这个工具有个bt的地方在于,每个文件的residue总数不能超过20w。
所以要是结果不太正常,那就实施输入少数的数目会是什么情况,结果发现,我们的residue数目是有限制的。。
targetp的README居然也没有提到这一点。 。。。太坑乐
Input exceeded maximal total residues : 200000
因此我的处理办法便是,让50个文件都
安装targetp之后,有以下说明都要按照上面一一写上:
uname (usually /bin/uname)
paste ( /bin/paste)
perl ( /usr/bin/perl)
nawk (or equivalent, e.g. gawk)
sh (usually /bin/sh)
echo ( /bin/echo)
-
Decide where you wish to keep the software. Uncompress and untar the
package in that location:cat TargetP-1.1.tar.Z | uncompress | tar xvf -
This will produce a directory 'TargetP-1.1'. The size of the installed
package is at most 7 Mb, depending on which binaries are included.
这里尤其要注意awk executable,ubuntu 15.0不要用awk文件,要
sudo apt-get install gawk
来下载gawk,并赋予gawk的路径! -
Edit the paragraph labelled "GENERAL SETTINGS, CUSTOMIZE" at the top of
the file "targetp". Configure the following variables:Variable Set to the full path to: ------------------------------------------- TARGETP 'targetp-1.1' directory TMP location for temporary data PASTE 'paste' executable PERL 'perl' executable AWK 'awk' executable SH POSIX-compliant shell ECHO 'echo' executable -------------------------------------------
Make sure that the settings you enter point at existing and operational
utilities. You might need to modify them after the testing (see below). -
Edit the paragraph labelled "HELPER APPLICATIONS, CUSTOMIZE" further
down in the same file. Configure the following variables:Variable Set to the full path to: ---------------------------------------- CHLOROP 'chlorop' executable SIGNALP 'signalp' executable
TargetP will need those softwares to produce the output as described in
the reference quoted above. They will be employed if the '-c' option is
used but not otherwise. The decision whether to install them should be
with the future users of TargetP:
./targetp -P test/twelve.fsa # many sequences