• Please provide both python source code AND sample output to receive full credit.
• Program must run with Python 3 and start with:
#!/usr/bin/env python3
• Please clean up any unused code and files – commented-out print statements are fine but remove anything else unused to keep your code easy to read.
• Avoid hardcoding values or filenames (except where the questions allow it).
• You should check expected input from the user to make sure it is valid.
• Code must be able to run on our class server
PLEASE READ THE TEXT OF THIS PROJECT COMPLETELY (RIGHT NOW) AND CONTACT ME ASAP IF YOU HAVE ANY QUESTIONS!!
The GFF3 format is a commonly-used one in bioinformatics for representing sequence annotation. You can find the specification here:
http://www.sequenceontology.org/gff3.shtml
The genome and annotation for Saccharomyces cerevisiae S288C are on the class server here:
/home/jorvis1/Saccharomyces_cerevisiae_S288C.annotation.gff
Note that this same file has both the annotation feature table and the FASTA sequence for the molecules referenced. (See the '##FASTA' directive in the specification.)
Within the feature table another column of note is the 9 th , where we can store any key=value pairs relevant to that row's feature such as ID, Ontology_term or Note.
Your task is to write a GFF3 feature exporter. A user should be able to run your script like this:
$ export_gff3_feature.py --source_gff=/path/to/some.gff3 --type=gene --attribute=ID --value=YAR003W
There are 4 arguments here that correspond to values in the GFF3 columns. In this case, your script should read the path to a GFF3 file, find any gene (column 3) which has an ID=YAR003W (column 9). When it finds this, it should use the coordinates for that feature (columns 4, 5 and 7) and the FASTA sequence at the end of the document to return its FASTA sequence.
Your script should work regardless of the parameter values passed, warning the user if no features were found that matched their query. (It should also check and warn if more than one feature matches the query.)
The output should just be printed on STDOUT (no writing to a file is necessary.) It should have a header that matches their query, like this:
>gene:ID:YAR003W
.... sequence here ...
As an extra challenge, you can format the sequence portion of the FASTA output as 60-characters per line, which follows the standard.
Provide the complete source code AND the output of the program as it runs. You should do test runs with 3 features that are present in the file and 1 where you intentionally enter a feature NOT present in the file. Your script should handle this gracefully.
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