Question: maize ESTs NCBI
0
gravatar for dinesh
5.2 years ago by
dinesh50
India
dinesh50 wrote:

my question looks simple but im new to bioinformatics. i have  a task of downloading maize ests which are around 20lakhs.So, how can i download this ESTs in batches 

for example : 50000 ESTs in one file and next 40000 ESTs  in one file like wise.

Thanks in advance

ncbi • 1.4k views
ADD COMMENTlink modified 5.2 years ago by Pierre Lindenbaum125k • written 5.2 years ago by dinesh50
0
gravatar for Pierre Lindenbaum
5.2 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum125k wrote:

go to http://www.ncbi.nlm.nih.gov/nucest?term=%22zea%20mays%22[Organism]

select 'send to -> file -> fasta ' & download

use awk to produce sequences with two lines (name+header) , and split .

awk '/^>/ {if(NR>1) printf("\n"); print;next;} {printf("%s",$0);}' your.fasta  |  split -l 100000 - prefix

 

 

ADD COMMENTlink written 5.2 years ago by Pierre Lindenbaum125k
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