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
file2 is this :
and i want result like this:
when i run this command :
i got no output or output file. why so?
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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
I have this tar file which has files of (.ksh, .ini &.sql) and their hard and soft links.
Later when the original files and their directories are deleted (or rather lost as in a system crash), I have this tar file as the only source to restore all of them.
In such a case when I do,
tar... (4 Replies)
Hi all,
I have a data file from which i would like to extract only certain fields, which are not adjacent to each other. Following is the format of data file (data.txt) that i have, which has about 6 fields delimited by "|"
HARRIS|23|IT|PROGRAMMER|CHICAGO|EMP
JOHN|35|IT|JAVA|NY|CON... (2 Replies)
I need to extract the character before the last "|" in the following lines, which are 'N' and 'U'. The last "|" shouldn't be extracted. Also the no.s of "|" may vary in a line, but I need only the character before the last one.
... (5 Replies)
Hello,
I need your help to extract text from following:
./sherg_fyd_rur:blkabl="R23.21_BL2008_0122_1"
./serge_a75:rlwual="/main/r23.21=26-Mar-2008.05:00:20UTC@R11.31_BL2008_0325"
./serge_a75:blkabl="R23.21_BL2008_0325"
./sherg_proto_npiv:bkguals="R23.21_BL2008_0302 I80_11.31_LR"
I... (11 Replies)
Hi,
Can you help me on this two problems?
how can i get :
from input: /ect/exp/hom/bin ==> output: exp
and
from input: aex1234 =====>output: ex
thanks, (1 Reply)
Hi everyone,
I have a large text file containing DNA sequences in fasta format as follows:
>someseq
GAACTTGAGATCCGGGGAGCAGTGGATCTC
CACCAGCGGCCAGAACTGGTGCACCTCCAG
GCCAGCCTCGTCCTGCGTGTC
>another seq
GGCATTTTTGTGTAATTTTTGGCTGGATGAGGT
GACATTTTCATTACTACCATTTTGGAGTACA
>seq3450... (4 Replies)
Hi all,
I have a file like this
ID 3BP5L_HUMAN Reviewed; 393 AA.
AC Q7L8J4; Q96FI5; Q9BQH8; Q9C0E3;
DT 05-FEB-2008, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 05-SEP-2012, entry version 71.
FT COILED 59 140 ... (1 Reply)
I am trying to extract a time from the below string in perl but not able to get the time properly
I just want to extract the time from the above line I am using the below syntax
x=~ /(.*) (\d+)\:(\d+)\:(\d+),(.*)\.com/
$time = $2 . ':' . $3 . ':' . $4;
print $time
Can... (1 Reply)
Hello, here I am posting my query again with modified data input files.
see my query is :
i have two input files file1 and file2.
file1 is smalldata.fasta
>gi|546671471|gb|AWWX01449637.1| Bubalus bubalis breed Mediterranean WGS:AWWX01:contig449636, whole genome shotgun sequence... (20 Replies)
Discussion started by: harpreetmanku04
20 Replies
LEARN ABOUT PHP
dio_seek
DIO_SEEK(3) 1 DIO_SEEK(3)dio_seek - Seeks to pos on fd from whenceSYNOPSIS
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)