Difference between revisions of "Eyanosch Week 3"
(The backbone behind the first part of the individual week 3 assignment, credit to Brandon for helping with this. He mentioned creating the three bases with a space between each other and showed me where/how to get Dondi's file) |
(added a space to make the coding look even) |
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* Removing all the spaces in-between the Amino Acids | * Removing all the spaces in-between the Amino Acids | ||
| − | cat sequence_file | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/ //g" | sed"s/[actg]//g" | + | cat sequence_file | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/ //g" | sed"s/[actg]//g" |
*Removes any bases accidentally left | *Removes any bases accidentally left | ||
Revision as of 06:42, 22 September 2015
In order to produce the complementary strands nucleotide sequence
cat sequence_file | sed "y/atgc/tacg/"
this follows the rule of y/<original characters>/<new characters>/
If sequence_file contains
agcggtatac
the output would be:
tcgccatatg
Write 6 sets of text processing commands that, when given a nucleotide sequence, returns the resulting amino acid sequence, one for each possible reading frame for the nucleotide sequence.
Using Dondi's already available translated code we first need to translate the DNA into RNA, then make a way so that the code can read each trinucleotide sequence. If it reads the entire block of code then I won't be able to use the sed commands in Dr. Dondi's page.
cat sequence_file
- The file of nucleotide sequences
cat sequence_file | sed "s/t/u/g"
- This will convert the Nucleotide sequence from DNA to RNA
cat sequence_file | sed "s/t/u/g" | sed "s/.../& /g"
- This command repeats every 3 nucleotides and adds a space inbetween each codon
cat sequence_file | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed
- by taking the codes from ~dondi/xmlpipedb/data directory in a file called genetic-code.sed, 64 chain commands are already taken care of.
cat sequence_file | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/ //g"
- Removing all the spaces in-between the Amino Acids
cat sequence_file | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/ //g" | sed"s/[actg]//g"
- Removes any bases accidentally left
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Eyanosch Week 3
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