Linux系统环境
• 查看CPU信息：lscpu
• 查看内存信息：free -h
• 查看硬盘信息：df -h
• 查看文件大小：du -h -d 1
• 查看文件大小：du -sh ~
• 查看系统进程：top 或者 ps -ef | grep "$LOGNAME"
htop
查看CPU信息：lscpu
$ lscpu
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 8 #8核
On-line CPU(s) list: 0-7
Thread(s) per core: 1 #8核8线程
Core(s) per socket: 8
Socket(s): 1
NUMA node(s): 1
Vendor ID: GenuineIntel
CPU family: 6
Model: 94
Model name: Intel(R) Xeon(R) Gold 61xx CPU #CPU型号
Stepping: 3
CPU MHz: 2494.130
BogoMIPS: 4988.26
Hypervisor vendor: KVM
Virtualization type: full
L1d cache: 32K
L1i cache: 32K
L2 cache: 4096K
NUMA node0 CPU(s): 0-7
Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl eagerfpu pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm 3dnowprefetch invpcid_single kaiser fsgsbase bmi1 hle avx2 smep bmi2 erms invpcid rtm mpx rdseed adx smap xsaveopt xsavec xgetbv1 arat
(base) Last2 10:14:39 ~
查看内存信息：free -h
$ free
total used free shared buff/cache available
Mem: 16300696 2142168 526548 165764 13631980 13597756
Swap: 0 0 0
(base) Last2 11:05:01 ~
$ free -h
total used free shared buff/cache available
Mem: 15G 2.0G 516M 161M 13G 12G
Swap: 0B 0B 0B
(base) Last2 11:05:41 ~
查看硬盘信息：df -h
$ df -h
Filesystem Size Used Avail Use% Mounted on
udev 7.8G 0 7.8G 0% /dev
tmpfs 1.6G 162M 1.4G 11% /run
/dev/vda1 50G 20G 28G 42% /
#/dev/vda1 相当于windowsC盘
tmpfs 7.8G 28K 7.8G 1% /dev/shm
tmpfs 5.0M 0 5.0M 0% /run/lock
tmpfs 7.8G 0 7.8G 0% /sys/fs/cgroup
/dev/vdd1 493G 334G 134G 72% /trainee1
#相当于windowsD盘
/dev/vdc1 493G 364G 104G 78% /trainee2
#相当于windowsE盘
/dev/vde1 148G 91G 50G 65% /teach
#相当于windowsF盘
tmpfs 1.6G 0 1.6G 0% /run/user/1003
tmpfs 1.6G 0 1.6G 0% /run/user/1027
tmpfs 1.6G 0 1.6G 0% /run/user/1011
tmpfs 1.6G 0 1.6G 0% /run/user/1057
tmpfs 1.6G 0 1.6G 0% /run/user/1074
tmpfs 1.6G 0 1.6G 0% /run/user/1080
tmpfs 1.6G 0 1.6G 0% /run/user/1103
tmpfs 1.6G 0 1.6G 0% /run/user/1101
tmpfs 1.6G 0 1.6G 0% /run/user/1093
tmpfs 1.6G 0 1.6G 0% /run/user/1091
tmpfs 1.6G 0 1.6G 0% /run/user/1125
tmpfs 1.6G 0 1.6G 0% /run/user/1131
tmpfs 1.6G 0 1.6G 0% /run/user/1172
tmpfs 1.6G 0 1.6G 0% /run/user/1173
tmpfs 1.6G 0 1.6G 0% /run/user/1157
tmpfs 1.6G 0 1.6G 0% /run/user/1207
tmpfs 1.6G 0 1.6G 0% /run/user/1209
tmpfs 1.6G 0 1.6G 0% /run/user/1208
(base) Last2 11:12:31 ~
查看家目录下文件大小
$ du -sh ~
3.6G /trainee1/Last2
(base) Last2 11:37:11 ~
查看家目录下Data文件,miniconda3文件大小
$ ls
biosoft config database filr1 filr3 filr5 miniconda3 myDir project readme.txt softlink test tmp
catFile Data file filr2 filr4 hisat2-2.1.0-Linux_x86_64.zip Miniconda3-latest-Linux-x86_64.sh pipline project_backup samtools-1.10.tar.bz2 sysoft test2 Trimmomatic-0.39.zip
(base) Last2 11:39:53 ~
$ du -sh Data
2.6M Data
(base) Last2 11:40:06 ~
$ du -sh miniconda3/
3.4G miniconda3/
(base) Last2 11:41:53 ~
显示出当前每个文件夹，当成固定用法即可
$ du -h -d 1
102M ./biosoft
3.4G ./miniconda3
36K ./project
8.0K ./.ssh
2.6M ./Data
20K ./database
4.0K ./myDir
8.0K ./.ncbi
4.0K ./softlink
4.0K ./sysoft
4.0K ./pipline
8.0K ./test2
4.0K ./test
8.0K ./project_backup
8.0K ./.conda
4.0K ./.cache
3.6G .
