find_url_ebi {ORFik} | R Documentation

## Locates and check if fastq files exists in ebi

### Description

Look for files in ebi following url: ftp://ftp.sra.ebi.ac.uk/vol1/fastq Paired end and single end fastq files.
EBI uses 3 ways to organize data inside vol1/fastq:
- 1: Most common: SRR(3 first)/0(2 last)/whole
- 2: less common: SRR(3 first)/00(1 last)/whole
- 3: least common SRR(3 first)/whole

### Usage

    find_url_ebi(SRR, stop.on.error = FALSE, study = NULL)

### Arguments

`SRR` | character, SRR, ERR or DRR numbers.
`stop.on.error` | logical FALSE, if TRUE will stop if all files are not found. If FALSE returns empty character vector if error is catched.
`study` | default NULL, optional PRJ (study id) to speed up search for URLs.

### Value

full url to fastq files, same length as input (2 urls for paired end data). Returns empty character() if all files not found.

### Examples

    # Test the 3 ways to get fastq files from EBI
    # Both single end and paired end data

    # Most common: SRR(3 first)/0(2 last)/whole
    # Single
    ORFik:::find_url_ebi("SRR10503056")
    # Paired
    ORFik:::find_url_ebi("SRR10500056")

    # less common: SRR(3 first)/00(1 last)/whole
    # Single
    #ORFik:::find_url_ebi("SRR1562873")
    # Paired
    #ORFik:::find_url_ebi("SRR1560083")
    # least common SRR(3 first)/whole
    # Single
    #ORFik:::find_url_ebi("SRR105687")
    # Paired
    #ORFik:::find_url_ebi("SRR105788")

[Package ORFik version 1.14.7 Index]