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
1用法: tar [选项...] [文件]...
2GNU '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。
3
4示例:
5 tar -cf archive.tar foo bar # 将foo和bar打包为archive.tar
6 tar -tvf archive.tar # 完整列出archive.tar中的文件.
7 tar -xf archive.tar # 将archive.tar中所有的文件解压出来
8
9 主要运行模式:
10
11 -A, --catenate, --concatenate 向已有的tar包中添加文件
12 -c, --create 创建一个新的tar包
13 -d, --diff, --compare 比较tar包和文件系统的差别
14 --delete delete from the archive (not on mag tapes!)
15 -r, --append 添加文件到包末尾
16 -t, --list 列出包中的内容
17 --test-label test the archive volume label and exit
18 -u, --update only append files newer than copy in archive
19 -x, --extract, --get extract files from an archive
20
21 Operation modifiers:
22
23 --check-device check device numbers when creating incremental
24 archives (default)
25 -g, --listed-incremental=FILE handle new GNU-format incremental backup
26 -G, --incremental handle old GNU-format incremental backup
27 --ignore-failed-read do not exit with nonzero on unreadable files
28 --level=NUMBER dump level for created listed-incremental archive
29 -n, --seek archive is seekable
30 --no-check-device do not check device numbers when creating
31 incremental archives
32 --no-seek archive is not seekable
33 --occurrence[=NUMBER] process only the NUMBERth occurrence of each file
34 in the archive; this option is valid only in
35 conjunction with one of the subcommands --delete,
36 --diff, --extract or --list and when a list of
37 files is given either on the command line or via
38 the -T option; NUMBER defaults to 1
39 --sparse-version=MAJOR[.MINOR]
40 set version of the sparse format to use (implies
41 --sparse)
42 -S, --sparse handle sparse files efficiently
43
44 Overwrite control:
45
46 -k, --keep-old-files don't replace existing files when extracting,
47 treat them as errors
48 --keep-directory-symlink preserve existing symlinks to directories when
49 extracting
50 --keep-newer-files don't replace existing files that are newer than
51 their archive copies
52 --no-overwrite-dir preserve metadata of existing directories
53 --one-top-level[=DIR] create a subdirectory to avoid having loose files
54 extracted
55 --overwrite overwrite existing files when extracting
56 --overwrite-dir overwrite metadata of existing directories when
57 extracting (default)
58 --recursive-unlink empty hierarchies prior to extracting directory
59 --remove-files remove files after adding them to the archive
60 --skip-old-files don't replace existing files when extracting,
61 silently skip over them
62 -U, --unlink-first remove each file prior to extracting over it
63 -W, --verify attempt to verify the archive after writing it
64
65 Select output stream:
66
67 --ignore-command-error ignore exit codes of children
68 --no-ignore-command-error treat non-zero exit codes of children as
69 error
70 -O, --to-stdout extract files to standard output
71 --to-command=COMMAND pipe extracted files to another program
72
73 Handling of file attributes:
74
75 --atime-preserve[=METHOD] preserve access times on dumped files, either
76 by restoring the times after reading
77 (METHOD='replace'; default) or by not setting the
78 times in the first place (METHOD='system')
79 --clamp-mtime only set time when the file is more recent than
80 what was given with --mtime
81 --delay-directory-restore delay setting modification times and
82 permissions of extracted directories until the end
83 of extraction
84 --group=NAME force NAME as group for added files
85 --mode=CHANGES force (symbolic) mode CHANGES for added files
86 --mtime=DATE-OR-FILE set mtime for added files from DATE-OR-FILE
87 -m, --touch don't extract file modified time
88 --no-delay-directory-restore
89 cancel the effect of --delay-directory-restore
90 option
91 --no-same-owner extract files as yourself (default for ordinary
92 users)
93 --no-same-permissions apply the user's umask when extracting permissions
94 from the archive (default for ordinary users)
95 --numeric-owner always use numbers for user/group names
96 --owner=NAME force NAME as owner for added files
