· 7 years ago · Feb 27, 2019, 07:58 AM
1gmod@gmod-VirtualBox:~$ mkdir wme_jan2013
2gmod@gmod-VirtualBox:~$ cd wme_jan2013/
3gmod@gmod-VirtualBox:~/wme_jan2013$ mkdir software
4gmod@gmod-VirtualBox:~/wme_jan2013$ ls .
5software
6gmod@gmod-VirtualBox:~/wme_jan2013$ ls ..
7Desktop examples.desktop PAG_2019_JBrowse.zip Templates
8Documents html Pictures Videos
9Downloads Music Public wme_jan2013
10gmod@gmod-VirtualBox:~/wme_jan2013$ tar zxcf ~/Downloads/ncbi-blast-2.8.1+-x64-linux.tar.gz
11tar: You may not specify more than one '-Acdtrux', '--delete' or '--test-label' option
12Try 'tar --help' or 'tar --usage' for more information.
13gmod@gmod-VirtualBox:~/wme_jan2013$ tar vxzf ~/Downloads/ncbi-blast-2.8.1+-x64-linux.tar.gz -C software
14ncbi-blast-2.8.1+/
15ncbi-blast-2.8.1+/doc/
16ncbi-blast-2.8.1+/doc/README.txt
17ncbi-blast-2.8.1+/bin/
18ncbi-blast-2.8.1+/bin/blastdbcheck
19ncbi-blast-2.8.1+/bin/update_blastdb.pl
20ncbi-blast-2.8.1+/bin/blast_formatter
21ncbi-blast-2.8.1+/bin/convert2blastmask
22ncbi-blast-2.8.1+/bin/psiblast
23ncbi-blast-2.8.1+/bin/blastn
24ncbi-blast-2.8.1+/bin/tblastn
25ncbi-blast-2.8.1+/bin/dustmasker
26ncbi-blast-2.8.1+/bin/blastdbcmd
27ncbi-blast-2.8.1+/bin/segmasker
28ncbi-blast-2.8.1+/bin/rpstblastn
29ncbi-blast-2.8.1+/bin/makembindex
30ncbi-blast-2.8.1+/bin/blastp
31ncbi-blast-2.8.1+/bin/legacy_blast.pl
32ncbi-blast-2.8.1+/bin/blastx
33ncbi-blast-2.8.1+/bin/rpsblast
34tar: ncbi-blast-2.8.1+/bin/rpsblast: Wrote only 3072 of 10240 bytes
35ncbi-blast-2.8.1+/bin/windowmasker
36tar: ncbi-blast-2.8.1+/bin/windowmasker: Cannot write: No space left on device
37ncbi-blast-2.8.1+/bin/makeprofiledb
38tar: ncbi-blast-2.8.1+/bin/makeprofiledb: Cannot write: No space left on device
39ncbi-blast-2.8.1+/bin/deltablast
40tar: ncbi-blast-2.8.1+/bin/deltablast: Cannot write: No space left on device
41ncbi-blast-2.8.1+/bin/get_species_taxids.sh
42tar: ncbi-blast-2.8.1+/bin/get_species_taxids.sh: Cannot write: No space left on device
43ncbi-blast-2.8.1+/bin/tblastx
44tar: ncbi-blast-2.8.1+/bin/tblastx: Cannot write: No space left on device
45ncbi-blast-2.8.1+/bin/makeblastdb
46tar: ncbi-blast-2.8.1+/bin/makeblastdb: Cannot write: No space left on device
47ncbi-blast-2.8.1+/bin/blastdb_aliastool
48tar: ncbi-blast-2.8.1+/bin/blastdb_aliastool: Cannot write: No space left on device
49ncbi-blast-2.8.1+/ChangeLog
50tar: ncbi-blast-2.8.1+/ChangeLog: Cannot write: No space left on device
51ncbi-blast-2.8.1+/LICENSE
52tar: ncbi-blast-2.8.1+/LICENSE: Cannot write: No space left on device
53ncbi-blast-2.8.1+/README
54tar: ncbi-blast-2.8.1+/README: Cannot write: No space left on device
55ncbi-blast-2.8.1+/ncbi_package_info
56tar: ncbi-blast-2.8.1+/ncbi_package_info: Cannot write: No space left on device
57tar: Exiting with failure status due to previous errors
58gmod@gmod-VirtualBox:~/wme_jan2013$ ls
59software
60gmod@gmod-VirtualBox:~/wme_jan2013$ ls softwbash: cannot create temp file for here-document: No space left on device
61bash: cannot create temp file for here-document: No space left on device
62^C
63gmod@gmod-VirtualBox:~/wme_jan2013$ tar vxzf ~/Downloads/ncbi-blast-2.8.1+-x64-linux.tar.gz -C software
64ncbi-blast-2.8.1+/
65ncbi-blast-2.8.1+/doc/
66ncbi-blast-2.8.1+/doc/README.txt
67ncbi-blast-2.8.1+/bin/
68ncbi-blast-2.8.1+/bin/blastdbcheck
69ncbi-blast-2.8.1+/bin/update_blastdb.pl
70ncbi-blast-2.8.1+/bin/blast_formatter
71ncbi-blast-2.8.1+/bin/convert2blastmask
72ncbi-blast-2.8.1+/bin/psiblast
73ncbi-blast-2.8.1+/bin/blastn
74ncbi-blast-2.8.1+/bin/tblastn
75ncbi-blast-2.8.1+/bin/dustmasker
76ncbi-blast-2.8.1+/bin/blastdbcmd
77ncbi-blast-2.8.1+/bin/segmasker
78ncbi-blast-2.8.1+/bin/rpstblastn
79ncbi-blast-2.8.1+/bin/makembindex
