生物信息學/linux操作與生物信息

第零階：命令入門

Linux命令共有選項

選項	含義
--help	顯示當前幫助後退出
--version	打印版本信息後退出

第一階：文件夾及文件管理命令

壓縮與解壓命令

tar命令的選項和參數

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

壓縮與解壓命令匯總

壓縮文件類型	壓縮文件命令示例	解壓縮命令示例
.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

第二階：文本文件處理命令

文本查看命令

cat和tac

cat命令將文件由前向後全部打印在屏幕上。

tac命令將文件由後向前全部打印在屏幕上。

cat的選項和參數

cat為Concatenate單詞的縮寫。

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的選項和參數

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

head 命令查看文件頭部， -n 選項可以指定查看前幾行。

tail 命令查看文件尾部， -n 選項可以指定查看後幾行。

head的選項和參數

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。

第三階：shell中的各種符號

• 元字符
• 通配符
• 擴展字符

第五階：任務管理

• 任務提交及批處理
• Shell腳本編寫

第六階：生信軟件安裝與管理

• 生信軟件安裝
• 使用conda管理生物信息軟件