日志 7.14.2008

 

1、  PROFphd结果

1）  提取结果，从文件夹中批量复制文件至另一文件夹

法一 find dir -name '*.c' | xargs -i cp {} dir_a   法二 #!/bin/sh for AA in `find . -name "*.c"` do cp -r $AA /a done

2）检查结果

结果有16526个，但理论结果16623，少了97个。

其中，选择序列

>2B5DX

再运行一次 ../prof  2B5DX  fileRdb=2B5DX.out  sec

错误如下：

*** ERROR prof: line number of error=106

*** ERROR failed prof:full:doOne dbfile=./2B5DX, chain=*!

*** ERROR msg from where it failed:

*** ERROR doOne: assHack1994 failed

*** ERROR assHack1994: SYSTEM call:

 /picb/home40/cyd/dys/backup/PROFphd/prof-tmp/prof/embl/phd.pl ./2B5DX sec exePhd=/picb/home40/cyd/dys/backup/PROFphd/prof-tmp/prof/bin/phd1994.UNKNOWN exeHsspFilter=/picb/home40/cyd/dys/backup/PROFphd/prof-tmp/prof/bin/filter_hssp.UNKNOWN exeHsspFilterPl=/picb/home40/cyd/dys/backup/PROFphd/prof-tmp/prof/scr/hssp_filter.pl exeHsspFilterPack=/picb/home40/cyd/dys/backup/PROFphd/prof-tmp/prof/scr/pack/hssp_filter.pm exeConvertSeq=/picb/home40/cyd/dys/backup/PROFphd/prof-tmp/prof/bin/convert_seq.UNKNOWN exeCopf=/picb/home40/cyd/dys/backup/PROFphd/prof-tmp/prof/scr/copf.pl exeCopfPack=/picb/home40/cyd/dys/backup/PROFphd/prof-tmp/prof/scr/pack/copf.pm exeConvHssp2saf=/picb/home40/cyd/dys/backup/PROFphd/prof-tmp/prof/embl/scr/conv_hssp2saf.pl ARCH=UNKNOWN filePhd=PROF14172.phdEMBL fileRdb=PROF14172.rdbPhdEMBL fileNotHtm=PROF14172.notHtm

failed producing output file=PROF14172.rdbPhdEMBL

 

1）  检查序列是否含非氨基酸字符（B、J、O、U、X、Z）

结果只发现X，但并非是预测出错的序列所特有。

 

2）  长度检查：出差的序列并非最长或最短

 

方法：用Excel找出错误序列

2、  安装prof

1）  根据readme安装出错

usage.c: In function `usage': usage.c:36: error: missing terminating " character usage.c:37: error: `o' undeclared (first use in this function) usage.c:37: error: (Each undeclared identifier is reported only once usage.c:37: error: for each function it appears in.) usage.c:37: error: `filename' undeclared (first use in this function) usage.c:37: error: syntax error before "for" usage.c:37: error: stray '/' in program usage.c:37: error: missing terminating " character usage.c:39: error: missing terminating " character usage.c:40: error: syntax error before "for" usage.c:40: error: stray '/' in program usage.c:40: error: missing terminating " character usage.c:43: error: missing terminating " character usage.c:44: error: `p' undeclared (first use in this function) usage.c:44: error: `Output' undeclared (first use in this function) usage.c:44: error: syntax error before "profil" usage.c:44: error: stray '/' in program usage.c:44: error: missing terminating " character usage.c:46: error: missing terminating " character usage.c:47: error: syntax error before "profil" usage.c:47: error: stray '/' in program usage.c:47: error: missing terminating " character make: *** [usage.o] Error 1

 

2）  修改usage.c 为：

#include<stdio.h>

#include<stdlib.h>

#include "Prof.h"

 

void usage(void)

{

   printf("In automatic mode :/n") ;

   printf("usage is Prof -A -v -d -m 0 -i  [filename in fasta format] -b [database name for psiblast] -o [filename for the output]/n");

   printf("Or if you want a casp format as output/n") ;

   printf("usage is Prof -c -v -d -m 0 -i  [filename in fasta format] -b [database name for psiblast] -o [filename for the output]/n");

   printf("/n------------------------------------------------------/n/n") ;

   printf("In non-automatic mode :/n") ;

   printf("usage is Prof -A -v -d -m 1  -a [Output from clustalw in aln format] -p [Output profil form psi-blast] -o [filename for the output]/n");

   printf("Or if you want a casp format as output/n") ;

   printf("usage is Prof -c -v -d -m 1  -a [Output from clustalw in aln format] -p [Output profil form psi-blast] -o [filename for the output]/n");

printf("/n/n") ;

 

if(mode == 1)

 {

 if(!file_clu)

 printf("file of multiple alignement in aln format not found. With option [-m 1] need option -a as well./n") ;

 if(!file_psi)

 printf("file of profil from psi-blast not found. With option [-m 1] need option -p as well./n") ;

 }

 if(!file_seq)

 printf("file of sequence not found. With option [-m 0] need file of sequence in fasta format./n") ;

 

 return ;

}

 

 

3）  安装blastpgb

注意：

1、    .cshrc只在csh下起作用，bash下起作用的是.bashrc

2、    .bash_profile与.bashrc作用的区别（zz）

1. /etc/profile:此文件为系统的每个用户设置环境信息,当用户第一次登 录时,该文件被执行.并从/etc/profile.d目录的配置文件中搜集shell的设置.

2. /etc/bashrc:为每一个运行bash shell的用户执行此文件.当bash shell被打开时,该文件被读取.

3. /.bash_profile:每个用户都可使用该文件输入专用于自己使用的shell信息,当用户登录时,该文件仅仅执行一次!默认情况下,他设置一些环境变量,执行用户的.bashrc文件.

4. /.bashrc:该文件包含专用于你的bash shell的bash信息,当登录时以及每次打开新的shell时,该该文件被读取.

5. /.bash_logout:当每次退出系统(退出bash shell)时,执行该文件.

6. /etc/profile中设定的变量(全局)的可以作用于任何用户,而~/.bashrc等中设定的变量(局部)只能继承/etc/profile中的变量,他们是"父子"关系.

7. /.bash_profile 是交互式、login 方式进入 bash 运行的/.bashrc 是交互式 non-login 方式进入 bash 运行的,通常二者设置大致相同，所以通常前者会调用后者。

 

3、    整合ssprod的结果：

1）  提取预测结果

> 1

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

CEEEEEECCCCEEEEECCCCCEHHHHHHHHHHHHCCCHHHEEEEECCEECCCCCECHHHCCCCCCEEEEEECCCCC

> 2

TLGALEFSLLYDQDNSNLQCIIRAKGLKPMDSNGLADPYVKLHLPGASKSNLRTKLRNTRNPVWNETLQYHGITEEDMQRKTLRISVCDEDKFGHNEFIGETRFSLKKLKANQRKNFNICLERVI

CCCEEEEEEEECCCCCCEEEEEEECCCCCCCCCCCCCCEEEEEECCCCCCCCCEEEECCCCCCECEEEEECCCCHHHHCCCEEEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCHHHHHHHHC

#include <stdio.h> #include <fstream> #include <iostream>   using namespace std;   int main() {     ifstream result("ssprod_result");     ofstream ss("ssprod_ss");     string line; int i=1;       while(!result.eof())     {        if(i%3==0)      //取3的整数倍行，即预测结果        {            result>>line;            ss<<line<<endl;            i++;                    }          else        {            result>>line;            i++;        }                                           } }

2）  整合数据combine

同前combine.cpp

#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("ssprod_ss");     ofstream combine("ssprod_final_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