97 -p, --preserve-permissions, --same-permissions
98 extract information about file permissions
99 (default for superuser)
100 --preserve same as both -p and -s
101 --same-owner try extracting files with the same ownership as
102 exists in the archive (default for superuser)
103 -s, --preserve-order, --same-order
104 member arguments are listed in the same order as
105 the files in the archive
106 --sort=ORDER directory sorting order: none (default), name or
107 inode
108
109 Handling of extended file attributes:
110
111 --acls Enable the POSIX ACLs support
112 --no-acls Disable the POSIX ACLs support
113 --no-selinux Disable the SELinux context support
114 --no-xattrs Disable extended attributes support
115 --selinux Enable the SELinux context support
116 --xattrs Enable extended attributes support
117 --xattrs-exclude=MASK specify the exclude pattern for xattr keys
118 --xattrs-include=MASK specify the include pattern for xattr keys
119
120 Device selection and switching:
121
122 -f, --file=ARCHIVE use archive file or device ARCHIVE
123 --force-local archive file is local even if it has a colon
124 -F, --info-script=NAME, --new-volume-script=NAME
125 run script at end of each tape (implies -M)
126 -L, --tape-length=NUMBER change tape after writing NUMBER x 1024 bytes
127 -M, --multi-volume create/list/extract multi-volume archive
128 --rmt-command=COMMAND use given rmt COMMAND instead of rmt
129 --rsh-command=COMMAND use remote COMMAND instead of rsh
130 --volno-file=FILE use/update the volume number in FILE
131
132 Device blocking:
133
134 -b, --blocking-factor=BLOCKS BLOCKS x 512 bytes per record
135 -B, --read-full-records reblock as we read (for 4.2BSD pipes)
136 -i, --ignore-zeros ignore zeroed blocks in archive (means EOF)
137 --record-size=NUMBER NUMBER of bytes per record, multiple of 512
138
139 Archive format selection:
140
141 -H, --format=FORMAT create archive of the given format
142
143 FORMAT is one of the following:
144
145 gnu GNU tar 1.13.x format
146 oldgnu GNU format as per tar <= 1.12
147 pax POSIX 1003.1-2001 (pax) format
148 posix same as pax
149 ustar POSIX 1003.1-1988 (ustar) format
150 v7 old V7 tar format
151
152 --old-archive, --portability
153 same as --format=v7
154 --pax-option=keyword[[:]=value][,keyword[[:]=value]]...
155 control pax keywords
156 --posix same as --format=posix
157 -V, --label=TEXT create archive with volume name TEXT; at
158 list/extract time, use TEXT as a globbing pattern
159 for volume name
160
161 Compression options:
162
163 -a, --auto-compress use archive suffix to determine the compression
164 program
165 -I, --use-compress-program=PROG
166 filter through PROG (must accept -d)
167 -j, --bzip2 filter the archive through bzip2
168 -J, --xz filter the archive through xz
169 --lzip filter the archive through lzip
170 --lzma filter the archive through xz
171 --lzop filter the archive through xz
172 --no-auto-compress do not use archive suffix to determine the
173 compression program
174 -z, --gzip, --gunzip, --ungzip filter the archive through gzip
175 -Z, --compress, --uncompress filter the archive through compress
176
177 Local file selection:
178
179 --add-file=FILE add given FILE to the archive (useful if its name
180 starts with a dash)
181 --backup[=CONTROL] backup before removal, choose version CONTROL
182 -C, --directory=DIR change to directory DIR
183 --exclude=PATTERN exclude files, given as a PATTERN
184 --exclude-backups exclude backup and lock files
185 --exclude-caches exclude contents of directories containing
186 CACHEDIR.TAG, except for the tag file itself
187 --exclude-caches-all exclude directories containing CACHEDIR.TAG
188 --exclude-caches-under exclude everything under directories containing
189 CACHEDIR.TAG
190 --exclude-ignore=FILE read exclude patterns for each directory from
191 FILE, if it exists
192 --exclude-ignore-recursive=FILE
193 read exclude patterns for each directory and its
194 subdirectories from FILE, if it exists
195 --exclude-tag=FILE exclude contents of directories containing FILE,
196 except for FILE itself
