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Full Discussion: Sequence extraction
Top Forums Shell Programming and Scripting Sequence extraction Post 302951305 by harpreetmanku04 on Wednesday 5th of August 2015 02:28:34 AM
Old 08-05-2015
Sequence extraction

i want to extract specific region of interest from big file. i have only start position, end position and seq id, see my query is:

I have file1 is this

Code:
>GL3482.1
GAACTTGAGATCCGGGGA
GCAGTGGATCTCCACCAG
CGGCCAGAACTGGTGCAC
CTCCAGGCCAGCCTCGTC
CTGCGTGTC
>GL3550.1
GGCATTTTTGTGTAATTTTTGGCTGGATGAGGT
GACATTTTCATTACTACCATTTTGGAGTACA
>GL3472.1
TTTTCCTGTTCACTGCTGCTTTTCTATAGACAGCA
GCAGCAAGCAGTAAGAGAAAGTA


file2 is this :

Code:
seq id     start    end
GL3482.1   323100   323743
GL3550.1   41911    40888
GL3472.1   274408   272617

and i want result like this:

Code:
>GL3482.1 
TTGAGA
>GL3550.1 
GGCATTTTTGTG
>GL3472.1
TTCCTGTT

when i run this command :

Code:
$ awk 'NR==FNR{if($0~/^>/){i=substr($0,2);getline};a[i]=a[i] $0;next}{print ">" $1 ORS substr(a[$1], $2, $3-$2+1)}' file1 FS=\\t file2

i got no output or output file. why so?
Moderator's Comments:
Mod Comment Please use CODE tags as required by the forum rules you agreed to when you joined this forum.


---------- Post updated at 01:28 AM ---------- Previous update was at 01:21 AM ----------

i am using Ubuntu OS

Last edited by Scrutinizer; 08-05-2015 at 04:07 AM.. Reason: Add CODE tags, remove extraneous closing COLOR tag. Removed spurious space and a newline from first sample file
 

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DIO_SEEK(3)								 1							       DIO_SEEK(3)

dio_seek - Seeks to pos on fd from whence

SYNOPSIS
int dio_seek (resource $fd, int $pos, [int $whence = SEEK_SET]) DESCRIPTION
The function dio_seek(3) is used to change the file position of the given file descriptor. PARAMETERS
o $fd - The file descriptor returned by dio_open(3). o $pos - The new position. o $whence - Specifies how the position $pos should be interpreted: o SEEK_SET (default) - specifies that $pos is specified from the beginning of the file. o SEEK_CUR - Specifies that $pos is a count of characters from the current file position. This count may be positive or nega- tive. o SEEK_END - Specifies that $pos is a count of characters from the end of the file. A negative count specifies a position within the current extent of the file; a positive count specifies a position past the current end. If you set the position past the current end, and actually write data, you will extend the file with zeros up to that position. RETURN VALUES
EXAMPLES
Example #1 Positioning in a file <?php $fd = dio_open('/dev/ttyS0', O_RDWR); dio_seek($fd, 10, SEEK_SET); // position is now at 10 characters from the start of the file dio_seek($fd, -2, SEEK_CUR); // position is now at 8 characters from the start of the file dio_seek($fd, -5, SEEK_END); // position is now at 5 characters from the end of the file dio_seek($fd, 10, SEEK_END); // position is now at 10 characters past the end of the file. // The 10 characters between the end of the file and the current // position are filled with zeros. dio_close($fd); ?> PHP Documentation Group DIO_SEEK(3)
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