生物信息学/linux操作与生物信息
< 生物信息学
第零阶：命令入门
[编辑]| 选项 | 含义 |
|---|---|
| --help | 显示当前帮助后退出 |
| --version | 打印版本信息后退出 |
第一阶：文件夹及文件管理命令
[编辑]
Ubutu还是CentOS
[编辑]压缩与解压命令
[编辑]tar命令的选项和参数
[编辑]用法: tar [选项...] [文件]...
GNU 'tar' 命令可以将多个文件打成一个压缩包，也可以从压缩包中将文件解压出来。
示例:
tar -cf archive.tar foo bar # 将foo和bar打包为archive.tar
tar -tvf archive.tar # 完整列出archive.tar中的文件.
tar -xf archive.tar # 将archive.tar中所有的文件解压出来
主要运行模式:
-A, --catenate, --concatenate 向已有的tar包中添加文件
-c, --create 创建一个新的tar包
-d, --diff, --compare 比较tar包和文件系统的差别
--delete delete from the archive (not on mag tapes!)
-r, --append 添加文件到包末尾
-t, --list 列出包中的内容
--test-label test the archive volume label and exit
-u, --update only append files newer than copy in archive
-x, --extract, --get extract files from an archive
Operation modifiers:
--check-device check device numbers when creating incremental
archives (default)
-g, --listed-incremental=FILE handle new GNU-format incremental backup
-G, --incremental handle old GNU-format incremental backup
--ignore-failed-read do not exit with nonzero on unreadable files
--level=NUMBER dump level for created listed-incremental archive
-n, --seek archive is seekable
--no-check-device do not check device numbers when creating
incremental archives
--no-seek archive is not seekable
--occurrence[=NUMBER] process only the NUMBERth occurrence of each file
in the archive; this option is valid only in
conjunction with one of the subcommands --delete,
--diff, --extract or --list and when a list of
files is given either on the command line or via
the -T option; NUMBER defaults to 1
--sparse-version=MAJOR[.MINOR]
set version of the sparse format to use (implies
--sparse)
-S, --sparse handle sparse files efficiently
Overwrite control:
-k, --keep-old-files don't replace existing files when extracting,
treat them as errors
--keep-directory-symlink preserve existing symlinks to directories when
extracting
--keep-newer-files don't replace existing files that are newer than
their archive copies
--no-overwrite-dir preserve metadata of existing directories
--one-top-level[=DIR] create a subdirectory to avoid having loose files
extracted
--overwrite overwrite existing files when extracting
--overwrite-dir overwrite metadata of existing directories when
extracting (default)
--recursive-unlink empty hierarchies prior to extracting directory
--remove-files remove files after adding them to the archive
--skip-old-files don't replace existing files when extracting,
silently skip over them
-U, --unlink-first remove each file prior to extracting over it
-W, --verify attempt to verify the archive after writing it
Select output stream:
--ignore-command-error ignore exit codes of children
--no-ignore-command-error treat non-zero exit codes of children as
error
-O, --to-stdout extract files to standard output
--to-command=COMMAND pipe extracted files to another program
Handling of file attributes:
--atime-preserve[=METHOD] preserve access times on dumped files, either
by restoring the times after reading
(METHOD='replace'; default) or by not setting the
times in the first place (METHOD='system')
--clamp-mtime only set time when the file is more recent than
what was given with --mtime
--delay-directory-restore delay setting modification times and
permissions of extracted directories until the end
of extraction
--group=NAME force NAME as group for added files
--mode=CHANGES force (symbolic) mode CHANGES for added files
--mtime=DATE-OR-FILE set mtime for added files from DATE-OR-FILE
-m, --touch don't extract file modified time
--no-delay-directory-restore
cancel the effect of --delay-directory-restore
option
--no-same-owner extract files as yourself (default for ordinary
users)
--no-same-permissions apply the user's umask when extracting permissions
from the archive (default for ordinary users)
--numeric-owner always use numbers for user/group names
--owner=NAME force NAME as owner for added files
-p, --preserve-permissions, --same-permissions
extract information about file permissions
(default for superuser)
--preserve same as both -p and -s
--same-owner try extracting files with the same ownership as
exists in the archive (default for superuser)
-s, --preserve-order, --same-order
