Skip to main content
Join the official Python Developers Survey 2018 and win valuable prizes: Start the survey!

Quickly parse genes and exons from a RefGene file

Project description

<h1 align="center">RefGene-Parser</h1>

<h3 align="center">Installation</h3>

Clone the respository and then install locally:

```bash
$ git clone https://github.com/clintval/refgene-parser.git
$ pip install refgene-parser
```

<h3 align="center">Dependencies</h3>

- None

<h3 align="center">Tutorial</h3>

Iterate over the records in a RefGene file:

```python

from refgene_parser import RefGene

refgene = RefGene('mm10.refGene.txt.gz')

for i, gene in enumerate(refgene):
if i >= 10: break
print(gene)
```

```python
Gene("chr2", 11705292, 11733985, "+", name="Il15ra", id="NM_001271498")
Gene("chr7", 142434976, 142440396, "+", name="Syt8", id="NM_001285857")
Gene("chr1", 78424744, 78488897, "-", name="Farsb", id="NM_011811")
Gene("chr11", 62574485, 62600305, "+", name="Trpv2", id="NM_011706")
Gene("chr12", 100199434, 100209824, "+", name="Calm1", id="NM_009790")
Gene("chr5", 30933142, 30945480, "-", name="Cgref1", id="NM_026770")
Gene("chr4", 142084297, 142088101, "+", name="Tmem51os1", id="NR_027137")
Gene("chr10", 77257772, 77259223, "-", name="Gm10941", id="NR_026944")
Gene("chr10", 77706586, 77706986, "+", name="Gm10272", id="NR_026831")
Gene("chr7", 100549116, 100607996, "-", name="Mrpl48", id="NR_003559")
Gene("chr7", 7212995, 7278289, "-", name="Vmn2r29", id="NR_003555")
```


<h5 align="center">Exact match for a gene symbol name</h5>

> Will return the first record matching with `name == Kras`

```python
Kras = refgene.gene_by_name('Kras')
print(Kras)
print(Kras.sam_interval)
print(Kras.num_exons)
```

```python
Gene("chr6", 145216698, 145250231, "-", name="Kras", id="NM_021284")
'chr6:145216698-145250231'
5
```


<h5 align="center">Exact match for a gene ID</h5>

> Will return the first record matching `id == NM_009085`

```python
NM_009085 = refgene.gene_by_id('NM_009085')
```

```python
Gene("chr17", 46243919, 46248045, "-", name="Polr1c", id="NM_009085")
```


<h5 align="center">Fuzzy match for a gene symbol name</h5>

```python
list(refgene.genes_by_name_pattern('^.ras$'))
```

```python
[Gene("chr3", 103058284, 103067914, "+", name="Nras", id="NM_010937"),
Gene("chr7", 45018006, 45021644, "+", name="Rras", id="NM_009101"),
Gene("chrX", 7924275, 7928607, "-", name="Eras", id="NM_181548"),
Gene("chr7", 141189933, 141194004, "-", name="Hras", id="NM_008284"),
Gene("chr6", 145216698, 145250231, "-", name="Kras", id="NM_021284"),
Gene("chr9", 99385419, 99436712, "-", name="Mras", id="NM_008624"),
Gene("chr7", 141189933, 141194004, "-", name="Hras", id="NM_001130444"),
Gene("chr7", 141189933, 141194004, "-", name="Hras", id="NM_001130443")]
```


<h5 align="center">Fuzzy match for a gene ID</h5>

```python
list(refgene.genes_by_id_pattern('NR_00355*'))
```

```python

[Gene("chr7", 100549116, 100607996, "-", name="Mrpl48", id="NR_003559"),
Gene("chr7", 7212995, 7278289, "-", name="Vmn2r29", id="NR_003555"),
Gene("chr15", 82636749, 82642045, "-", name="Cyp2d13", id="NR_003552"),
Gene("chr3", 92373914, 92375229, "+", name="Sprr2g", id="NR_003548"),
Gene("chr13", 104173720, 104178466, "-", name="Trappc13", id="NR_003546"),
Gene("chr5", 30950065, 30955095, "+", name="Abhd1", id="NR_003522"),
Gene("chr17", 3064317, 3084183, "-", name="Pisd-ps2", id="NR_003519"),
Gene("chrUn_JH584304", 52673, 59689, "-", name="Pisd-ps3", id="NR_003518"),
Gene("chr11", 3124020, 3131944, "+", name="Pisd-ps1", id="NR_003517"),
Gene("chr16", 97536080, 97560901, "+", name="Mx2", id="NR_003508"),
Gene("chr5", 120812634, 120824160, "+", name="Oas1b", id="NR_003507"),
Gene("chr5", 10865028, 10870808, "+", name="Gm6455", id="NR_003596"),
Gene("chr19", 5842295, 5845480, "-", name="Neat1", id="NR_003513"),
Gene("chr15", 62217540, 62219451, "-", name="H2afy3", id="NR_003523"),
Gene("chrX_GL456233_random", 268798, 270075, "+", name="Zf12", id="NR_003547"),
Gene("chr16", 97447034, 97462906, "-", name="Mx1", id="NR_003520"),
Gene("chr11", 88964665, 88966917, "-", name="Gm15698", id="NR_003564"),
Gene("chr13", 12614064, 12650395, "-", name="Gpr137b-ps", id="NR_003568")]
```

Project details


Release history Release notifications

This version
History Node

0.0.1

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
refgene_parser-0.0.1.tar.gz (4.5 kB) Copy SHA256 hash SHA256 Source None Oct 3, 2017

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page