find_url_ebi: Locates and check if fastq files exists in ebi

In JokingHero/ORFik: Open Reading Frames in Genomics

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")

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.