README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# pfamscanr

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The goal of pfamscanr is to ...

## Installation

You can download the development version from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("USCbiostats/pfamscanr")
```
## Example

This is an example extracted directly from the website https://www.ebi.ac.uk/Tools/pfa/pfamscan/

```{r example, eval=FALSE}
library(pfamscanr)
ans <- pfamscan(
  fasta_str = ">sp|P35858|ALS_HUMAN OS=Homo sapiens GN=IGFALS PE=1 SV=1
  MALRKGGLALALLLLSWVALGPRSLEGADPGTPGEAEGPACPAACVCSYDDDADEL
  SVFCSSRNLTRLPDGVPGGTQALWLDGNNLSSVPPAAFQNLSSLGFLNLQGGQLGS
  LEPQALLGLENLCHLHLERNQLRSLALGTFAHTPALASLGLSNNRLSRLEDGLFEG
  LGSLWDLNLGWNSLAVLPDAAFRGLGSLRELVLAGNRLAYLQPALFSGLAELRELD
  LSRNALRAIKANVFVQLPRLQKLYLDRNLIAAVAPGAFLGLKALRWLDLSHNRVAG
  LLEDTFPGLLGLRVLRLSHNAIASLRPRTFKDLHFLEELQLGHNRIRQLAERSFEG
  LGQLEVLTLDHNQLQEVKAGAFLGLTNVAVMNLSGNCLRNLPEQVFRGLGKLHSLH
  LEGSCLGRIRPHTFTGLSGLRRLFLKDNGLVGIEEQSLWGLAELLELDLTSNQLTH
  LPHRLFQGLGKLEYLLLSRNRLAELPADALGPLQRAFWLDVSHNRLEALPNSLLAP
  LGRLRYLSLRNNSLRTFTPQPPGLERLWLEGNPWDCGCPLKALRDFALQNPSAVPR
  FVQAICEGDDCQPPAYTYNNITCASPPEVVGLDLRDLSEAHFAPC",
  email = "your@email.com",
  httr::config(connecttimeout=60)
)
```

```{r echo=FALSE}
data("P35858", package="pfamscanr")
ans <- P35858
```

```{r}
ans
```