separated by a comma

Examples

  • You can provide a list of amino acids which will keep default isotopic abundance:

Supposing peptides.txt :

YAQEISR
VGFPVLSVKEHK
LAMVIIKEFVDDLK

The command

$ python seq_to_first_iso.py peptides.txt -n V,W

will create peptides.tsv :

sequence mass formula formula_X M0_NC M1_NC M0_12C M1_12C
YAQEISR 865.42938099921 C37H59O13N11 C37H59O13N11 0.6206414140575179 0.280870823368276 0.9206561231798033 0.05161907174495234
VGFPVLSVKEHK 1338.7659712609 C63H102O16N16 C48H102O16N16X15 0.4550358985377136 0.34506032928190855 0.7589558393662944 0.18515489894512063
LAMVIIKEFVDDLK 1632.91606619252 C76H128O21N16S1 C66H128O21N16S1X10 0.36994021481230627 0.3373188347614264 0.7475090558698947 0.15292723586285323

Where, in 12C enrichment conditions, the isotopologue intensity M0_12C and M1_12C are computed with unlabelled Valine and Tryptophan (V and W have default isotopic abundance)

  • You can change the name of the output file:
$ python seq_to_first_iso.py peptides.txt -o sequence

will create a file named sequence.tsv

Credits

  • Bioconda:

    • Grüning, Björn, Ryan Dale, Andreas Sjödin, Brad A. Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, the Bioconda Team, and Johannes Köster. 2018. “Bioconda: Sustainable and Comprehensive Software Distribution for the Life Sciences”. Nature Methods, 2018 doi:10.1038/s41592-018-0046-7.
  • pyteomics:

    • Goloborodko, A.A.; Levitsky, L.I.; Ivanov, M.V.; and Gorshkov, M.V. (2013) “Pyteomics - a Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics”, Journal of The American Society for Mass Spectrometry, 24(2), 301–304. DOI: 10.1007/s13361-012-0516-6

    • Levitsky, L.I.; Klein, J.; Ivanov, M.V.; and Gorshkov, M.V. (2018) “Pyteomics 4.0: five years of development of a Python proteomics framework”, Journal of Proteome Research. DOI: 10.1021/acs.jproteome.8b00717

  • MIDAs:

    • Alves G, Ogurtsov AY, Yu YK (2014) Molecular Isotopic Distribution Analysis (MIDAs) with adjustable mass accuracy. J Am Soc Mass Spectrom, 25: 57-70. DOI: 10.1007/s13361-013-0733-7

Changelog

Dev

0.4.0 (2019-06-21)

Changed

  • Add support for Xtandem Parsing
    • Breaking change: sequence_parser() now returns a dict with "annotations", "raw_sequences", "sequences", "modifications" and "ignored_lines"
    • Add get_mods_composition() that returns a composition from a list of Unimod PTMs
    • Remove the appended "_stfi" if -o flag is provided

0.3.0 (2019-04-18)

Changed

  • Add support for files with annotations before the sequences
    • Breaking change: sequence_parser() now returns (annotations, sequences, ignored_lines)
    • seq_to_tsv() now accepts (sequences, unlabelled_aa, annotations=None)

Fixed

  • Output files now have "_stfi" appended to differentiate from .tsv input files with the same name

0.2.1 (2019-04-17)

  • Format CHANGELOG

0.2.0 (2019-04-17)

  • Add bumpversion

Changed

  • seq_to_tsv() no longer writes a file, instead it returns a dataframe

0.1.0 (2019-04-08)

  • First release

BSD 3-Clause License

Copyright (c) 2019, Lilian Yang-crosson All rights reserved. Copyright (c) 2019, Pierre Poulain All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

  • Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

  • Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

  • Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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