[BioC] retrieve genomic coordinates of FASTA file

[James W. MacDonald]

Hi João,

João Fadista wrote:
> Hi,
>  
> I would like to know if there is any bioconductor (or other) tool that is able to retrieve a batch of sequences from a fasta file, given the desired genomic coordinates.
>  
> Desired genomic coordinates: 
> chr1 1 5
> chr2 8 13
>  
> Example of a fasta input file:
>> pig_chr1
> acacactagagata
>> pig_chr2
> gagagagcgcgcatgtgt
>  
> Example of a fasta output file:
>> pig_chr1_start1_end5
>  acaca
>> pig_chr2_start8_end13
> cgcgca

 > library(Biostrings)
 > tmp <- read.DNAStringSet("pig.fa","fasta")
Read 4 items
 > tmp
   A DNAStringSet instance of length 2
     width seq                                               names 

[1]    14 ACACACTAGAGATA                                    pig_chr1
[2]    18 GAGAGAGCGCGCATGTGT                                pig_chr2
 > tmp[[1]][1:5]
   5-letter "DNAString" instance
seq: ACACA
 > tmp[[2]][8:13]
   6-letter "DNAString" instance
seq: CGCGCA
 > as.character(tmp[[1]][1:5])
[1] "ACACA"

Best,

Jim



>  
>  
>  
>  
> 
> Med venlig hilsen / Regards
> 
> João Fadista
> Ph.d. studerende / Ph.d. student
> 
> 
>  	
>  	 AARHUS UNIVERSITET / UNIVERSITY OF AARHUS	
> Det Jordbrugsvidenskabelige Fakultet / Faculty of Agricultural Sciences	
> Inst. for Genetik og Bioteknologi / Dept. of Genetics and Biotechnology	
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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662