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Is it possible to do something on Emacs where I put in the file I want to run (perl process_genbank.pl) and then after it put in the specific NC_ file that I want it run on (almost as a command-line)...
Sorry, I have never used Emacs.
In vim, however, if you type this:
at the editor prompt ":", then it will execute the shell_command and paste the output in your vim file at the cursor position.
You may want to check the Emacs documentation for the equivalent set of keystrokes.
Quote:
...
(2) If I needed at some point in time the output to be more specific, so each line after genes: said something like
If you look on that NCBI file, the left margin has gene for each new gene and then under it says either CDS if it's coding a protein, or tRNA, or I believe there might be a few rRNA's in other files, and then has each exon and intron for that particular gene before going onto the next gene. Is it possible to have that output like I said above (one gene per line, just double spaces in between things like the gene name, the CDS/tRNA/rRNA, etc)?
...
This is with references to "sequences.gb" from ""http://www.ncbi.nlm.nih.gov/nuccore/NC_010093"
(1) The gene name was picked from the line right below / gene / e.g. for this excerpt:
The name in bold red was picked for gene name; the name in bold blue was *NOT*.
(2) In cases where none of CDS, tRNA or rRNA was found for a gene, the value "DEFAULT" is being displayed e.g. for this excerpt:
you'd see "DEFAULT" as the gene type. You can set it to NULL or something else.
The updated script is as follows:
And the execution on the "sequences.gb" mentioned above is as follows:
Hope that helps,
tyler_durden
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"And the eighth and final rule: if this is your first time at Fight Club, you have to fight."
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