197 --exclude-tag-all=FILE exclude directories containing FILE
198 --exclude-tag-under=FILE exclude everything under directories
199 containing FILE
200 --exclude-vcs exclude version control system directories
201 --exclude-vcs-ignores read exclude patterns from the VCS ignore files
202 -h, --dereference follow symlinks; archive and dump the files they
203 point to
204 --hard-dereference follow hard links; archive and dump the files they
205 refer to
206 -K, --starting-file=MEMBER-NAME
207 begin at member MEMBER-NAME when reading the
208 archive
209 --newer-mtime=DATE compare date and time when data changed only
210 --no-null disable the effect of the previous --null option
211 --no-recursion avoid descending automatically in directories
212 --no-unquote do not unquote input file or member names
213 --null -T reads null-terminated names, disable -C
214 -N, --newer=DATE-OR-FILE, --after-date=DATE-OR-FILE
215 only store files newer than DATE-OR-FILE
216 --one-file-system stay in local file system when creating archive
217 -P, --absolute-names don't strip leading '/'s from file names
218 --recursion recurse into directories (default)
219 --suffix=STRING backup before removal, override usual suffix ('~'
220 unless overridden by environment variable
221 SIMPLE_BACKUP_SUFFIX)
222 -T, --files-from=FILE get names to extract or create from FILE
223 --unquote unquote input file or member names (default)
224 -X, --exclude-from=FILE exclude patterns listed in FILE
225
226 File name transformations:
227
228 --strip-components=NUMBER strip NUMBER leading components from file
229 names on extraction
230 --transform=EXPRESSION, --xform=EXPRESSION
231 use sed replace EXPRESSION to transform file
232 names
233
234 File name matching options (affect both exclude and include patterns):
235
236 --anchored patterns match file name start
237 --ignore-case ignore case
238 --no-anchored patterns match after any '/' (default for
239 exclusion)
240 --no-ignore-case case sensitive matching (default)
241 --no-wildcards verbatim string matching
242 --no-wildcards-match-slash wildcards do not match '/'
243 --wildcards use wildcards (default for exclusion)
244 --wildcards-match-slash wildcards match '/' (default for exclusion)
245
246 Informative output:
247
248 --checkpoint[=NUMBER] display progress messages every NUMBERth record
249 (default 10)
250 --checkpoint-action=ACTION execute ACTION on each checkpoint
251 --full-time print file time to its full resolution
252 --index-file=FILE send verbose output to FILE
253 -l, --check-links print a message if not all links are dumped
254 --no-quote-chars=STRING disable quoting for characters from STRING
255 --quote-chars=STRING additionally quote characters from STRING
256 --quoting-style=STYLE set name quoting style; see below for valid STYLE
257 values
258 -R, --block-number show block number within archive with each message
259
260 --show-defaults show tar defaults
261 --show-omitted-dirs when listing or extracting, list each directory
262 that does not match search criteria
263 --show-snapshot-field-ranges
264 show valid ranges for snapshot-file fields
265 --show-transformed-names, --show-stored-names
266 show file or archive names after transformation
267 --totals[=SIGNAL] print total bytes after processing the archive;
268 with an argument - print total bytes when this
269 SIGNAL is delivered; Allowed signals are: SIGHUP,
270 SIGQUIT, SIGINT, SIGUSR1 and SIGUSR2; the names
271 without SIG prefix are also accepted
272 --utc print file modification times in UTC
273 -v, --verbose verbosely list files processed
274 --warning=KEYWORD warning control
275 -w, --interactive, --confirmation
276 ask for confirmation for every action
277
278 Compatibility options:
279
280 -o when creating, same as --old-archive; when
281 extracting, same as --no-same-owner
282
283 Other options:
284
285 -?, --help 打印当前帮助文档
286 --restrict disable use of some potentially harmful options
287 --usage 打印简短的使用信息
288 --version 打印程序版本
289
290Mandatory or optional arguments to long options are also mandatory or optional
291for any corresponding short options.
