Script to download fasta seqeuences for FGF1 to FGF12

Question

[Shicheng Guo]

Hi All,

Who can share a script to download human gene fasta/sequences for FGF1, FGF2, FGF3, FGF4, FGF5, FGF6 and FGF7 at the same time?

Thanks.

[Ankit]

You can try using bedtools getfasta.

1. First obtain coordinates of the gene (eg. FGF1 and genome version hg19).

   chr5 141971743 142077635 FGF1(GRCh37/hg19) (note: tab-separated)

2. Run getfasta using fasta file hg19 version:

bedtools getfasta -fi hg19.fa -bed FGF1.bed -fo FGF1.fa

FGF1.fa will be your fasta sequence.

And you can do the same for other genes by making a shell script and it will extract all at the same time. Make a bed of file of all coordinates of the gene of your interest and run getfasta.

Answer 1

[swbarnes2]

Why won't BioMart at ensembl do what you want?

[Shicheng Guo]

Thanks. any script to share?

[swbarnes2]

Why didn't Biomart work for you?

Answer 2

[GenoMax]

Using EntrezDirect. Following will get you only RefSeq entries (which is what I assume would be of interest).

$  esearch -db nuccore -query "FGF1 [GENE] AND Homo sapiens [ORGN]" | efetch -format docsum | xtract -pattern DocumentSummary -if SourceDb -contains refseq -element Caption | xargs -n 1 sh -c 'efetch -db nuccore -id "$0" -format fasta_cds_na'