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
1 maintainer
Metadata
1 maintainer
Release files for MembProtFinder 0.0.3
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| membprotfinder-0.0.3.tar.gz | 4.0 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| MembProtFinder-0.0.3-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 8.5 kB
Release files / membprotfinder-0.0.3.tar.gz
| Download URL | membprotfinder-0.0.3.tar.gz |
|---|---|
| Size | 4.0 kB |
| Tags | Source |
|
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| Uploaded via |
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Release files / MembProtFinder-0.0.3-py3-none-any.whl
| Download URL | MembProtFinder-0.0.3-py3-none-any.whl |
|---|---|
| Size | 4.5 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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No |
| Uploaded via |
twine/5.1.0 CPython/3.12.3
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