292
293The backup suffix is '~', unless set with --suffix or SIMPLE_BACKUP_SUFFIX.
294The version control may be set with --backup or VERSION_CONTROL, values are:
295
296 none, off never make backups
297 t, numbered make numbered backups
298 nil, existing numbered if numbered backups exist, simple otherwise
299 never, simple always make simple backups
300
301Valid arguments for the --quoting-style option are:
302
303 literal
304 shell
305 shell-always
306 c
307 c-maybe
308 escape
309 locale
310 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。
1用法: cat [选项]... [文件]...
2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
3
4没有[文件], 或当[文件]为-, 读取标准输入。
5
6 -A, --show-all 等同于 -vET
7 -b, --number-nonblank 为非空输出行编号， 优先级高于 -n选项
8 -e 等同于 -vE
9 -E, --show-ends 每行结尾显示 $
10 -n, --number 为输出的每行编号
11 -s, --squeeze-blank 有连续两行以上的空白行，就替换为一行的空白行
12 -t 等同于 -vT
13 -T, --show-tabs 将TAB符显示为^I
14 -u (ignored)
15 -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
16
17
18Examples:
19 cat f - g 输出f的内容，然后标准输入，最后是g的内容
20 cat 将标准输入输出到标准输出
tac的选项和参数编辑
1用法: tac [选项]... [文件]...
2将每个[文件]打印到标准输出，最后一行先打印。
3
4没有[文件], 或当[文件]为-, 读取标准输入。
5
6 -b, --before 分隔符放在开头而不是结尾
7 -r, --regex 分隔符采用正则表达式
8 -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
1用法:
2 head/tail [选项]... [文件]...
3打印每个文件的前/后10行道标准输出
4当[文件]多于一个时，打印前/后10行的同时打印文件名。
5
6没有[文件], 或当[文件]为-, 读取标准输入。
7
8head和taill共有选项：
9 -c, --bytes=[-]NUM 打印每个文件的前NUM个字节(bytes);
10 在NUM前加'-', 打印除最后NUM个字节的所有内容
11 -n, --lines=[-]NUM 打印前NUM行;
12 在NUM前加'-', 打印除最后NUM行的所有行
13 -q, --quiet, --silent 打印前NUM行时不给出文件名
14head的选项：
15
16
17 -v, --verbose 打印前NUM行时给出文件名
18 -z, --zero-terminated 行分隔符是NULL，而非换行符
19tail的选项：
20Mandatory arguments to long options are mandatory for short options too.
21 -c, --bytes=[+]NUM output the last NUM bytes; or use -c +NUM to
22 output starting with byte NUM of each file
23 -f, --follow[={name|descriptor}]
24 output appended data as the file grows;
25 an absent option argument means 'descriptor'
26 -F same as --follow=name --retry
27 -n, --lines=[+]NUM output the last NUM lines, instead of the last 10;
28 or use -n +NUM to output starting with line NUM
29 --max-unchanged-stats=N
30 with --follow=name, reopen a FILE which has not
31 changed size after N (default 5) iterations
32 to see if it has been unlinked or renamed
33 (this is the usual case of rotated log files);
34 with inotify, this option is rarely useful
35 --pid=PID with -f, terminate after process ID, PID dies
36 -q, --quiet, --silent never output headers giving file names
37 --retry keep trying to open a file if it is inaccessible
38 -s, --sleep-interval=N with -f, sleep for approximately N seconds
39 (default 1.0) between iterations;
40 with inotify and --pid=P, check process P at
41 least once every N seconds
42 -v, --verbose always output headers giving file names
43 -z, --zero-terminated line delimiter is NUL, not newline
44NUM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