member arguments are listed in the same order as
the files in the archive
--sort=ORDER directory sorting order: none (default), name or
inode
Handling of extended file attributes:
--acls Enable the POSIX ACLs support
--no-acls Disable the POSIX ACLs support
--no-selinux Disable the SELinux context support
--no-xattrs Disable extended attributes support
--selinux Enable the SELinux context support
--xattrs Enable extended attributes support
--xattrs-exclude=MASK specify the exclude pattern for xattr keys
--xattrs-include=MASK specify the include pattern for xattr keys
Device selection and switching:
-f, --file=ARCHIVE use archive file or device ARCHIVE
--force-local archive file is local even if it has a colon
-F, --info-script=NAME, --new-volume-script=NAME
run script at end of each tape (implies -M)
-L, --tape-length=NUMBER change tape after writing NUMBER x 1024 bytes
-M, --multi-volume create/list/extract multi-volume archive
--rmt-command=COMMAND use given rmt COMMAND instead of rmt
--rsh-command=COMMAND use remote COMMAND instead of rsh
--volno-file=FILE use/update the volume number in FILE
Device blocking:
-b, --blocking-factor=BLOCKS BLOCKS x 512 bytes per record
-B, --read-full-records reblock as we read (for 4.2BSD pipes)
-i, --ignore-zeros ignore zeroed blocks in archive (means EOF)
--record-size=NUMBER NUMBER of bytes per record, multiple of 512
Archive format selection:
-H, --format=FORMAT create archive of the given format
FORMAT is one of the following:
gnu GNU tar 1.13.x format
oldgnu GNU format as per tar <= 1.12
pax POSIX 1003.1-2001 (pax) format
posix same as pax
ustar POSIX 1003.1-1988 (ustar) format
v7 old V7 tar format
--old-archive, --portability
same as --format=v7
--pax-option=keyword[[:]=value][,keyword[[:]=value]]...
control pax keywords
--posix same as --format=posix
-V, --label=TEXT create archive with volume name TEXT; at
list/extract time, use TEXT as a globbing pattern
for volume name
Compression options:
-a, --auto-compress use archive suffix to determine the compression
program
-I, --use-compress-program=PROG
filter through PROG (must accept -d)
-j, --bzip2 filter the archive through bzip2
-J, --xz filter the archive through xz
--lzip filter the archive through lzip
--lzma filter the archive through xz
--lzop filter the archive through xz
--no-auto-compress do not use archive suffix to determine the
compression program
-z, --gzip, --gunzip, --ungzip filter the archive through gzip
-Z, --compress, --uncompress filter the archive through compress
Local file selection:
--add-file=FILE add given FILE to the archive (useful if its name
starts with a dash)
--backup[=CONTROL] backup before removal, choose version CONTROL
-C, --directory=DIR change to directory DIR
--exclude=PATTERN exclude files, given as a PATTERN
--exclude-backups exclude backup and lock files
--exclude-caches exclude contents of directories containing
CACHEDIR.TAG, except for the tag file itself
--exclude-caches-all exclude directories containing CACHEDIR.TAG
--exclude-caches-under exclude everything under directories containing
CACHEDIR.TAG
--exclude-ignore=FILE read exclude patterns for each directory from
FILE, if it exists
--exclude-ignore-recursive=FILE
read exclude patterns for each directory and its
subdirectories from FILE, if it exists
--exclude-tag=FILE exclude contents of directories containing FILE,
except for FILE itself
--exclude-tag-all=FILE exclude directories containing FILE
--exclude-tag-under=FILE exclude everything under directories
containing FILE
--exclude-vcs exclude version control system directories
--exclude-vcs-ignores read exclude patterns from the VCS ignore files
-h, --dereference follow symlinks; archive and dump the files they
point to
--hard-dereference follow hard links; archive and dump the files they
refer to
-K, --starting-file=MEMBER-NAME
begin at member MEMBER-NAME when reading the
archive
--newer-mtime=DATE compare date and time when data changed only
--no-null disable the effect of the previous --null option
--no-recursion avoid descending automatically in directories
--no-unquote do not unquote input file or member names
--null -T reads null-terminated names, disable -C
-N, --newer=DATE-OR-FILE, --after-date=DATE-OR-FILE