(base) Last2 11:52:11 ~
查看系统进程top，类似于windows的任务资源管理器
image.png
按q退出
查看具体某一个人的系统进程
$ top -u Last2 #u是user
image.png
查看系统进程htop
$ htop
image.png
查看具体某一个人的系统进程
$ htop -u Last2
image.png
$ ps -ef
image.png
$ ps -ef | grep 'Last2'
Last2 5453 29645 0 15:45 pts/17 00:00:00 ps -ef
Last2 5454 29645 0 15:45 pts/17 00:00:00 -bash
root 29580 1491 0 14:54 ? 00:00:00 sshd: Last2 [priv]
Last2 29587 1 0 14:54 ? 00:00:00 /lib/systemd/systemd --user
Last2 29592 29587 0 14:54 ? 00:00:00 (sd-pam)
Last2 29644 29580 0 14:54 ? 00:00:00 sshd: Last2@pts/17
Last2 29645 29644 0 14:54 pts/17 00:00:00 -bash
(base) Last2 15:45:03 ~
变量
自定义变量
$ a=gene
(base) Last2 15:53:15 ~
$ echo 'This is a $a'
This is a $a
(base) Last2 15:54:59 ~
$ echo "This is a $a"
This is a gene
(base) Last2 15:55:15 ~
单引号：变量不会被解释,不动脑子
双引号：变量被解释
环境变量
注意大小写
$ echo $HOME
/trainee1/Last2
(base) Last2 16:19:46 ~
$ echo $SHELL
/bin/bash
(base) Last2 16:19:57 ~
$ echo $LOGNAME
Last2
(base) Last2 16:20:12 ~
$PS1：修改命令行配色
~/.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，该文件被读取和执行。
Linux export 命令https://www.runoob.com/linux/linux-comm-export.html
Linux export 命令用于设置或显示环境变量。
在 shell 中执行程序时，shell 会提供一组环境变量。export 可新增，修改或删除环境变量，供后续执行的程序使用。export 的效力仅限于该次登陆操作。写入bashrc，被永久保存。
export仅设置环境变量，要echo来输出，才能写入bashrc
image.png
image.png
验证export 的效力仅限于该次登陆操作
$ export A=3
(base) Last2 16:46:57 ~
$ export -p
declare -x A="3"
declare -x CONDA_DEFAULT_ENV="base"
declare -x CONDA_EXE="/trainee1/Last2/miniconda3/bin/conda"
declare -x CONDA_PREFIX="/trainee1/Last2/miniconda3"
declare -x CONDA_PROMPT_MODIFIER="(base) "
declare -x CONDA_PYTHON_EXE="/trainee1/Last2/miniconda3/bin/python"
declare -x CONDA_SHLVL="1"
declare -x HISTSIZE="3000"
declare -x HISTTIMEFORMAT="%F %T "
declare -x HOME="/trainee1/Last2"
declare -x LANG="en_US.utf8"
declare -x LESSCLOSE="/usr/bin/lesspipe %s %s"
declare -x LESSOPEN="| /usr/bin/lesspipe %s"
declare -x LOGNAME="Last2"
......