80ncbi-blast-2.8.1+/bin/blastp
81ncbi-blast-2.8.1+/bin/legacy_blast.pl
82ncbi-blast-2.8.1+/bin/blastx
83ncbi-blast-2.8.1+/bin/rpsblast
84ncbi-blast-2.8.1+/bin/windowmasker
85ncbi-blast-2.8.1+/bin/makeprofiledb
86ncbi-blast-2.8.1+/bin/deltablast
87ncbi-blast-2.8.1+/bin/get_species_taxids.sh
88ncbi-blast-2.8.1+/bin/tblastx
89ncbi-blast-2.8.1+/bin/makeblastdb
90ncbi-blast-2.8.1+/bin/blastdb_aliastool
91ncbi-blast-2.8.1+/ChangeLog
92ncbi-blast-2.8.1+/LICENSE
93ncbi-blast-2.8.1+/README
94ncbi-blast-2.8.1+/ncbi_package_info
95gmod@gmod-VirtualBox:~/wme_jan2013$
96
97
98v - verbose
99x - extract
100z -
101f -
102
103gmod@gmod-VirtualBox:~/wme_jan2013$ tar --help
104Usage: tar [OPTION...] [FILE]...
105GNU 'tar' saves many files together into a single tape or disk archive, and can
106restore individual files from the archive.
107
108Examples:
109 tar -cf archive.tar foo bar # Create archive.tar from files foo and bar.
110 tar -tvf archive.tar # List all files in archive.tar verbosely.
111 tar -xf archive.tar # Extract all files from archive.tar.
112
113 Local file name selection:
114
115 --add-file=FILE add given FILE to the archive (useful if its name
116 starts with a dash)
117 -C, --directory=DIR change to directory DIR
118 --exclude=PATTERN exclude files, given as a PATTERN
119 --exclude-backups exclude backup and lock files
120 --exclude-caches exclude contents of directories containing
121 CACHEDIR.TAG, except for the tag file itself
122 --exclude-caches-all exclude directories containing CACHEDIR.TAG
123 --exclude-caches-under exclude everything under directories containing
124 CACHEDIR.TAG
125 --exclude-ignore=FILE read exclude patterns for each directory from
126 FILE, if it exists
127 --exclude-ignore-recursive=FILE
128 read exclude patterns for each directory and its
129 subdirectories from FILE, if it exists
130 --exclude-tag=FILE exclude contents of directories containing FILE,
131 except for FILE itself
132 --exclude-tag-all=FILE exclude directories containing FILE
133 --exclude-tag-under=FILE exclude everything under directories
134 containing FILE
135 --exclude-vcs exclude version control system directories
136 --exclude-vcs-ignores read exclude patterns from the VCS ignore files
137 --no-null disable the effect of the previous --null option
138 --no-recursion avoid descending automatically in directories
139 --no-unquote do not unquote input file or member names
140 --no-verbatim-files-from -T treats file names starting with dash as
141 options (default)
142 --null -T reads null-terminated names; implies
143 --verbatim-files-from
144 --recursion recurse into directories (default)
145 -T, --files-from=FILE get names to extract or create from FILE
146 --unquote unquote input file or member names (default)
147 --verbatim-files-from -T reads file names verbatim (no option handling)
148 -X, --exclude-from=FILE exclude patterns listed in FILE
149
150 File name matching options (affect both exclude and include patterns):
151
152 --anchored patterns match file name start
153 --ignore-case ignore case
154 --no-anchored patterns match after any '/' (default for
155 exclusion)
156 --no-ignore-case case sensitive matching (default)
157 --no-wildcards verbatim string matching
158 --no-wildcards-match-slash wildcards do not match '/'
159 --wildcards use wildcards (default for exclusion)
160 --wildcards-match-slash wildcards match '/' (default for exclusion)
161
162 Main operation mode:
163
164 -A, --catenate, --concatenate append tar files to an archive
165 -c, --create create a new archive
166 -d, --diff, --compare find differences between archive and file system
167 --delete delete from the archive (not on mag tapes!)
