Command for getting a fragment from a sequence file

[chariko]

Hi all,

Could anyone tell me how to get from a sequence file the sequence which is delimited from certain positions? As an example:

Original file:

asdfgh
qwert


Get sequence from positions 2 to 8:

I tried the following:

cat original.txt | cut -c 2-8 >result file

Result file:

sdfgh
wert

Instead of that I would like to obtain:

sdfghqwe

Can anyone help me?

[mastal]

How long are the actual sequences you are working with?

It looks like your command would work if your sequence was all on one line.

[chariko]

How long are the actual sequences you are working with?

It looks like your command would work if your sequence was all on one line.

You are right mastal, the command works if my sequence is all on one line, the problem is that sometimes it´s not.

Actually my sequences are contigs with about 235000 nucleotides...

[Richard Finney]

Consider tr command

tr -d "\n" to eliminate carriage returns.

Example:
cat file | tr -d "\n" | cut -b1-7

[TiborNagy]

Seqret from Emboss package can handle it:
seqret input.fasta -sbegin -send

[chariko]

# Richard This could be an option thanks!!

# TiborNagy I just installed the Emboss package run your command and your option is just what I was looking for. thank you very much!!!

[santhilalsubhash]

Try this

cat original.txt | sed 's/\n//g' | cut -c 2-8 >result file

OR

Other option will be, you can parse your BED file through this command with a simple perl or bash script.
fastacmd -d input.fasta -s Chromosome -L start,stop

Download fastacmd linux binary from here. Because in new BLAST tool this has been replace by blastdbcmd which does not supports this and not available in NCBI website.