Efetch extracting large fasta data from positon

Question

[bengoaluoni]

Hello, I am new in bioinformatics and I need to run a little command line to help me to extract fasta sequences. I download Edirect in my Ubuntu, and I read a lot of Efread command.

I try run this line:

efetch -db nuccore -format fasta -id NC_035437.1 -chr_start 214621161 -chr_stop 214618066

And it works, but I need around 200 of these lines, How I do it?

My table of input data is something like that:

NC_035437.1 214621161   214618066
NC_035437.1 209015121   209019563
NC_035437.1 208791830   208794856
NC_035437.1 194797143   194795212
NC_035437.1 187148585   187150444
NC_035437.1 167068722   167071843
NC_035433.1 131712739   131714461

Thank ;)

Answer 1

[Pierre Lindenbaum]

cat input.txt | while read A B E; do efetch -db nuccore -format fasta -id "${A}" -chr_start "${B}" -chr_stop "${E}" ; done

Answer 2

[GenoMax]

Try this (assumes your input file of co-ordinates is space separated) :

$ awk -F ' ' '{print $1,$2,$3}' input_coord_file | xargs -n 3 sh -c 'efetch -db nuccore -format fasta -id $0 -chr_start $1 -chr_stop $2'

[bengoaluoni]

Thank you so much!!! It works ;)

[Ram]

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