7.10.2008

 

1、安装PROFphd

下载网址：http://www.predictprotein.org/download.php

有新的软件即其安装文件PROFphd.run

安装：

   1） Create a folder on the file system named prof-tmp

 

   2） Download the prof package (either the LINUX or the OS X version) into        the prof-tmp folder

 

   3） Make the package executable by typing    chmod u+x PROFphd.run

 

   4） ./PROFphd.run follow the instructions to install

 

报错：

-bash-3.00$ ../prof ./single_seq.fasta fileRdb=single_rdbProfSec sec

Newline in left-justified string for sprintf at /picb/home40/cyd/dys/backup/PROFphd/prof-tmp/prof/scr/lib/lib-col.pl line 183.

Newline in left-justified string for sprintf at /picb/home40/cyd/dys/backup/PROFphd/prof-tmp/prof/scr/lib/lib-col.pl line 183.

Newline in left-justified string for sprintf at /picb/home40/cyd/dys/backup/PROFphd/prof-tmp/prof/scr/lib/lib-col.pl line 183.

Newline in left-justified string for sprintf at /picb/home40/cyd/dys/backup/PROFphd/prof-tmp/prof/scr/lib/lib-col.pl line 183.

Newline in left-justified string for sprintf at /picb/home40/cyd/dys/backup/PROFphd/prof-tmp/prof/scr/lib/lib-col.pl line 183.

Use of uninitialized value in concatenation (.) or string at /picb/home40/cyd/dys/backup/PROFphd/prof-tmp/prof/scr/lib/prof.pm line 1218.

*** ERROR prof: after package prof:full (/picb/home40/cyd/dys/backup/PROFphd/prof-tmp/prof/scr/lib/prof.pm)

*** ERROR prof:full: failed initialising (prof:full:ini)58

*** ERROR prof:ini: after setfinal

*** ERROR prof:iniSetFinal: failed iniSetFinalFileIn:

*** ERROR prof:iniSetFinalFileIn: input format '' (of files in file=./single_seq.fasta) unsupported

 

 

2、psipred结果整合

PSIPRED Version 2.61

方法同jnet：

/*

combine.cpp

By DYS

Function:Combine name real structure and prediction structure

Inputfile:name.txt real_structure prediction_structure

Onputfile:result.txt

*/

 

#include <stdio.h>

#include <fstream>

#include <iostream>

 

using namespace std;

 

int main()

{

    ifstream name("name.txt");

    ifstream aa("protein.txt");

    ifstream real_structure("re_sturcture.txt");

    ifstream prediction("psipred_prediction_result.txt");

    ofstream combine("result.txt");

   

    string name_str,aa_str,real_structure_str,prediction_str;

   

    name>>name_str;

    while(!name.eof())

    {

         

          aa>>aa_str;

          real_structure>>real_structure_str;

          prediction>>prediction_str;

         

          //name_str>>endl>>aa_str>>endl>>real_structure_str>>endl>>prediction_str>>endl>>combine; 

          combine<<name_str<<endl<<aa_str<<endl<<real_structure_str<<endl<<prediction_str<<endl;

          

          name>>name_str;           

    }

}//int main