168 -r, --append append files to the end of an archive
169 -t, --list list the contents of an archive
170 --test-label test the archive volume label and exit
171 -u, --update only append files newer than copy in archive
172 -x, --extract, --get extract files from an archive
173
174 Operation modifiers:
175
176 --check-device check device numbers when creating incremental
177 archives (default)
178 -g, --listed-incremental=FILE handle new GNU-format incremental backup
179 -G, --incremental handle old GNU-format incremental backup
180 --hole-detection=TYPE technique to detect holes
181 --ignore-failed-read do not exit with nonzero on unreadable files
182 --level=NUMBER dump level for created listed-incremental archive
183 -n, --seek archive is seekable
184 --no-check-device do not check device numbers when creating
185 incremental archives
186 --no-seek archive is not seekable
187 --occurrence[=NUMBER] process only the NUMBERth occurrence of each file
188 in the archive; this option is valid only in
189 conjunction with one of the subcommands --delete,
190 --diff, --extract or --list and when a list of
191 files is given either on the command line or via
192 the -T option; NUMBER defaults to 1
193 --sparse-version=MAJOR[.MINOR]
194 set version of the sparse format to use (implies
195 --sparse)
196 -S, --sparse handle sparse files efficiently
197
198 Overwrite control:
199
200 -k, --keep-old-files don't replace existing files when extracting,
201 treat them as errors
202 --keep-directory-symlink preserve existing symlinks to directories when
203 extracting
204 --keep-newer-files don't replace existing files that are newer than
205 their archive copies
206 --no-overwrite-dir preserve metadata of existing directories
207 --one-top-level[=DIR] create a subdirectory to avoid having loose files
208 extracted
209 --overwrite overwrite existing files when extracting
210 --overwrite-dir overwrite metadata of existing directories when
211 extracting (default)
212 --recursive-unlink empty hierarchies prior to extracting directory
213 --remove-files remove files after adding them to the archive
214 --skip-old-files don't replace existing files when extracting,
215 silently skip over them
216 -U, --unlink-first remove each file prior to extracting over it
217 -W, --verify attempt to verify the archive after writing it
218
219 Select output stream:
220
221 --ignore-command-error ignore exit codes of children
222 --no-ignore-command-error treat non-zero exit codes of children as
223 error
224 -O, --to-stdout extract files to standard output
225 --to-command=COMMAND pipe extracted files to another program
226
227 Handling of file attributes:
228
229 --atime-preserve[=METHOD] preserve access times on dumped files, either
230 by restoring the times after reading
231 (METHOD='replace'; default) or by not setting the
232 times in the first place (METHOD='system')
233 --clamp-mtime only set time when the file is more recent than
234 what was given with --mtime
235 --delay-directory-restore delay setting modification times and
236 permissions of extracted directories until the end
237 of extraction
238 --group=NAME force NAME as group for added files
239 --group-map=FILE use FILE to map file owner GIDs and names
240 --mode=CHANGES force (symbolic) mode CHANGES for added files
241 --mtime=DATE-OR-FILE set mtime for added files from DATE-OR-FILE
242 -m, --touch don't extract file modified time
243 --no-delay-directory-restore
244 cancel the effect of --delay-directory-restore
245 option
246 --no-same-owner extract files as yourself (default for ordinary
247 users)
248 --no-same-permissions apply the user's umask when extracting permissions
249 from the archive (default for ordinary users)
250 --numeric-owner always use numbers for user/group names
251 --owner=NAME force NAME as owner for added files
252 --owner-map=FILE use FILE to map file owner UIDs and names
253 -p, --preserve-permissions, --same-permissions
254 extract information about file permissions
255 (default for superuser)
256 --same-owner try extracting files with the same ownership as
257 exists in the archive (default for superuser)
258 -s, --preserve-order, --same-order
259 member arguments are listed in the same order as
260 the files in the archive
261 --sort=ORDER directory sorting order: none (default), name or
262 inode
263
264 Handling of extended file attributes:
265
266 --acls Enable the POSIX ACLs support
267 --no-acls Disable the POSIX ACLs support
268 --no-selinux Disable the SELinux context support
269 --no-xattrs Disable extended attributes support
270 --selinux Enable the SELinux context support
271 --xattrs Enable extended attributes support
272 --xattrs-exclude=MASK specify the exclude pattern for xattr keys
273 --xattrs-include=MASK specify the include pattern for xattr keys
274
275 Device selection and switching:
276
277 -f, --file=ARCHIVE use archive file or device ARCHIVE
278 --force-local archive file is local even if it has a colon
279 -F, --info-script=NAME, --new-volume-script=NAME
280 run script at end of each tape (implies -M)
281 -L, --tape-length=NUMBER change tape after writing NUMBER x 1024 bytes
282 -M, --multi-volume create/list/extract multi-volume archive
283 --rmt-command=COMMAND use given rmt COMMAND instead of rmt
284 --rsh-command=COMMAND use remote COMMAND instead of rsh
285 --volno-file=FILE use/update the volume number in FILE
286
287 Device blocking:
288
289 -b, --blocking-factor=BLOCKS BLOCKS x 512 bytes per record
290 -B, --read-full-records reblock as we read (for 4.2BSD pipes)
291 -i, --ignore-zeros ignore zeroed blocks in archive (means EOF)
292 --record-size=NUMBER NUMBER of bytes per record, multiple of 512
293
294 Archive format selection:
295
296 -H, --format=FORMAT create archive of the given format
297
298 FORMAT is one of the following:
299
300 gnu GNU tar 1.13.x format
301 oldgnu GNU format as per tar <= 1.12
302 pax POSIX 1003.1-2001 (pax) format
303 posix same as pax
304 ustar POSIX 1003.1-1988 (ustar) format
305 v7 old V7 tar format
306
307 --old-archive, --portability
308 same as --format=v7
309 --pax-option=keyword[[:]=value][,keyword[[:]=value]]...
