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annoPipeline-0.0.1
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API-enabled Gene Annotation
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | annoPipeline-0.0.1 |
| نام | annoPipeline |
| نسخه کتابخانه | 0.0.1 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Jim Arnold |
| ایمیل نویسنده | jimmyjamesarnold@gmail.com |
| آدرس صفحه اصلی | https://github.com/jimmyjamesarnold/annoPipeline |
| آدرس اینترنتی | https://pypi.org/project/annoPipeline/ |
| مجوز | MIT |
# annoPipeline - an API-enabled gene annotation pipeline
***annoPipeline*** uses APIs from [mygene.info](http://mygene.info/) and [Entrez esummary](https://dataguide.nlm.nih.gov/eutilities/utilities.html#esummary) to annotate a user-provided list of gene symbols.
Generates a pandas DataFrame with gene symbol, gene name, EntrezID, and bibliographic info for up to 5 pubmed publications where a functional reference was provided (more about functional references at [GeneRIF](https://www.ncbi.nlm.nih.gov/gene/about-generif)).
Designed to be useful for tasks such as:
* identifying relevant publications for a given function
* analyzing publications trends for genes belonging to a common pathway
* identifying influential PIs for a given gene network.
## Reqirements:
* Written for use with Python 3.7, not tested on other versions.
* *annoPipeline* requires:
- numpy >= 1.16.2
- pandas >= 0.24.2
- Biopython >= 1.73
- openpyxl >= 2.6.1
- requests >= 2.21.0
## To Install:
```
pip install annoPipeline
```
Or clone the repo from github.
Then, in the annoPipeline directory, run:
```
python setup.py install
```
Required dependencies will be installed if missing, may take a few seconds.
## Example usage:
Execute the full annotation pipeline on a list of gene symbols like this:
```python
import annoPipeline as ap
# define a list of genes you would like annotated
geneList = ['CDK2', 'FGFR1', 'SLC6A4']
# annoPipeline will execute full annotation pipeline (see individual functions below).
df = ap.annoPipeline(geneList) # returns pandas df with annotations for gene and bibliographic info.
```
- ***ap.annoPipeline*** will default save annotation output to Excel file named by geneList symbols separated by '_'.
### Warning!
If querying a **single gene**, still pass as a list. For example:
```python
import annoPipeline as ap
df = ap.annoPipeline(['CDK2']) # for single gene queries still include [] - will be fixed in later version
```
## v0.0.1 Functionality
### Task 1:
1. From the MyGeneInfo API, use the “Gene query service" GET method to return details on a given list of human gene symbols.
2. From the returned json, parse out the “name", “symbol" and “entrezgene" values and print to screen
Use *queryGenes()*:
```python
import annoPipeline as ap
geneList = ['CDK2', 'FGFR1', 'SLC6A4']
l1 = ap.queryGenes(geneList) # returns list of dicts where keys are default mygene fields (symbol,name,taxid,entrezgene,ensemblgene)
```
### Task 2:
1. Using the appropriate identifier from the above result, send a query to the MyGeneInfo “Gene annotation services" method for each gene
2. From the resulting json, collate up to 5 generif descriptions per gene
3. Write the results to an Excel spreadsheet with columns: gene_symbol, gene_name, entrez_id, generifs
Use *getAnno()*:
```python
import annoPipeline as ap
geneList = ['CDK2', 'FGFR1', 'SLC6A4']
l1 = ap.queryGenes(geneList)
l2 = ap.getAnno(l1, saveExcel=True) # saveExcel defaults False
```
- returns pandas df with genes and up to 5 generifs from mygene.info.
- default **saveExcel**=*False*, to save output to Excel must state *True*
- if *True*, Excel file will be named by geneList symbols separated by '_'.
### Task 3:
1. Use the Pubmed IDs associated with the above generif content to extract additional bibliographic information.
Use *addBibs()*:
```python
import annoPipeline as ap
geneList = ['CDK2', 'FGFR1', 'SLC6A4']
l1 = ap.queryGenes(geneList)
l2 = ap.getAnno(l1)
l3 = ap.addBibs(l2) # will return df with genes and up to 5 generifs from mygene.info
```
* Currently returns the following bibliographic information when available:
* PubDate
* Source
* Title
* LastAuthor
* DOI
* PmcRefCount
نیازمندی
| مقدار | نام |
|---|---|
| >=1.16.2 | numpy |
| >=0.24.2 | pandas |
| >=1.73 | Biopython |
| >=2.6.1 | openpyxl |
| >=2.21.0 | requests |
نحوه نصب
نصب پکیج whl annoPipeline-0.0.1:
pip install annoPipeline-0.0.1.whl
نصب پکیج tar.gz annoPipeline-0.0.1:
pip install annoPipeline-0.0.1.tar.gz