02-11-2013
My apologies, I didn't intend to be vague. That summary is correct. This is an aligned Next-gen sequencing file that I am attempting to manipulate. There is a family of repeat genes on chr3 in the range of 112,937,439 -113,437,438 that I am interested in exploring within my data. The file will have millions of "reads" on chr3, but I want to only extract the reads that fall:
1. only lines with field3="chr3" as Don already mentioned
2. The value of field 4 is in the mentioned range
Then I would like to have the whole line printed to a separate file.
Thank you for all of your help.
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LEARN ABOUT OPENSOLARIS
scrollkeeper-preinstall
scrollkeeper-devel(1) User Commands scrollkeeper-devel(1)
NAME
scrollkeeper-devel, scrollkeeper-extract, scrollkeeper-gen-seriesid, scrollkeeper-preinstall - utilities for working with OMF documents and
the scrollkeeper database
SYNOPSIS
scrollkeeper-extract file stylesheet output [stylesheet output...]
scrollkeeper-gen-seriesid
scrollkeeper-preinstall docfile omf-file1 omf-file2
DESCRIPTION
scrollkeeper-extract is used internally by scrollkeeper to convert DocBook/SGML files to Docbook/XML files if necessary, and to apply a
number of transformations to the XML file to extract information from the XML file.
scrollkeeper-gen-seriesid generates a globally unique series ID for an OMF file.
scrollkeeper-preinstall reads omf_file1, changes the URL attribute of the identifier tag to doc_file and writes the output to omf_file2.
scrollkeeper-preinstall can be used during the document installation process to point OMF files to the correct location on the target
machine before registration in the scrollkeeper database.
OPTIONS
None.
OPERANDS
The following operands are supported:
docfile Specifies the file path to the document that omf-file1 describes.
file Specifies the XML file that is to be used as input for XSLT transformations.
omf-file1 Specifies the OMF file that contains metadata for docfile.
omf-file2 Specifies the file created by scrollkeeper-preinstall, which contains the same data as omf-file1 except that the URL
attribute of the identifier tag is changed to docfile.
output Specifies the file that contains the result when the preceding stylesheet has been applied to file.
stylesheet Specifies an XSLT transformation to apply.
EXAMPLES
Example 1: Creating a New scrollkeeper Series ID
example% scrollkeeper-gen-seriesid
Example 2: Extracting a TOC From a Document
example% scrollkeeper-extract /path/to/xml/file.xml /usr/share/scrollkeeper/stylesheets/toc.xsl /path/to/toc.xml
EXIT STATUS
The following exit values are returned:
0 Application exited successfully
>0 Application exited with failure
FILES
The following files are used by this application:
/usr/bin/scrollkeeper-extract
The command-line executable for the scrollkeeper-extract application.
/usr/bin/scrollkeeper-gen-seriesid
The command-line executable for the scrollkeeper-gen-seriesid application.
/usr/bin/scrollkeeper-preinstall
The command-line executable for the scrollkeeper-preinstall application.
ATTRIBUTES
See attributes(5) for descriptions of the following attributes:
+-----------------------------+-----------------------------+
| ATTRIBUTE TYPE | ATTRIBUTE VALUE |
+-----------------------------+-----------------------------+
|Availability |SUNWgnome-libs-devel |
+-----------------------------+-----------------------------+
|Interface stability |Obsolete |
+-----------------------------+-----------------------------+
SEE ALSO
scrollkeeper(1)
NOTES
Written by Sander Vesik, Sun Microsystems Inc., 2003.
Updated by Ghee Teo, Sun Microsystems Inc., 2007.
SunOS 5.11 01 Apr 2003 scrollkeeper-devel(1)