重新登录一次，发现环境变量没有A
$ export -p
declare -x CONDA_DEFAULT_ENV="base"
declare -x CONDA_EXE="/trainee1/Last2/miniconda3/bin/conda"
declare -x CONDA_PREFIX="/trainee1/Last2/miniconda3"
declare -x CONDA_PROMPT_MODIFIER="(base) "
declare -x CONDA_PYTHON_EXE="/trainee1/Last2/miniconda3/bin/python"
declare -x CONDA_SHLVL="1"
declare -x HISTSIZE="3000"
declare -x HISTTIMEFORMAT="%F %T "
declare -x HOME="/trainee1/Last2"
declare -x LANG="en_US.utf8"
declare -x LESSCLOSE="/usr/bin/lesspipe %s %s"
declare -x LESSOPEN="| /usr/bin/lesspipe %s"
declare -x LOGNAME="Last2"
状态变量
$? 获取执行上一个指令的执行状态返回值，返回0表示上一个命令或者程序执行成功，返回的值为非0则表示上一个命令执行失败。只有0和非0的区别。
$ ls
biosoft config database filr1 filr3 filr5 miniconda3 myDir project readme.txt softlink test tmp
catFile Data file filr2 filr4 hisat2-2.1.0-Linux_x86_64.zip Miniconda3-latest-Linux-x86_64.sh pipline project_backup samtools-1.10.tar.bz2 sysoft test2 Trimmomatic-0.39.zip
(base) Last2 17:25:45 ~
$ echo $?
0
(base) Last2 17:25:56 ~
$ pppp
No command 'pppp' found, did you mean:
Command 'pppd' from package 'ppp' (main)
Command 'kppp' from package 'kppp' (universe)
Command 'pptp' from package 'pptp-linux' (main)
Command 'pspp' from package 'pspp' (universe)
pppp: command not found
(base) Last2 17:26:01 ~
$ echo $?
127
(base) Last2 17:26:04 ~
03.结构化语句
可以写成一段，也可以以；分隔写成一行
$ ls
biosoft config database filr1 filr3 filr5 miniconda3 myDir project readme.txt softlink test tmp
catFile Data file filr2 filr4 hisat2-2.1.0-Linux_x86_64.zip Miniconda3-latest-Linux-x86_64.sh pipline project_backup samtools-1.10.tar.bz2 sysoft test2 Trimmomatic-0.39.zip
(base) Last2 17:42:54 ~
$ if [ $? -eq 0 ]
> then
> echo 'Yes!'
> fi
Yes!
(base) Last2 17:44:51 ~
$ ls
biosoft config database filr1 filr3 filr5 miniconda3 myDir project readme.txt softlink test tmp
catFile Data file filr2 filr4 hisat2-2.1.0-Linux_x86_64.zip Miniconda3-latest-Linux-x86_64.sh pipline project_backup samtools-1.10.tar.bz2 sysoft test2 Trimmomatic-0.39.zip
(base) Last2 17:45:26 ~
$ if [ $? -eq 0 ];then echo 'Yes!';fi
Yes!
(base) Last2 17:47:58 ~
for循环语句
反引号里必须放一个可执行的命令，优先执行。不是可执行命令会报错。
image.png
$ for i in `file*`; do echo ${i} ; done
file1:
empty
file10:
empty
file2:
empty
file3:
empty
file4:
empty
file5:
empty
file6:
empty
file7:
empty
file8:
empty
file9:
empty
(base) Last2 20:26:11 ~
$ for i in `ls file*`; do echo ${i} ; done
file
file1
file10
file2
file3
file4
file5
file6
file7
file8
file9
(base) Last2 20:26:33 ~
$ for i in `ls ../file*`; do echo ${i} ; done
ls: cannot access '../file*': No such file or directory
(base) Last2 20:27:03 ~
04.Shell 脚本编程
vim很智能。写入.sh脚本，它可以识别哪句命令是对的，显示一个颜色。哪句命令是错的，显示一个颜色。写入.py脚本，print("Hi!")就显示对的颜色，echo就显示错的颜色。
如果是python脚本该如何指定？
$ which python
/usr/bin/python
Last2 18:40:20 ~
$ vim test.py
#!/usr/bin/python
print("Hi!")
~
~
~
~
~
~
~
~
-- INSERT --
$ python test.py
Hi!
Last2 18:46:10 ~
结构化语句练习：
在群文件，Linux结构化语句练习题
- 软件安装与环境变量：请安装一个二进制软件 bowtie2，包括下载、解压、调用 bowtie2 命令的帮助文档，修改环境变量 PATH
不需要下载这个软件，因为服务器上已经有了，拷贝一份即可 `/home/hcguo/tmp/biosoft/bowtie2-2.3.4.3-linux-x86_64.zip
# 提示，添加环境变量需要改一下安装路径
echo 'export PATH="安装路径:$PATH"' >> ~/.bashrc
echo 'export PATH="/home/hcguo/bowtie2-2.3.4.3-linux-x86_64:$PATH"' >> ~/.bashrc
echo 'export PATH="/trainee2/Sep14/bowtie2-2.3.4.3-linux-x86_64/:$PATH"' >> ~/.bashrc
我的解题
$ cd biosoft
Last2 21:28:41 ~/biosoft
$ cp /home/hcguo/tmp/biosoft/bowtie2-2.3.4.3-linux-x86_64.zip .
