Sponsored Content
Top Forums Shell Programming and Scripting Convert a DNA sequence into Amino Acid Post 302957627 by cjcox on Tuesday 13th of October 2015 10:50:43 AM
Old 10-13-2015
The sed script file can be represented as a set of sed command "-e". You can use multiple -e's or use semicolon to separate the commands.
 

9 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

escape sequence for $

Hi all, I have a requirement where the variable name starts with $, like $Amd=/home/student/test/ How to work wit it? can some one help me, am in gr8 confusion:confused: (5 Replies)
Discussion started by: shreekrishnagd
5 Replies

2. Shell Programming and Scripting

How to remove those sequence with same amino acid?What command line I should type?

My input is listed as: giNumber RefAminoAcid VarAminoAcid 10190711 P P 10190711 D D 109255248 I A 110349771 A ... (4 Replies)
Discussion started by: patrick chia
4 Replies

3. Shell Programming and Scripting

Extracting DNA sequences from GenBank files using Perl

Hi all, Using Perl, I need to extract DNA bases from a GenBank file for a given plant species. A sample GenBank file is here... Nucleotide This is saved on my computer as NC_001666.gb. I also have a file that is saved on my computer as NC_001666.txt. This text file has a list of all... (5 Replies)
Discussion started by: akreibich07
5 Replies

4. Shell Programming and Scripting

Tricky task with DNA sequences.

I am trying to reverse and complement my DNA sequences. The file format is FASTA, something like this: Now, to reverse the sequence, I should start reading from right to left. At the same should be complemented. Thus, "A" should be read as "T"; "C" should be read as "G"; "T" should be converted... (8 Replies)
Discussion started by: Xterra
8 Replies

5. Shell Programming and Scripting

find common entries and match the number with long sequence and cut that sequence in output

Hi all, I have a file like this ID 3BP5L_HUMAN Reviewed; 393 AA. AC Q7L8J4; Q96FI5; Q9BQH8; Q9C0E3; DT 05-FEB-2008, integrated into UniProtKB/Swiss-Prot. DT 05-JUL-2004, sequence version 1. DT 05-SEP-2012, entry version 71. FT COILED 59 140 ... (1 Reply)
Discussion started by: manigrover
1 Replies

6. Shell Programming and Scripting

How to convert multiple number ranges into sequence?

Looking for a simple way to convert ranges to a numerical sequence that would assign the original value of the range to the individual numbers that are on the range. Thank you given data 13196-13199 0 13200 4 13201 10 13202-13207 3 13208-13210 7 desired... (3 Replies)
Discussion started by: jcue25
3 Replies

7. Shell Programming and Scripting

Sequence generator

Thanks Guys This really helped (5 Replies)
Discussion started by: robert89
5 Replies

8. Shell Programming and Scripting

Shell script for changing the accession number of DNA sequences in a FASTA file

Hi, I am having a file of dna sequences in fasta format which look like this: >admin_1_45 atatagcaga >admin_1_46 atatagcagaatatatat with many such thousands of sequences in a single file. I want to the replace the accession Id "admin_1_45" similarly in following sequences to... (5 Replies)
Discussion started by: margarita
5 Replies

9. Red Hat

Rm -rf * sequence

If I run rm -rf * command under one parent directory. /data > rm -rf * Is there anyway to know which files will be deleted first ? Start using code tags please, ty. (2 Replies)
Discussion started by: sameermohite
2 Replies
SED(1)								   User Commands							    SED(1)