310 control pax keywords
311 --posix same as --format=posix
312 -V, --label=TEXT create archive with volume name TEXT; at
313 list/extract time, use TEXT as a globbing pattern
314 for volume name
315
316 Compression options:
317
318 -a, --auto-compress use archive suffix to determine the compression
319 program
320 -I, --use-compress-program=PROG
321 filter through PROG (must accept -d)
322 -j, --bzip2 filter the archive through bzip2
323 -J, --xz filter the archive through xz
324 --lzip filter the archive through lzip
325 --lzma filter the archive through xz
326 --lzop filter the archive through xz
327 --no-auto-compress do not use archive suffix to determine the
328 compression program
329 -z, --gzip, --gunzip, --ungzip filter the archive through gzip
330 -Z, --compress, --uncompress filter the archive through compress
331
332 Local file selection:
333
334 --backup[=CONTROL] backup before removal, choose version CONTROL
335 -h, --dereference follow symlinks; archive and dump the files they
336 point to
337 --hard-dereference follow hard links; archive and dump the files they
338 refer to
339 -K, --starting-file=MEMBER-NAME
340 begin at member MEMBER-NAME when reading the
341 archive
342 --newer-mtime=DATE compare date and time when data changed only
343 -N, --newer=DATE-OR-FILE, --after-date=DATE-OR-FILE
344 only store files newer than DATE-OR-FILE
345 --one-file-system stay in local file system when creating archive
346 -P, --absolute-names don't strip leading '/'s from file names
347 --suffix=STRING backup before removal, override usual suffix ('~'
348 unless overridden by environment variable
349 SIMPLE_BACKUP_SUFFIX)
350
351 File name transformations:
352
353 --strip-components=NUMBER strip NUMBER leading components from file
354 names on extraction
355 --transform=EXPRESSION, --xform=EXPRESSION
356 use sed replace EXPRESSION to transform file
357 names
358
359 Informative output:
360
361 --checkpoint[=NUMBER] display progress messages every NUMBERth record
362 (default 10)
363 --checkpoint-action=ACTION execute ACTION on each checkpoint
364 --full-time print file time to its full resolution
365 --index-file=FILE send verbose output to FILE
366 -l, --check-links print a message if not all links are dumped
367 --no-quote-chars=STRING disable quoting for characters from STRING
368 --quote-chars=STRING additionally quote characters from STRING
369 --quoting-style=STYLE set name quoting style; see below for valid STYLE
370 values
371 -R, --block-number show block number within archive with each message
372
373 --show-defaults show tar defaults
374 --show-omitted-dirs when listing or extracting, list each directory
375 that does not match search criteria
376 --show-snapshot-field-ranges
377 show valid ranges for snapshot-file fields
378 --show-transformed-names, --show-stored-names
379 show file or archive names after transformation
380 --totals[=SIGNAL] print total bytes after processing the archive;
381 with an argument - print total bytes when this
382 SIGNAL is delivered; Allowed signals are: SIGHUP,
383 SIGQUIT, SIGINT, SIGUSR1 and SIGUSR2; the names
384 without SIG prefix are also accepted
385 --utc print file modification times in UTC
386 -v, --verbose verbosely list files processed
387 --warning=KEYWORD warning control
388 -w, --interactive, --confirmation
389 ask for confirmation for every action
390
391 Compatibility options:
392
393 -o when creating, same as --old-archive; when
394 extracting, same as --no-same-owner
395
396 Other options:
397
398 -?, --help give this help list
399 --restrict disable use of some potentially harmful options
400 --usage give a short usage message
401 --version print program version
402
403Mandatory or optional arguments to long options are also mandatory or optional
404for any corresponding short options.
405
406The backup suffix is '~', unless set with --suffix or SIMPLE_BACKUP_SUFFIX.
407The version control may be set with --backup or VERSION_CONTROL, values are:
408
409 none, off never make backups
410 t, numbered make numbered backups
411 nil, existing numbered if numbered backups exist, simple otherwise
412 never, simple always make simple backups
413
414Valid arguments for the --quoting-style option are:
415
416 literal
417 shell
418 shell-always
419 c
420 c-maybe
421 escape
422 locale
423 clocale
424
425*This* tar defaults to:
426--format=gnu -f- -b20 --quoting-style=escape --rmt-command=/usr/lib/tar/rmt
427--rsh-command=/usr/bin/rsh
428gmod@gmod-VirtualBox:~/wme_jan2013$
429
430
431
432
433** set a path variable --> use 2 variables, echo and ">>" to append something (concatenate)
434- source = read this file / refresh this file
435
436
437
438
439
440
441
442
443
444
445
446
447####
448
449
450gmod@gmod-VirtualBox:~/wme_jan2013$ ls software
451ncbi-blast-2.8.1+
452gmod@gmod-VirtualBox:~/wme_jan2013$ ls software/ncbi-blast-2.8.1+/
453bin ChangeLog doc LICENSE ncbi_package_info README
454gmod@gmod-VirtualBox:~/wme_jan2013$ ls -l software/ncbi-blast-2.8.1+/
455total 36
456drwxr-xr-x 2 gmod gmod 4096 Nov 26 09:45 bin
457-rw-r--r-- 1 gmod gmod 85 Nov 26 09:45 ChangeLog
458drwxr-xr-x 2 gmod gmod 4096 Nov 26 13:10 doc
459-rw-r--r-- 1 gmod gmod 1055 Nov 26 09:45 LICENSE
460-rw-r--r-- 1 gmod gmod 15540 Nov 26 09:45 ncbi_package_info
461-rw-r--r-- 1 gmod gmod 465 Nov 26 09:45 README
462gmod@gmod-VirtualBox:~/wme_jan2013$ echo PATH=$PATH:~/wme_jan2013/software/ncbi-blast-2.8.1+/bin >>.bashrc
463gmod@gmod-VirtualBox:~/wme_jan2013$ echo export PATH >>.bashrc
464gmod@gmod-VirtualBox:~/wme_jan2013$ source .bashrc
465
466
467(to check if installed)
468gmod@gmod-VirtualBox:~/wme_jan2013$ blastn
469BLAST query/options error: Either a BLAST database or subject sequence(s) must be specified
470Please refer to the BLAST+ user manual.
471gmod@gmod-VirtualBox:~/wme_jan2013$ blastp
472BLAST query/options error: Either a BLAST database or subject sequence(s) must be specified
473Please refer to the BLAST+ user manual.
474
475gmod@gmod-VirtualBox:~/wme_jan2013$ unzip ~/Downloads/blastplus.zip
476Archive: /home/gmod/Downloads/blastplus.zip
477 creating: blastplus/
478 creating: blastplus/db/
479 inflating: blastplus/db/pdbaa
480 creating: __MACOSX/
481 creating: __MACOSX/blastplus/
482 creating: __MACOSX/blastplus/db/
483 inflating: __MACOSX/blastplus/db/._pdbaa
484 inflating: blastplus/db/pdbaa.fasta
485 inflating: __MACOSX/blastplus/db/._pdbaa.fasta
486 inflating: blastplus/db/pdbaa.phr
487 inflating: blastplus/db/pdbaa.pin
488 inflating: blastplus/db/pdbaa.pnd
489 inflating: blastplus/db/pdbaa.pni
490 inflating: blastplus/db/pdbaa.pog
491 inflating: blastplus/db/pdbaa.psd
492 inflating: blastplus/db/pdbaa.psi
493 inflating: blastplus/db/pdbaa.psq
494 inflating: blastplus/proteins.fasta
495 inflating: __MACOSX/blastplus/._proteins.fasta
496gmod@gmod-VirtualBox:~/wme_jan2013$
497
498gmod@gmod-VirtualBox:~/wme_jan2013$ ls -l
499total 12
500drwxr-xr-x 3 gmod gmod 4096 Jan 24 2013 blastplus
501drwxrwxr-x 3 gmod gmod 4096 Jan 24 2013 __MACOSX
502drwxr-xr-x 3 gmod gmod 4096 Feb 26 22:58 software
503gmod@gmod-VirtualBox:~/wme_jan2013$ ls blastplus
504db proteins.fasta
505gmod@gmod-VirtualBox:~/wme_jan2013$ cd blastplus
506gmod@gmod-VirtualBox:~/wme_jan2013/blastplus$ blastp -query proteins.fasta -db db/pdbaa -out proteins_blastp.txt
507gmod@gmod-VirtualBox:~/wme_jan2013/blastplus$ ls
508db proteins_blastp.txt proteins.fasta
509gmod@gmod-VirtualBox:~/wme_jan2013/blastplus$ gedit proteins_blastp.txt
510gmod@gmod-VirtualBox:~/wme_jan2013/blastplus$ blastp -help
511USAGE
512 blastp [-h] [-help] [-import_search_strategy filename]
513 [-export_search_strategy filename] [-task task_name] [-db database_name]
514 [-dbsize num_letters] [-gilist filename] [-seqidlist filename]
515 [-negative_gilist filename] [-negative_seqidlist filename]
516 [-taxids taxids] [-negative_taxids taxids] [-taxidlist filename]
517 [-negative_taxidlist filename] [-entrez_query entrez_query]
518 [-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm]
519 [-subject subject_input_file] [-subject_loc range] [-query input_file]
520 [-out output_file] [-evalue evalue] [-word_size int_value]
521 [-gapopen open_penalty] [-gapextend extend_penalty]
522 [-qcov_hsp_perc float_value] [-max_hsps int_value]
523 [-xdrop_ungap float_value] [-xdrop_gap float_value]
524 [-xdrop_gap_final float_value] [-searchsp int_value] [-seg SEG_options]
525 [-soft_masking soft_masking] [-matrix matrix_name]
526 [-threshold float_value] [-culling_limit int_value]
527 [-best_hit_overhang float_value] [-best_hit_score_edge float_value]
528 [-subject_besthit] [-window_size int_value] [-lcase_masking]
529 [-query_loc range] [-parse_deflines] [-outfmt format] [-show_gis]
530 [-num_descriptions int_value] [-num_alignments int_value]
531 [-line_length line_length] [-html] [-max_target_seqs num_sequences]
532 [-num_threads int_value] [-ungapped] [-remote] [-comp_based_stats compo]
533 [-use_sw_tback] [-version]
534
535DESCRIPTION
536 Protein-Protein BLAST 2.8.1+
537
538OPTIONAL ARGUMENTS
539 -h
540 Print USAGE and DESCRIPTION; ignore all other parameters
541 -help
542 Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
543 -version
544 Print version number; ignore other arguments
545
546 *** Input query options
547 -query <File_In>
548 Input file name
549 Default = `-'
550 -query_loc <String>
551 Location on the query sequence in 1-based offsets (Format: start-stop)
552
553 *** General search options
554 -task <String, Permissible values: 'blastp' 'blastp-fast' 'blastp-short' >
555 Task to execute
556 Default = `blastp'
557 -db <String>
558 BLAST database name
559 * Incompatible with: subject, subject_loc
560 -out <File_Out>
561 Output file name
562 Default = `-'
563 -evalue <Real>
564 Expectation value (E) threshold for saving hits
565 Default = `10'
566 -word_size <Integer, >=2>
567 Word size for wordfinder algorithm
568 -gapopen <Integer>
569 Cost to open a gap
570 -gapextend <Integer>
571 Cost to extend a gap
572 -matrix <String>
573 Scoring matrix name (normally BLOSUM62)
574 -threshold <Real, >=0>
575 Minimum word score such that the word is added to the BLAST lookup table
576 -comp_based_stats <String>
577 Use composition-based statistics:
578 D or d: default (equivalent to 2 )
579 0 or F or f: No composition-based statistics
580 1: Composition-based statistics as in NAR 29:2994-3005, 2001
581 2 or T or t : Composition-based score adjustment as in Bioinformatics
582 21:902-911,
583 2005, conditioned on sequence properties
584 3: Composition-based score adjustment as in Bioinformatics 21:902-911,
585 2005, unconditionally
586 Default = `2'
587
588 *** BLAST-2-Sequences options
589 -subject <File_In>
590 Subject sequence(s) to search
591 * Incompatible with: db, gilist, seqidlist, negative_gilist,
592 negative_seqidlist, taxids, taxidlist, negative_taxids, negative_taxidlist,
593 db_soft_mask, db_hard_mask
594 -subject_loc <String>
595 Location on the subject sequence in 1-based offsets (Format: start-stop)
596 * Incompatible with: db, gilist, seqidlist, negative_gilist,
597 negative_seqidlist, taxids, taxidlist, negative_taxids, negative_taxidlist,
598 db_soft_mask, db_hard_mask, remote
599
600 *** Formatting options
601 -outfmt <String>
602 alignment view options:
603 0 = Pairwise,
604 1 = Query-anchored showing identities,
605 2 = Query-anchored no identities,
606 3 = Flat query-anchored showing identities,
607 4 = Flat query-anchored no identities,
608 5 = BLAST XML,
609 6 = Tabular,
610 7 = Tabular with comment lines,
611 8 = Seqalign (Text ASN.1),
612 9 = Seqalign (Binary ASN.1),
613 10 = Comma-separated values,
614 11 = BLAST archive (ASN.1),
615 12 = Seqalign (JSON),
616 13 = Multiple-file BLAST JSON,
617 14 = Multiple-file BLAST XML2,
618 15 = Single-file BLAST JSON,
619 16 = Single-file BLAST XML2,
620 18 = Organism Report
621
622 Options 6, 7 and 10 can be additionally configured to produce
623 a custom format specified by space delimited format specifiers.
624 The supported format specifiers are:
625 qseqid means Query Seq-id
626 qgi means Query GI
627 qacc means Query accesion
628 qaccver means Query accesion.version
629 qlen means Query sequence length
630 sseqid means Subject Seq-id
631 sallseqid means All subject Seq-id(s), separated by a ';'
632 sgi means Subject GI
633 sallgi means All subject GIs
634 sacc means Subject accession
635 saccver means Subject accession.version
636 sallacc means All subject accessions
637 slen means Subject sequence length
638 qstart means Start of alignment in query
639 qend means End of alignment in query
640 sstart means Start of alignment in subject
641 send means End of alignment in subject
642 qseq means Aligned part of query sequence
643 sseq means Aligned part of subject sequence
644 evalue means Expect value
645 bitscore means Bit score
646 score means Raw score
647 length means Alignment length
648 pident means Percentage of identical matches
649 nident means Number of identical matches
650 mismatch means Number of mismatches
651 positive means Number of positive-scoring matches
652 gapopen means Number of gap openings
653 gaps means Total number of gaps
654 ppos means Percentage of positive-scoring matches
655 frames means Query and subject frames separated by a '/'
656 qframe means Query frame
657 sframe means Subject frame
658 btop means Blast traceback operations (BTOP)
659 staxid means Subject Taxonomy ID
660 ssciname means Subject Scientific Name
661 scomname means Subject Common Name
662 sblastname means Subject Blast Name
663 sskingdom means Subject Super Kingdom
664 staxids means unique Subject Taxonomy ID(s), separated by a ';'
665 (in numerical order)
666 sscinames means unique Subject Scientific Name(s), separated by a ';'
667 scomnames means unique Subject Common Name(s), separated by a ';'
668 sblastnames means unique Subject Blast Name(s), separated by a ';'
669 (in alphabetical order)
670 sskingdoms means unique Subject Super Kingdom(s), separated by a ';'
671 (in alphabetical order)
672 stitle means Subject Title
673 salltitles means All Subject Title(s), separated by a '<>'
674 sstrand means Subject Strand
675 qcovs means Query Coverage Per Subject
676 qcovhsp means Query Coverage Per HSP
677 qcovus means Query Coverage Per Unique Subject (blastn only)
678 When not provided, the default value is:
679 'qaccver saccver pident length mismatch gapopen qstart qend sstart send
680 evalue bitscore', which is equivalent to the keyword 'std'
681 Default = `0'
682 -show_gis
683 Show NCBI GIs in deflines?
684 -num_descriptions <Integer, >=0>
685 Number of database sequences to show one-line descriptions for
686 Not applicable for outfmt > 4
687 Default = `500'
688 * Incompatible with: max_target_seqs
689 -num_alignments <Integer, >=0>
690 Number of database sequences to show alignments for
691 Default = `250'
692 * Incompatible with: max_target_seqs
693 -line_length <Integer, >=1>
694 Line length for formatting alignments
695 Not applicable for outfmt > 4
696 Default = `60'
697 -html
698 Produce HTML output?
699
700 *** Query filtering options
701 -seg <String>
702 Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or
703 'no' to disable)
704 Default = `no'
705 -soft_masking <Boolean>
706 Apply filtering locations as soft masks
707 Default = `false'
708 -lcase_masking
709 Use lower case filtering in query and subject sequence(s)?
710
711 *** Restrict search or results
712 -gilist <String>
713 Restrict search of database to list of GIs
714 * Incompatible with: seqidlist, taxids, taxidlist, negative_gilist,
715 negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
716 subject_loc
717 -seqidlist <String>
718 Restrict search of database to list of SeqIDs
719 * Incompatible with: gilist, taxids, taxidlist, negative_gilist,
720 negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
721 subject_loc
722 -negative_gilist <String>
723 Restrict search of database to everything except the specified GIs
724 * Incompatible with: gilist, seqidlist, taxids, taxidlist,
725 negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
726 subject_loc
727 -negative_seqidlist <String>
728 Restrict search of database to everything except the specified SeqIDs
729 * Incompatible with: gilist, seqidlist, taxids, taxidlist,
730 negative_gilist, negative_taxids, negative_taxidlist, remote, subject,
731 subject_loc
732 -taxids <String>
733 Restrict search of database to include only the specified taxonomy IDs
734 (multiple IDs delimited by ',')
735 * Incompatible with: gilist, seqidlist, taxidlist, negative_gilist,
736 negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
737 subject_loc
738 -negative_taxids <String>
739 Restrict search of database to everything except the specified taxonomy IDs
740 (multiple IDs delimited by ',')