Last2 21:29:01 ~/biosoft
$ ls
bowtie2-2.3.4.3-linux-x86_64.zip hisat2-2.1.0 hisat2-2.1.0-Linux_x86_64.zip
Last2 21:29:02 ~/biosoft
$ unzip bowtie2-2.3.4.3-linux-x86_64.zip
Archive: bowtie2-2.3.4.3-linux-x86_64.zip
creating: bowtie2-2.3.4.3-linux-x86_64/
inflating: bowtie2-2.3.4.3-linux-x86_64/bowtie2-align-l
inflating: bowtie2-2.3.4.3-linux-x86_64/bowtie2-align-l-debug
inflating: bowtie2-2.3.4.3-linux-x86_64/bowtie2-inspect-l-debug
inflating: bowtie2-2.3.4.3-linux-x86_64/TUTORIAL
inflating: bowtie2-2.3.4.3-linux-x86_64/bowtie2-align-s-debug
inflating: bowtie2-2.3.4.3-linux-x86_64/bowtie2-inspect-s-debug
inflating: bowtie2-2.3.4.3-linux-x86_64/bowtie2-build-l
inflating: bowtie2-2.3.4.3-linux-x86_64/LICENSE
inflating: bowtie2-2.3.4.3-linux-x86_64/bowtie2
inflating: bowtie2-2.3.4.3-linux-x86_64/AUTHORS
inflating: bowtie2-2.3.4.3-linux-x86_64/bowtie2-build-l-debug
creating: bowtie2-2.3.4.3-linux-x86_64/example/
creating: bowtie2-2.3.4.3-linux-x86_64/example/reads/
......
$ ls
bowtie2-2.3.4.3-linux-x86_64 bowtie2-2.3.4.3-linux-x86_64.zip hisat2-2.1.0 hisat2-2.1.0-Linux_x86_64.zip
Last2 21:35:20 ~/biosoft
$ ls bowtie2-2.3.4.3-linux-x86_64
AUTHORS bowtie2-align-l bowtie2-align-s bowtie2-build bowtie2-build-l-debug bowtie2-build-s-debug bowtie2-inspect-l bowtie2-inspect-s doc LICENSE MANUAL.markdown scripts VERSION
bowtie2 bowtie2-align-l-debug bowtie2-align-s-debug bowtie2-build-l bowtie2-build-s bowtie2-inspect bowtie2-inspect-l-debug bowtie2-inspect-s-debug example MANUAL NEWS TUTORIAL
Last2 21:37:34 ~/biosoft
$ cd bowtie2-2.3.4.3-linux-x86_64
Last2 21:44:01 ~/biosoft/bowtie2-2.3.4.3-linux-x86_64
$ ./bowtie2 --help
Bowtie 2 version 2.3.4.3 by Ben Langmead ([email protected], www.cs.jhu.edu/~langmea)
Usage:
bowtie2 [options]* -x {-1 -2 | -U | --interleaved } [-S ]
Index filename prefix (minus trailing .X.bt2).
NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.
Files with #1 mates, paired with files in .
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
Files with #2 mates, paired with files in .
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
Files with unpaired reads.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
Files with interleaved paired-end FASTQ reads
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
File for SAM output (default: stdout)
, , can be comma-separated lists (no whitespace) and can be
specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'.
......