NAME
sed - stream editor for filtering and transforming text SYNOPSIS
sed [OPTION]... {script-only-if-no-other-script} [input-file]... DESCRIPTION
Sed is a stream editor. A stream editor is used to perform basic text transformations on an input stream (a file or input from a pipe- line). While in some ways similar to an editor which permits scripted edits (such as ed), sed works by making only one pass over the input(s), and is consequently more efficient. But it is sed's ability to filter text in a pipeline which particularly distinguishes it from other types of editors. -n, --quiet, --silent suppress automatic printing of pattern space -e script, --expression=script add the script to the commands to be executed -f script-file, --file=script-file add the contents of script-file to the commands to be executed --follow-symlinks follow symlinks when processing in place -i[SUFFIX], --in-place[=SUFFIX] edit files in place (makes backup if extension supplied) -l N, --line-length=N specify the desired line-wrap length for the `l' command --posix disable all GNU extensions. -r, --regexp-extended use extended regular expressions in the script. -s, --separate consider files as separate rather than as a single continuous long stream. -u, --unbuffered load minimal amounts of data from the input files and flush the output buffers more often --help display this help and exit --version output version information and exit If no -e, --expression, -f, or --file option is given, then the first non-option argument is taken as the sed script to interpret. All remaining arguments are names of input files; if no input files are specified, then the standard input is read. GNU sed home page: <http://www.gnu.org/software/sed/>. General help using GNU software: <http://www.gnu.org/gethelp/>. E-mail bug reports to: <bug-gnu-utils@gnu.org>. Be sure to include the word ``sed'' somewhere in the ``Subject:'' field. COMMAND SYNOPSIS
This is just a brief synopsis of sed commands to serve as a reminder to those who already know sed; other documentation (such as the tex- info document) must be consulted for fuller descriptions. Zero-address ``commands'' : label Label for b and t commands. #comment The comment extends until the next newline (or the end of a -e script fragment). } The closing bracket of a { } block. Zero- or One- address commands = Print the current line number. a text Append text, which has each embedded newline preceded by a backslash. i text Insert text, which has each embedded newline preceded by a backslash. q [exit-code] Immediately quit the sed script without processing any more input, except that if auto-print is not disabled the current pattern space will be printed. The exit code argument is a GNU extension. Q [exit-code] Immediately quit the sed script without processing any more input. This is a GNU extension. r filename Append text read from filename. R filename Append a line read from filename. Each invocation of the command reads a line from the file. This is a GNU extension. Commands which accept address ranges { Begin a block of commands (end with a }). b label Branch to label; if label is omitted, branch to end of script. c text Replace the selected lines with text, which has each embedded newline preceded by a backslash. d Delete pattern space. Start next cycle. D Delete up to the first embedded newline in the pattern space. Start next cycle, but skip reading from the input if there is still data in the pattern space. h H Copy/append pattern space to hold space. g G Copy/append hold space to pattern space. l List out the current line in a ``visually unambiguous'' form. l width List out the current line in a ``visually unambiguous'' form, breaking it at width characters. This is a GNU extension. n N Read/append the next line of input into the pattern space. p Print the current pattern space. P Print up to the first embedded newline of the current pattern space. s/regexp/replacement/ Attempt to match regexp against the pattern space. If successful, replace that portion matched with replacement. The replacement may contain the special character & to refer to that portion of the pattern space which matched, and the special escapes 1 through 9 to refer to the corresponding matching sub-expressions in the regexp. t label If a s/// has done a successful substitution since the last input line was read and since the last t or T command, then branch to label; if label is omitted, branch to end of script. T label If no s/// has done a successful substitution since the last input line was read and since the last t or T command, then branch to label; if label is omitted, branch to end of script. This is a GNU extension. w filename Write the current pattern space to filename. W filename Write the first line of the current pattern space to filename. This is a GNU extension. x Exchange the contents of the hold and pattern spaces. y/source/dest/ Transliterate the characters in the pattern space which appear in source to the corresponding character in dest. Addresses Sed commands can be given with no addresses, in which case the command will be executed for all input lines; with one address, in which case the command will only be executed for input lines which match that address; or with two addresses, in which case the command will be executed for all input lines which match the inclusive range of lines starting from the first address and continuing to the second address. Three things to note about address ranges: the syntax is addr1,addr2 (i.e., the addresses are separated by a comma); the line which addr1 matched will always be accepted, even if addr2 selects an earlier line; and if addr2 is a regexp, it will not be tested against the line that addr1 matched. After the address (or address-range), and before the command, a ! may be inserted, which specifies that the command shall only be executed if the address (or address-range) does not match. The following address types are supported: number Match only the specified line number. first~step Match every step'th line starting with line first. For example, ``sed -n 1~2p'' will print all the odd-numbered lines in the input stream, and the address 2~5 will match every fifth line, starting with the second. first can be zero; in this case, sed operates as if it were equal to step. (This is an extension.) $ Match the last line. /regexp/ Match lines matching the regular expression regexp. cregexpc Match lines matching the regular expression regexp. The c may be any character. GNU sed also supports some special 2-address forms: 0,addr2 Start out in "matched first address" state, until addr2 is found. This is similar to 1,addr2, except that if addr2 matches the very first line of input the 0,addr2 form will be at the end of its range, whereas the 1,addr2 form will still be at the beginning of its range. This works only when addr2 is a regular expression. addr1,+N Will match addr1 and the N lines following addr1. addr1,~N Will match addr1 and the lines following addr1 until the next line whose input line number is a multiple of N. REGULAR EXPRESSIONS
POSIX.2 BREs should be supported, but they aren't completely because of performance problems. The sequence in a regular expression matches the newline character, and similarly for a, , and other sequences. BUGS
E-mail bug reports to bonzini@gnu.org. Be sure to include the word ``sed'' somewhere in the ``Subject:'' field. Also, please include the output of ``sed --version'' in the body of your report if at all possible. COPYRIGHT
Copyright (C) 2009 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICU- LAR PURPOSE, to the extent permitted by law. GNU sed home page: <http://www.gnu.org/software/sed/>. General help using GNU software: <http://www.gnu.org/gethelp/>. E-mail bug reports to: <bug-gnu-utils@gnu.org>. Be sure to include the word ``sed'' somewhere in the ``Subject:'' field. SEE ALSO
awk(1), ed(1), grep(1), tr(1), perlre(1), sed.info, any of various books on sed, the sed FAQ (http://sed.sf.net/grabbag/tutorials/sed- faq.txt), http://sed.sf.net/grabbag/. The full documentation for sed is maintained as a Texinfo manual. If the info and sed programs are properly installed at your site, the command info sed should give you access to the complete manual. sed 4.2.1 December 2010 SED(1)
All times are GMT -4. The time now is 02:08 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy