I have a large text file that is has a bunch of records. Each record starts with a header line that starts with the ">" character. Then there are several lines under that line that contain sequences of letters.
For example, a file might look like:
I can send you the actual file if you would like to see it. All I want is a PERL script that inputs a file in the following format:
Where ID is an identifier for the record (in the above record 1 has identifier of 2L and record 2 has identifier of 3R and start and stop are first and last positions of a subsequence in the record. Then there is a space and a SEQUENCE. I can send you an actual file for testing.
I want the script to use the ranges to pull out the subsequence from the big record text file and then see if it matches the SEQUENCE in the input. The big record file is large so you can't load the whole file into memory, you need to stream it.
The output would be the subsequence from the record and a space and a YES or NO for where it matches.
Thanks in advance
Last edited by Franklin52; 04-09-2010 at 05:09 AM..
Reason: Please use code tags!
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I would like to take a fasta file formated like
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Discussion started by: newbie_01
3 Replies
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tclsh
tclsh(1) Tcl Applications tclsh(1)__________________________________________________________________________________________________________________________________________________NAME
tclsh - Simple shell containing Tcl interpreter
SYNOPSIS
tclsh ?-encoding name? ?fileName arg arg ...?
_________________________________________________________________DESCRIPTION
Tclsh is a shell-like application that reads Tcl commands from its standard input or from a file and evaluates them. If invoked with no
arguments then it runs interactively, reading Tcl commands from standard input and printing command results and error messages to standard
output. It runs until the exit command is invoked or until it reaches end-of-file on its standard input. If there exists a file .tclshrc
(or tclshrc.tcl on the Windows platforms) in the home directory of the user, interactive tclsh evaluates the file as a Tcl script just
before reading the first command from standard input.
SCRIPT FILES
If tclsh is invoked with arguments then the first few arguments specify the name of a script file, and, optionally, the encoding of the |
text data stored in that script file. Any additional arguments are made available to the script as variables (see below). Instead of
reading commands from standard input tclsh will read Tcl commands from the named file; tclsh will exit when it reaches the end of the
file. The end of the file may be marked either by the physical end of the medium, or by the character, "