添加到PATH，这里出现了一些问题
$ $PATH
-bash: /trainee1/Last2/bin:/trainee1/Last2/.local/bin:/trainee1/Last2/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin: No such file or directory
本想输出PATH看一看，发现有No such file or directory，原来是忘了写echo
image.png
$ PATH=
Last2 22:01:30 ~
#作死的我执行了这一步命令，然后PATH就空了
$ PATH=~/biosoft/bowtie2-2.3.4.3-linux-x86_64:$PATH
Last2 22:04:17 ~
$ echo $PATH
/trainee1/Last2/biosoft/bowtie2-2.3.4.3-linux-x86_64:
Last2 22:16:48 ~
后知后觉的我还在给PATH添加路径，到这里才发现
咨询了优秀的卖萌哥，新开了一个窗口，就好了。因为修改变量的值，不写入~/.bashrc，就只对这次登陆有效。不过，记得把bashrc给备份一下，cp ~/.bashrc ~/.bashrc_bak
image.png
备份了一下
$ cp ~/.bashrc ~/.bashrc_bak
(base) Last2 10:09:27 ~
$ ll
total 123408
drwxr-xr-x 19 Last2 Last 4096 Jan 30 10:09 ./
drwxr-xr-x 135 root root 4096 Jan 30 10:09 ../
-rw------- 1 Last2 Last2 40819 Jan 30 10:09 .bash_history
-rw-r--r-- 1 Last2 root 4390 Jan 22 20:42 .bashrc
-rw-r--r-- 1 Last2 Last2 4390 Jan 30 10:09 .bashrc_bak
drwxrwxr-x 4 Last2 Last2 4096 Jan 29 21:30 biosoft/
drwx------ 2 Last2 Last2 4096 Jan 18 20:26 .cache/
-rw-rw-r-- 1 Last2 Last2 0 Jan 19 21:00 catFile
drwxrwxr-x 2 Last2 Last2 4096 Jan 22 20:41 .conda/
-rw-rw-r-- 1 Last2 Last2 255 Jan 25 10:02 .condarc
-rw-rw-r-- 1 Last2 Last2 150 Jan 23 21:20 config
drwx------ 3 Last2 Last2 4096 Jan 29 15:08 .config/
drwxr-xr-x 3 Last2 Last2 4096 Jan 23 15:25 Data/
drwxrwxr-x 3 Last2 Last2 4096 Jan 25 22:08 database/
-rw-rw-r-- 1 Last2 Last2 27104162 Jan 22 14:40 hisat2-2.1.0-Linux_x86_64.zip
drwxrwxr-x 18 Last2 Last2 4096 Jan 22 22:12 miniconda3/
-rw-rw-r-- 1 Last2 Last2 94235922 Nov 24 03:21 Miniconda3-latest-Linux-x86_64.sh
drwxrwxr-x 2 Last2 Last2 4096 Jan 18 22:16 myDir/
drwx------ 2 Last2 Last2 4096 Jan 25 10:56 .ncbi/
drwxrwxr-x 2 Last2 Last2 4096 Jan 25 22:16 pipline/
-rw-r--r-- 1 Last2 root 655 Jan 17 16:51 .profile
drwxrwxr-x 6 Last2 Last2 4096 Jan 25 22:10 project/
drwxrwxr-x 3 Last2 Last2 4096 Jan 25 22:15 project_backup/
-rw-r--r-- 1 Last2 root 206 Jan 17 16:51 readme.txt
-rw-rw-r-- 1 Last2 Last2 4721173 Dec 7 2019 samtools-1.10.tar.bz2
drwxrwxr-x 2 Last2 Last2 4096 Jan 25 13:07 softlink/
drwx------ 2 Last2 Last2 4096 Jan 22 14:54 .ssh/
drwxrwxr-x 2 Last2 Last2 4096 Jan 25 13:07 sysoft/
drwxrwxr-x 2 Last2 Last2 4096 Jan 22 10:22 test/
drwxrwxr-x 3 Last2 Last2 4096 Jan 18 22:40 test2/
-rw-rw-r-- 1 Last2 Last2 209 Jan 22 14:03 tmp
-rw-rw-r-- 1 Last2 Last2 133596 Apr 8 2019 Trimmomatic-0.39.zip
-rw------- 1 Last2 Last2 5001 Jan 25 10:03 .viminfo
(base) Last2 10:09:29 ~
添加到PATH
$ PATH=~/biosoft/bowtie2-2.3.4.3-linux-x86_64:$PATH
(base) Last2 10:12:11 ~/biosoft
$ echo $PATH
/trainee1/Last2/biosoft/bowtie2-2.3.4.3-linux-x86_64:/trainee1/Last2/bin:/trainee1/Last2/.local/bin:/trainee1/Last2/miniconda3/bin:/trainee1/Last2/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
(base) Last2 10:12:22 ~/biosoft
加入PATH之后就可以直接调用 bowtie2 命令的帮助文档了
$ bowtie2 -h
Bowtie 2 version 2.3.4.3 by Ben Langmead ([email protected], www.cs.jhu.edu/~langmea)
Usage:
bowtie2 [options]* -x {-1 -2 | -U | --interleaved } [-S ]
Index filename prefix (minus trailing .X.bt2).
NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.
