Answered step by step
Verified Expert Solution
Link Copied!

Question

1 Approved Answer

Problem Statement The GFF3 format is a commonly-used one in bioinformatics for representing sequence annotation. You can find the specification here: The genome and annotation

image text in transcribed
Problem Statement The GFF3 format is a commonly-used one in bioinformatics for representing sequence annotation. You can find the specification here: The genome and annotation for Saccharomyces cerevisiae S288C is on the class server here: /home/jorvisl/Saccharomyces_cerevisiae_5288C.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 --tvpe=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 which matches their query, like this: rgene:ID:YARODIW o 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 which are present in the file and 1 where you intentionally enter a feature NOT present in the file. Your script should handle this gracefully

Step by Step Solution

There are 3 Steps involved in it

Step: 1

blur-text-image

Get Instant Access to Expert-Tailored Solutions

See step-by-step solutions with expert insights and AI powered tools for academic success

Step: 2

blur-text-image

Step: 3

blur-text-image

Ace Your Homework with AI

Get the answers you need in no time with our AI-driven, step-by-step assistance

Get Started

Recommended Textbook for

Mathematics for Economics and Business

Authors: Ian Jacques

9th edition

129219166X, 9781292191706 , 978-1292191669

More Books

Students also viewed these Mathematics questions

Question

Discuss the role of data analytics in future supply chains

Answered: 1 week ago