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Top Forums Shell Programming and Scripting Convert a DNA sequence into Amino Acid Post 302957300 by faizlo on Thursday 8th of October 2015 06:50:02 PM
Old 10-08-2015
Here is what I did:
  • Created a file dna.sed
  • Created another bash script file with your code (starting with the usual #!)
  • Called the shell script "conversion.sh" and chmod it to excutable
  • ran it like this: ./conversion.sh < dna_input.dna
  • Got my result as expected for the test input file.
Thank you for your help.
How would one put this into a single script file?
 

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MARK(1)                                                              [nmh-1.5]                                                             MARK(1)

NAME
mark - manipulate message sequences SYNOPSIS
mark [+folder] [msgs] [-sequence name ...] [-add | -delete] [-list] [-public | -nopublic] [-zero | -nozero] [-version] [-help] DESCRIPTION
The mark command manipulates message sequences by adding or deleting message numbers from folder-specific message sequences, or by listing those sequences and messages. A message sequence is a keyword, just like one of the "reserved" message names, such as "first" or "next". Unlike the "reserved" message names, which have a fixed semantics on a per-folder basis, the semantics of a message sequence may be defined, modified, and removed by the user. Message sequences are folder-specific, e.g., the sequence name "seen" in the context of folder "+inbox" need not have any relation whatsoever to the sequence of the same name in a folder of a different name. Three action switches direct the operation of mark. These switches are mutually exclusive: the last occurrence of any of them overrides any previous occurrence of the other two. The -add switch tells mark to add messages to sequences or to create a new sequence. For each sequence named via the -sequence name argu- ment (which must occur at least once) the messages named via msgs (which defaults to "cur" if no msgs are given), are added to the sequence. The messages to be added need not be absent from the sequence. If the -zero switch is specified, the sequence will be emptied prior to adding the messages. Hence, -add -zero means that each sequence should be initialized to the indicated messages, while -add -nozero means that each sequence should be appended to by the indicated messages. The -delete switch tells mark to delete messages from sequences, and is the dual of -add. For each of the named sequences, the named mes- sages are removed from the sequence. These messages need not be already present in the sequence. If the -zero switch is specified, then all messages in the folder are added to the sequence (first creating the sequence, if necessary) before removing the messages. Hence, -delete -zero means that each sequence should contain all messages except those indicated, while -delete -nozero means that only the indi- cated messages should be removed from each sequence. As expected, the command "mark -sequence foo -delete all" deletes the sequence "foo" from the current folder. When creating or modifying sequences, you can specify the switches -public or -nopublic to force the new or modified sequences to be "pub- lic" or "private". The switch -public indicates that the sequences should be made "public". These sequences will then be readable by all nmh users with permission to read the relevant folders. In contrast, the -nopublic switch indicates that the sequences should be made "private", and will only be accessible by you. If neither of these switches is specified, then existing sequences will maintain their cur- rent status, and new sequences will default to "public" if you have write permission for the relevant folder. Check the mh-sequence(5) man page for more details about the difference between "public" and "private" sequences. The -list switch tells mark to list both the sequences defined for the folder and the messages associated with those sequences. Mark will list the name of each sequence given by -sequence name and the messages associated with that sequence. If the sequence is private, this will also be indicated. If no sequence is specified by the -sequence switch, then all sequences for this folder will be listed. The -zero switch does not affect the operation of -list. The current restrictions on sequences are: o The name used to denote a message sequence must consist of an alphabetic character followed by zero or more alphanumeric characters, and cannot be one of the (reserved) message names "new", "first", "last", "all", "next", or "prev". o Only a certain number of sequences may be defined for a given folder. This number is usually limited to 27 (11 on small systems). (The internal implementation relies on bitmasks, with some bits set aside for internal use.) o Message ranges with user-defined sequence names are restricted to the form "name:n", "name:+n", or "name:-n", and refer to the first or last `n' messages of the sequence `name', respectively. Constructs of the form "name1-name2" are forbidden for user defined sequences. FILES
$HOME/.mh_profile The user profile PROFILE COMPONENTS
Path: To determine the user's nmh directory Current-Folder: To find the default current folder SEE ALSO
flist(1), pick(1), mh-sequence(5) DEFAULTS
`+folder' defaults to the current folder `-add' if -sequence is specified, -list otherwise `msgs' defaults to cur (or all if -list is specified) `-nozero' CONTEXT
If a folder is given, it will become the current folder. HELPFUL HINTS
Use flist to find folders with a given sequence, and "pick sequence -list" to enumerate those messages in the sequence (such as for use by a shell script). MH.6.8 11 June 2012 MARK(1)
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