A tool to identify transmembrane proteins from a given list of gene or protein IDs.

Project description

MembProtFinder

A tool to identify transmembrane proteins from a given list of gene or protein IDs.

Usage

$ MembProtFinder [-h] --infile INFILE --infile-index-column INFILE_INDEX_COLUMN --givenIDs GIVENIDS --outfile OUTFILE [--TMcount] [--TMcoordinates] [--filter]

Options

-h, --help: Show this help message and exit
--infile INFILE: Input file containing gene or protein identifiers
--infile-index-column INFILE_INDEX_COLUMN: Index of the column containing gene or protein identifiers in the input file (0-based)
--givenIDs GIVENIDS: Type of identifiers to search for in the database
--outfile OUTFILE: Output file with the results
--filter: Filter out entries that are not transmembrane proteins

Example

Input File

Genes
ENSG00000075624
ENST00000275493
ENSG00000141510
ENST00000342462
ENSG00000184895
ENSG00000184895
ENSG00000184895
ENSG00000184895
ENSG00000184895
ENSG00000184895
ENSG00000184895
ENSG00000184895
ENSG00000184895
ENSG00000184895
ENSG00000184895
ENSG00000184895
ENSG00000184895

Output File

Genes	Gene Name	Transmembrane Protein?	Transmembrane_Helices_Count	Transmembrane_Helices_Positions
ENST00000275493	EGFR	True	1	TM1: TRANSMEM 646..668
ENST00000342462	TMPPE	True	5	TM1: TRANSMEM 7..27 TM2: TRANSMEM 43..63 TM3: TRANSMEM 87..107 TM4: TRANSMEM 114..134 TM5: TRANSMEM 162..182

Installation

$ pip install MembProtFinder

Project details

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This version

0.0.3

Jun 6, 2024

0.0.2

Jun 6, 2024

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