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Top Forums Shell Programming and Scripting Using sed on 1st column of tab delimited file Post 302540050 by Hkins552 on Tuesday 19th of July 2011 12:12:29 PM
Old 07-19-2011
Java Using sed on 1st column of tab delimited file

Hi all,
I'm new to Unix and work primarily in bioinformatics. I am in need of a script which will allow me to replace "1" with "chr1" in only the first column of a file which looks like such:
Code:
1       10327   rs112750067     T       C       .       PASS    ASP;RSPOS=10327;
SAO=0;SCS=0;SSR=0;VC=SNP;VP=050000000005000000000100;WGT=1;dbSNPBuildID=132
1       10433   rs56289060      A       AC      .       PASS    ASP;RSPOS=10433;
SAO=0;SCS=0;SSR=0;VC=INDEL;VP=050000000005000000000200;WGT=1;dbSNPBuildID=129

I would like it to be:
Code:
chr1       10327   rs112750067     T       C       .       PASS    ASP;RSPOS=10327;
SAO=0;SCS=0;SSR=0;VC=SNP;VP=050000000005000000000100;WGT=1;dbSNPBuildID=132
chr1       10433   rs56289060      A       AC      .       PASS    ASP;RSPOS=10433;
SAO=0;SCS=0;SSR=0;VC=INDEL;VP=050000000005000000000200;WGT=1;dbSNPBuildID=129

Any ideas?

Last edited by Scott; 07-19-2011 at 01:19 PM.. Reason: Please use code tags
 

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Net::Config(3pm)					 Perl Programmers Reference Guide					  Net::Config(3pm)

NAME
Net::Config - Local configuration data for libnet SYNOPSYS
use Net::Config qw(%NetConfig); DESCRIPTION
"Net::Config" holds configuration data for the modules in the libnet distribution. During installation you will be asked for these values. The configuration data is held globally in a file in the perl installation tree, but a user may override any of these values by providing their own. This can be done by having a ".libnetrc" file in their home directory. This file should return a reference to a HASH containing the keys described below. For example # .libnetrc { nntp_hosts => [ "my_preferred_host" ], ph_hosts => [ "my_ph_server" ], } __END__ METHODS
"Net::Config" defines the following methods. They are methods as they are invoked as class methods. This is because "Net::Config" inherits from "Net::LocalCfg" so you can override these methods if you want. requires_firewall HOST Attempts to determine if a given host is outside your firewall. Possible return values are. -1 Cannot lookup hostname 0 Host is inside firewall (or there is no ftp_firewall entry) 1 Host is outside the firewall This is done by using hostname lookup and the "local_netmask" entry in the configuration data. NetConfig VALUES nntp_hosts snpp_hosts pop3_hosts smtp_hosts ph_hosts daytime_hosts time_hosts Each is a reference to an array of hostnames (in order of preference), which should be used for the given protocol inet_domain Your internet domain name ftp_firewall If you have an FTP proxy firewall (NOT an HTTP or SOCKS firewall) then this value should be set to the firewall hostname. If your firewall does not listen to port 21, then this value should be set to "hostname:port" (eg "hostname:99") ftp_firewall_type There are many different ftp firewall products available. But unfortunately there is no standard for how to traverse a firewall. The list below shows the sequence of commands that Net::FTP will use user Username for remote host pass Password for remote host fwuser Username for firewall fwpass Password for firewall remote.host The hostname of the remote ftp server 0 There is no firewall 1 USER user@remote.host PASS pass 2 USER fwuser PASS fwpass USER user@remote.host PASS pass 3 USER fwuser PASS fwpass SITE remote.site USER user PASS pass 4 USER fwuser PASS fwpass OPEN remote.site USER user PASS pass 5 USER user@fwuser@remote.site PASS pass@fwpass 6 USER fwuser@remote.site PASS fwpass USER user PASS pass 7 USER user@remote.host PASS pass AUTH fwuser RESP fwpass ftp_ext_passive ftp_int_passive FTP servers can work in passive or active mode. Active mode is when you want to transfer data you have to tell the server the address and port to connect to. Passive mode is when the server provide the address and port and you establish the connection. With some firewalls active mode does not work as the server cannot connect to your machine (because you are behind a firewall) and the firewall does not re-write the command. In this case you should set "ftp_ext_passive" to a true value. Some servers are configured to only work in passive mode. If you have one of these you can force "Net::FTP" to always transfer in passive mode; when not going via a firewall, by setting "ftp_int_passive" to a true value. local_netmask A reference to a list of netmask strings in the form "134.99.4.0/24". These are used by the "requires_firewall" function to determine if a given host is inside or outside your firewall. The following entries are used during installation & testing on the libnet package test_hosts If true then "make test" may attempt to connect to hosts given in the configuration. test_exists If true then "Configure" will check each hostname given that it exists perl v5.16.3 2014-06-17 Net::Config(3pm)
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