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Top Forums UNIX for Advanced & Expert Users Map snps into a ref gene file Post 302989917 by marwah on Thursday 19th of January 2017 07:27:29 PM
Old 01-19-2017
Map snps into a ref gene file

I have the following data set about the snps ID txt file

Code:
   POS ID	
    	78599583	rs987435
    	33395779	rs345783
    	189807684	rs955894
    	33907909	rs6088791
    	75664046	rs11180435
    	218890658	rs17571465
    	127630276	rs17011450
    	90919465	rs6919430

and a gene reference file, txt file

Code:
 genename	name	chrom	strand	txstart	txend
    CDK1	NM_001786	chr10	+	62208217	62224616
    CALB2	NM_001740	chr16	+	69950116	69981843
    STK38	NM_007271	chr6	-	36569637	36623271
    YWHAE	NM_006761	chr17	-	1194583	1250306
    SYT1	NM_005639	chr12	+	77782579	78369919
    ARHGAP22	NM_001347736	chr10	-	49452323	49534316
    PRMT2	NM_001535	chr21	+	46879934	46909464
    CELSR3	NM_001407	chr3	-	48648899	48675352

I'm trying to match the genes with the SNps using snps location, so include the snps that has

POS >= txstart and POS<= txend

for example I want a data set that has the following columns

Code:
genename   SNPID   chrom   position   txstart   txend


Last edited by Don Cragun; 01-19-2017 at 09:48 PM.. Reason: Add more CODE and ICODE tags.
 

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IO::Seekable(3pm)					 Perl Programmers Reference Guide					 IO::Seekable(3pm)

NAME
IO::Seekable - supply seek based methods for I/O objects SYNOPSIS
use IO::Seekable; package IO::Something; @ISA = qw(IO::Seekable); DESCRIPTION
"IO::Seekable" does not have a constructor of its own as it is intended to be inherited by other "IO::Handle" based objects. It provides methods which allow seeking of the file descriptors. $io->getpos Returns an opaque value that represents the current position of the IO::File, or "undef" if this is not possible (eg an unseekable stream such as a terminal, pipe or socket). If the fgetpos() function is available in your C library it is used to implements getpos, else perl emulates getpos using C's ftell() function. $io->setpos Uses the value of a previous getpos call to return to a previously visited position. Returns "0 but true" on success, "undef" on failure. See perlfunc for complete descriptions of each of the following supported "IO::Seekable" methods, which are just front ends for the corresponding built-in functions: $io->seek ( POS, WHENCE ) Seek the IO::File to position POS, relative to WHENCE: WHENCE=0 (SEEK_SET) POS is absolute position. (Seek relative to the start of the file) WHENCE=1 (SEEK_CUR) POS is an offset from the current position. (Seek relative to current) WHENCE=2 (SEEK_END) POS is an offset from the end of the file. (Seek relative to end) The SEEK_* constants can be imported from the "Fcntl" module if you don't wish to use the numbers 0 1 or 2 in your code. Returns 1 upon success, 0 otherwise. $io->sysseek( POS, WHENCE ) Similar to $io->seek, but sets the IO::File's position using the system call lseek(2) directly, so will confuse most perl IO operators except sysread and syswrite (see perlfunc for full details) Returns the new position, or "undef" on failure. A position of zero is returned as the string "0 but true" $io->tell Returns the IO::File's current position, or -1 on error. SEE ALSO
perlfunc, "I/O Operators" in perlop, IO::Handle IO::File HISTORY
Derived from FileHandle.pm by Graham Barr <gbarr@pobox.com> perl v5.18.2 2013-11-04 IO::Seekable(3pm)
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