only store files newer than DATE-OR-FILE
--one-file-system stay in local file system when creating archive
-P, --absolute-names don't strip leading '/'s from file names
--recursion recurse into directories (default)
--suffix=STRING backup before removal, override usual suffix ('~'
unless overridden by environment variable
SIMPLE_BACKUP_SUFFIX)
-T, --files-from=FILE get names to extract or create from FILE
--unquote unquote input file or member names (default)
-X, --exclude-from=FILE exclude patterns listed in FILE
File name transformations:
--strip-components=NUMBER strip NUMBER leading components from file
names on extraction
--transform=EXPRESSION, --xform=EXPRESSION
use sed replace EXPRESSION to transform file
names
File name matching options (affect both exclude and include patterns):
--anchored patterns match file name start
--ignore-case ignore case
--no-anchored patterns match after any '/' (default for
exclusion)
--no-ignore-case case sensitive matching (default)
--no-wildcards verbatim string matching
--no-wildcards-match-slash wildcards do not match '/'
--wildcards use wildcards (default for exclusion)
--wildcards-match-slash wildcards match '/' (default for exclusion)
Informative output:
--checkpoint[=NUMBER] display progress messages every NUMBERth record
(default 10)
--checkpoint-action=ACTION execute ACTION on each checkpoint
--full-time print file time to its full resolution
--index-file=FILE send verbose output to FILE
-l, --check-links print a message if not all links are dumped
--no-quote-chars=STRING disable quoting for characters from STRING
--quote-chars=STRING additionally quote characters from STRING
--quoting-style=STYLE set name quoting style; see below for valid STYLE
values
-R, --block-number show block number within archive with each message
--show-defaults show tar defaults
--show-omitted-dirs when listing or extracting, list each directory
that does not match search criteria
--show-snapshot-field-ranges
show valid ranges for snapshot-file fields
--show-transformed-names, --show-stored-names
show file or archive names after transformation
--totals[=SIGNAL] print total bytes after processing the archive;
with an argument - print total bytes when this
SIGNAL is delivered; Allowed signals are: SIGHUP,
SIGQUIT, SIGINT, SIGUSR1 and SIGUSR2; the names
without SIG prefix are also accepted
--utc print file modification times in UTC
-v, --verbose verbosely list files processed
--warning=KEYWORD warning control
-w, --interactive, --confirmation
ask for confirmation for every action
Compatibility options:
-o when creating, same as --old-archive; when
extracting, same as --no-same-owner
Other options:
-?, --help 打印当前帮助文档
--restrict disable use of some potentially harmful options
--usage 打印简短的使用信息
--version 打印程序版本
Mandatory or optional arguments to long options are also mandatory or optional
for any corresponding short options.
The backup suffix is '~', unless set with --suffix or SIMPLE_BACKUP_SUFFIX.
The version control may be set with --backup or VERSION_CONTROL, values are:
none, off never make backups
t, numbered make numbered backups
nil, existing numbered if numbered backups exist, simple otherwise
never, simple always make simple backups
Valid arguments for the --quoting-style option are:
literal
shell
shell-always
c
c-maybe
escape
locale
clocale
| 压缩文件类型 | 压缩文件命令示例 | 解压缩命令示例 |
| .tar.gz/.tgz | tar zcvf FileName.tar.gz DirName | tar zxvf FileName.tar.gz |
| .tar.bz2 | tar jcvf FileName.tar.bz2 DirName | tar jxvf FileName.tar.bz2 |
| .bz2 | bzip2 -z FileName | bzip2 -d/bunzip2 FileName.bz2 |
| .tar | tar cf FileName.tar DirName | tar xvf FileName.tar |
| .gz | gzip FileName | gzip -d/gunzip FileName.gz |
| .tar.xz | tar zcvf FileName.tar.gz DirName | tar xvJf FileName.tar.xz |
| .Z | tar zcvf FileName.tar.gz DirName | uncompress FileName.Z |
| .tar.Z | tar zcvf FileName.tar.gz DirName | tar xzf FileName.tar.Z |
| .rar | tar zcvf FileName.tar.gz DirName | unrar e FileName.rar |
| .zip | tar zcvf FileName.tar.gz DirName | unzip FileName.zip |
第二阶：文本文件处理命令
[编辑]文本查看命令
[编辑]cat和tac
[编辑]cat命令将文件由前向后全部打印在屏幕上。
tac命令将文件由后向前全部打印在屏幕上。
cat的选项和参数
[编辑]cat为Concatenate单词的缩写。
用法: cat [选项]... [文件]...