741 * Incompatible with: gilist, seqidlist, taxids, taxidlist,
742 negative_gilist, negative_seqidlist, negative_taxidlist, remote, subject,
743 subject_loc
744 -taxidlist <String>
745 Restrict search of database to include only the specified taxonomy IDs
746 * Incompatible with: gilist, seqidlist, taxids, negative_gilist,
747 negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
748 subject_loc
749 -negative_taxidlist <String>
750 Restrict search of database to everything except the specified taxonomy IDs
751 * Incompatible with: gilist, seqidlist, taxids, taxidlist,
752 negative_gilist, negative_seqidlist, negative_taxids, remote, subject,
753 subject_loc
754 -entrez_query <String>
755 Restrict search with the given Entrez query
756 * Requires: remote
757 -db_soft_mask <String>
758 Filtering algorithm ID to apply to the BLAST database as soft masking
759 * Incompatible with: db_hard_mask, subject, subject_loc
760 -db_hard_mask <String>
761 Filtering algorithm ID to apply to the BLAST database as hard masking
762 * Incompatible with: db_soft_mask, subject, subject_loc
763 -qcov_hsp_perc <Real, 0..100>
764 Percent query coverage per hsp
765 -max_hsps <Integer, >=1>
766 Set maximum number of HSPs per subject sequence to save for each query
767 -culling_limit <Integer, >=0>
768 If the query range of a hit is enveloped by that of at least this many
769 higher-scoring hits, delete the hit
770 * Incompatible with: best_hit_overhang, best_hit_score_edge
771 -best_hit_overhang <Real, (>0 and <0.5)>
772 Best Hit algorithm overhang value (recommended value: 0.1)
773 * Incompatible with: culling_limit
774 -best_hit_score_edge <Real, (>0 and <0.5)>
775 Best Hit algorithm score edge value (recommended value: 0.1)
776 * Incompatible with: culling_limit
777 -subject_besthit
778 Turn on best hit per subject sequence
779 -max_target_seqs <Integer, >=1>
780 Maximum number of aligned sequences to keep
781 (value of 5 or more is recommended)
782 Default = `500'
783 * Incompatible with: num_descriptions, num_alignments
784
785 *** Statistical options
786 -dbsize <Int8>
787 Effective length of the database
788 -searchsp <Int8, >=0>
789 Effective length of the search space
790
791 *** Search strategy options
792 -import_search_strategy <File_In>
793 Search strategy to use
794 * Incompatible with: export_search_strategy
795 -export_search_strategy <File_Out>
796 File name to record the search strategy used
797 * Incompatible with: import_search_strategy
798
799 *** Extension options
800 -xdrop_ungap <Real>
801 X-dropoff value (in bits) for ungapped extensions
802 -xdrop_gap <Real>
803 X-dropoff value (in bits) for preliminary gapped extensions
804 -xdrop_gap_final <Real>
805 X-dropoff value (in bits) for final gapped alignment
806 -window_size <Integer, >=0>
807 Multiple hits window size, use 0 to specify 1-hit algorithm
808 -ungapped
809 Perform ungapped alignment only?
810
811 *** Miscellaneous options
812 -parse_deflines
813 Should the query and subject defline(s) be parsed?
814 -num_threads <Integer, >=1>
815 Number of threads (CPUs) to use in the BLAST search
816 Default = `1'
817 * Incompatible with: remote
818 -remote
819 Execute search remotely?
820 * Incompatible with: gilist, seqidlist, taxids, taxidlist,
821 negative_gilist, negative_seqidlist, negative_taxids, negative_taxidlist,
822 subject_loc, num_threads
823 -use_sw_tback
824 Compute locally optimal Smith-Waterman alignments?
825
826gmod@gmod-VirtualBox:~/wme_jan2013/blastplus$
827
828
829gmod@gmod-VirtualBox:~/wme_jan2013/blastplus$ blastp -query proteins.fasta -db db/pdbaa -out proteins_blastp_1align.txt -num_alignments 1
830gmod@gmod-VirtualBox:~/wme_jan2013/blastplus$ gedit proteins_blastp_1align.txt
831gmod@gmod-VirtualBox:~/wme_jan2013/blastplus$ ls
832db proteins_blastp_1align.txt proteins_blastp.txt proteins.fasta
833
834
835=== exercise 4
836gmod@gmod-VirtualBox:~/wme_jan2013/blastplus$ mkdir db2
837gmod@gmod-VirtualBox:~/wme_jan2013/blastplus$ cp db/pdbaa.fasta db2/
838gmod@gmod-VirtualBox:~/wme_jan2013/blastplus$ ls
839db proteins_blastp_1e-30_table.txt
840db2 proteins_blastp.txt
841proteins_blastp_1align_1e-30.txt proteins.fasta
842proteins_blastp_1align.txt
843gmod@gmod-VirtualBox:~/wme_jan2013/blastplus$ ls db2
844pdbaa.fasta
845gmod@gmod-VirtualBox:~/wme_jan2013/blastplus$ cd db2
846gmod@gmod-VirtualBox:~/wme_jan2013/blastplus/db2$ makeblastdb -in pdbaa.fasta -title pdbaa -dbtype prot -out pdbaa -parse_seqids
847
848
849Building a new DB, current time: 02/26/2019 23:35:24
850New DB name: /home/gmod/wme_jan2013/blastplus/db2/pdbaa
851New DB title: pdbaa
852Sequence type: Protein
853Keep MBits: T
854Maximum file size: 1000000000B
855Adding sequences from FASTA; added 61866 sequences in 3.39984 seconds.
856gmod@gmod-VirtualBox:~/wme_jan2013/blastplus/db2$
857
858
859=== exercise 5