Files with #1 mates, paired with files in .
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
Files with #2 mates, paired with files in .
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
Files with unpaired reads.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
Files with interleaved paired-end FASTQ reads
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
File for SAM output (default: stdout)
, , can be comma-separated lists (no whitespace) and can be
specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'.
......
(base) Last2 10:17:14 ~/biosoft
写入~/.bashrc,永久保存
$ echo 'export PATH="/trainee1/Last2/biosoft/bowtie2-2.3.4.3-linux-x86_64:$PATH"'>> ~/.bashrc
(base) Last2 10:24:45 ~/biosoft
$ source ~/.bashrc
(base) Last2 10:53:16 ~/biosoft
2.if 语句与状态参数：在上一题修改好了环境变量之后，回到家目录，再次调用 bowtie2 命令的帮助文档，然后使用 if 语句判断是否调用成功（提示：状态参数变量），如果成功，输出：yes ，否则输出 no
if [ $? -eq 0 ] ; then echo yes; else echo no; fi
我的答题
第一次尝试，错误，if 和command之间必须要加空格
$ if[ $? -eq 0 ]
if[ 0 -eq 0 ]: command not found
(base) Last2 11:26:37 ~
$ bowtie2 -h
Bowtie 2 version 2.3.4.3 by Ben Langmead ([email protected], www.cs.jhu.edu/~langmea)
Usage:
bowtie2 [options]* -x {-1 -2 | -U | --interleaved } [-S ]
Index filename prefix (minus trailing .X.bt2).
NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.
Files with #1 mates, paired with files in .
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
Files with #2 mates, paired with files in .
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
Files with unpaired reads.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
Files with interleaved paired-end FASTQ reads
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
File for SAM output (default: stdout)
, , can be comma-separated lists (no whitespace) and can be
specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'.
......
$ if [ $? -eq 0 ]; then echo 'yes'; else echo 'no'; fi
yes
(base) Last2 11:29:30 ~
3.if 语句与自定义变量：
- 创建文件 file1
- 然后判断当前目录下是否有 file1 这个文件
- 如果是，输出：yes ；否则什么都不做
touch file1
if [ -f file1 ]; then echo yes; fi
我的答案
$ touch file1
(base) Last2 11:38:22 ~
$ if [ -f file1 ]
> then
> echo yes
> fi
yes
(base) Last2 11:41:40 ~
4.创建 10 个文件 test_file_1 ~ test_file_10 ，使用循环语句（建议用 while read id），将上面的 test_file_1 ~ test_file_10 进行重命名，如：test_file_1 改为 test_1
我的答案
使用参数拓展里的替换，将file_替换为空即可。因为要变的地方在中间，无法掐头去尾，无法索引切片。
$ touch test_file_{1..10}
(base) Last2 12:14:38 ~
$ ls
biosoft Data hisat2-2.1.0-Linux_x86_64.zip myDir project_backup softlink test2 test_file_2 test_file_5 test_file_8 Trimmomatic-0.39.zip
catFile database miniconda3 pipline readme.txt sysoft test_file_1 test_file_3 test_file_6 test_file_9
config file1 Miniconda3-latest-Linux-x86_64.sh project samtools-1.10.tar.bz2 test test_file_10 test_file_4 test_file_7 tmp
(base) Last2 12:14:40 ~
$ ls test_file_*
test_file_1 test_file_10 test_file_2 test_file_3 test_file_4 test_file_5 test_file_6 test_file_7 test_file_8 test_file_9
(base) Last2 12:19:23 ~
$ ls test_file_* | while read id
> do
> mv ${id} ${id//file_/}
> done
(base) Last2 12:33:52 ~
$ ls
biosoft config database hisat2-2.1.0-Linux_x86_64.zip Miniconda3-latest-Linux-x86_64.sh pipline project_backup samtools-1.10.tar.bz2 sysoft test_1 test2 test_3 test_5 test_7 test_9 Trimmomatic-0.39.zip
catFile Data file1 miniconda3 myDir project readme.txt softlink test test_10 test_2 test_4 test_6 test_8 tmp
(base) Last2 12:33:54 ~
$ ls test_*
test_1 test_10 test_2 test_3 test_4 test_5 test_6 test_7 test_8 test_9
(base) Last2 12:39:35 ~
科研利器
飞鸟flybird
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A survey of best practices for RNA-seq data analysis
DOI号：10.1186/s13059-016-0881-8