把一个或者多个文件(或者标准输入)连接在一起,并标准输出
没有[文件], 或当[文件]为-, 读取标准输入。
-A, --show-all 等同于 -vET
-b, --number-nonblank 为非空输出行编号， 优先级高于 -n选项
-e 等同于 -vE
-E, --show-ends 每行结尾显示 $
-n, --number 为输出的每行编号
-s, --squeeze-blank 有连续两行以上的空白行，就替换为一行的空白行
-t 等同于 -vT
-T, --show-tabs 将TAB符显示为^I
-u (ignored)
-v, --show-nonprinting 使用^和M-符号显示不能打印的字符（不在ASCII码内的字符），尤其是LFD和TAB
Examples:
cat f - g 输出f的内容，然后标准输入，最后是g的内容
cat 将标准输入输出到标准输出
tac的选项和参数
[编辑]用法: tac [选项]... [文件]...
将每个[文件]打印到标准输出，最后一行先打印。
没有[文件], 或当[文件]为-, 读取标准输入。
-b, --before 分隔符放在开头而不是结尾
-r, --regex 分隔符采用正则表达式
-s, --separator=STRING 用STRING代替newLine作为分隔符
head和tail
[编辑]head 命令查看文件头部， -n 选项可以指定查看前几行。
tail 命令查看文件尾部， -n 选项可以指定查看后几行。
head的选项和参数
[编辑]用法:
head/tail [选项]... [文件]...
打印每个文件的前/后10行道标准输出
当[文件]多于一个时，打印前/后10行的同时打印文件名。
没有[文件], 或当[文件]为-, 读取标准输入。
head和taill共有选项：
-c, --bytes=[-]NUM 打印每个文件的前NUM个字节(bytes);
在NUM前加'-', 打印除最后NUM个字节的所有内容
-n, --lines=[-]NUM 打印前NUM行;
在NUM前加'-', 打印除最后NUM行的所有行
-q, --quiet, --silent 打印前NUM行时不给出文件名
head的选项：
-v, --verbose 打印前NUM行时给出文件名
-z, --zero-terminated 行分隔符是NULL，而非换行符
tail的选项：
Mandatory arguments to long options are mandatory for short options too.
-c, --bytes=[+]NUM output the last NUM bytes; or use -c +NUM to
output starting with byte NUM of each file
-f, --follow[={name|descriptor}]
output appended data as the file grows;
an absent option argument means 'descriptor'
-F same as --follow=name --retry
-n, --lines=[+]NUM output the last NUM lines, instead of the last 10;
or use -n +NUM to output starting with line NUM
--max-unchanged-stats=N
with --follow=name, reopen a FILE which has not
changed size after N (default 5) iterations
to see if it has been unlinked or renamed
(this is the usual case of rotated log files);
with inotify, this option is rarely useful
--pid=PID with -f, terminate after process ID, PID dies
-q, --quiet, --silent never output headers giving file names
--retry keep trying to open a file if it is inaccessible
-s, --sleep-interval=N with -f, sleep for approximately N seconds
(default 1.0) between iterations;
with inotify and --pid=P, check process P at
least once every N seconds
-v, --verbose always output headers giving file names
-z, --zero-terminated line delimiter is NUL, not newline
NUM可以有一个乘法器后缀:b 512, kB 1000, K 1024, MB 1000*1000, M 1024*1024, GB 1000*1000*1000, G 1024*1024*1024，等等，用于T, P, E, Z, Y。
tail的选项和参数
[编辑]
文本处理命令
[编辑]第三阶：shell中的各种符号
[编辑]- 元字符
- 通配符
- 扩展字符
第四阶：高级目录管理
[编辑]第五阶：任务管理
[编辑]- 任务提交及批处理
- Shell脚本编写
第六阶：生信软件安装与管理
[编辑]- 生信软件安装
- 使用conda管理生物信息软件