CSV2MIPE(1) User Contributed Perl Documentation CSV2MIPE(1)NAME
csv2mipe.pl - Generates MIPE file based on 3 tab-delimited files
based on MIPE version v1.1
arguments: * tab-delimited file with PCR-level data
* tab-delimited file with SNP-level data
* tab-delimited file with assay-level data
Columns in file with PCR-level data:
pcr_id
pcr_modified (might be multiple, divided by semi-colon ";")
pcr_project (might be multiple, divided by semi-colon ";")
pcr_researcher (might be multiple, divided by semi-colon ";")
pcr_species
source_type
source_id
design_seq
primer1_oligo
primer1_seq
primer1_tm
primer2_oligo
primer2_seq
primer2_tm
design_remark (might be multiple, divided by semi-colon ";")
use_seq
use_revcomp
use_remark (might be multiple, divided by semi-colon ";")
pcr_remark (might be multiple, divided by semi-colon ";")
Columns in file with SNP-level data:
pcr_id
snp_id
snp_pos
snp_amb
snp_remark (might be multiple, divided by semi-colon ";")
Columns in file with assay-level data:
pcr_id
snp_id
assay_id
assay_type
assay_enzyme
assay_oligo
assay_specific
assay_tail
assay_strand
assay_remark (might be multiple, divided by semi-colon ";")
SYNOPSIS
csv2mipe.pl <pcr_file.csv> <snp_file.csv> <assay_file.csv>
ADDITIONAL INFO
See http://mipe.sourceforge.net
AUTHOR
Jan Aerts (jan.aerts@bbsrc.ac.uk)
perl v5.14.2 2005-07-20 CSV2MIPE(1)
Check Out this Related Man Page
Regexp::Common::URI::ftp(3) User Contributed Perl Documentation Regexp::Common::URI::ftp(3)NAME
Regexp::Common::URI::ftp -- Returns a pattern for FTP URIs.
SYNOPSIS
use Regexp::Common qw /URI/;
while (<>) {
/$RE{URI}{FTP}/ and print "Contains an FTP URI.
";
}
DESCRIPTION
$RE{URI}{FTP}{-type}{-password};
Returns a regex for FTP URIs. Note: FTP URIs are not formally defined. RFC 1738 defines FTP URLs, but parts of that RFC have been
obsoleted by RFC 2396. However, the differences between RFC 1738 and RFC 2396 are such that they aren't applicable straightforwardly to FTP
URIs.
There are two main problems:
Passwords.
RFC 1738 allowed an optional username and an optional password (separated by a colon) in the FTP URL. Hence, colons were not allowed in
either the username or the password. RFC 2396 strongly recommends passwords should not be used in URIs. It does allow for userinfo
instead. This userinfo part may contain colons, and hence contain more than one colon. The regexp returned follows the RFC 2396
specification, unless the {-password} option is given; then the regex allows for an optional username and password, separated by a
colon.
The ;type specifier.
RFC 1738 does not allow semi-colons in FTP path names, because a semi-colon is a reserved character for FTP URIs. The semi-colon is
used to separate the path from the option type specifier. However, in RFC 2396, paths consist of slash separated segments, and each
segment is a semi-colon separated group of parameters. Straigthforward application of RFC 2396 would mean that a trailing type
specifier couldn't be distinguished from the last segment of the path having a two parameters, the last one starting with type=.
Therefore we have opted to disallow a semi-colon in the path part of an FTP URI.
Furthermore, RFC 1738 allows three values for the type specifier, A, I and D (either upper case or lower case). However, the internet
draft about FTP URIs [DRAFT-FTP-URL] (which expired in May 1997) notes the lack of consistent implementation of the D parameter and
drops D from the set of possible values. We follow this practise; however, RFC 1738 behaviour can be archieved by using the -type =
"[ADIadi]"> parameter.
FTP URIs have the following syntax:
"ftp:" "//" [ userinfo "@" ] host [ ":" port ]
[ "/" path [ ";type=" value ]]
When using {-password}, we have the syntax:
"ftp:" "//" [ user [ ":" password ] "@" ] host [ ":" port ]
[ "/" path [ ";type=" value ]]
Under "{-keep}", the following are returned:
$1 The complete URI.
$2 The scheme.
$3 The userinfo, or if {-password} is used, the username.
$4 If {-password} is used, the password, else "undef".
$5 The hostname or IP address.
$6 The port number.
$7 The full path and type specification, including the leading slash.
$8 The full path and type specification, without the leading slash.
$9 The full path, without the type specification nor the leading slash.
$10 The value of the type specification.
REFERENCES
[DRAFT-URL-FTP]
Casey, James: A FTP URL Format. November 1996.
[RFC 1738]
Berners-Lee, Tim, Masinter, L., McCahill, M.: Uniform Resource Locators (URL). December 1994.
[RFC 2396]
Berners-Lee, Tim, Fielding, R., and Masinter, L.: Uniform Resource Identifiers (URI): Generic Syntax. August 1998.
SEE ALSO
Regexp::Common::URI for other supported URIs.
AUTHOR
Damian Conway (damian@conway.org)
MAINTAINANCE
This package is maintained by Abigail (regexp-common@abigail.be).
BUGS AND IRRITATIONS
Bound to be plenty.
LICENSE and COPYRIGHT
This software is Copyright (c) 2001 - 2009, Damian Conway and Abigail.
This module is free software, and maybe used under any of the following licenses:
1) The Perl Artistic License. See the file COPYRIGHT.AL.
2) The Perl Artistic License 2.0. See the file COPYRIGHT.AL2.
3) The BSD Licence. See the file COPYRIGHT.BSD.
4) The MIT Licence. See the file COPYRIGHT.MIT.
perl v5.16.2 2010-02-23 Regexp::Common::URI::ftp(3)