Question 1:

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 which matches their query, like this:

>gene:ID:YAR003W
.... sequence here ...

Some bonus points will be awarded if you 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.

QUESTION 2:

Write a program that will open a BLASTN (nucleotide to nucleotide search) output file, parse out specific information, and produce formatted output that will be written to STDOUT (i.e. Standard Output; the terminal window / command line). Before writing your program, copy the BLASTP output file, /home/jorvis1/example_blast.txt to your home directory. Look through the file and explore the format.

Your program should start by opening the input file (you may hardcode the filename in this case), parsing and storing both the query sequence ID (from near the top of the file; look for the string following "Query=") and the query length (found on the line below the query sequence), and displaying them both to STDOUT. Add some additional characters and formatting to your output such that these two fields appear exactly like this in STDOUT:

Then, it is time to parse information about the significant alignments for this query. Each alignment begins with the ">" symbol. For just the first ten hits, parse out only the accession (located between the first set of pipe symbols, | | ), length and score. For each of these hits, these three fields should then be written to STDOUT in exactly this format including capitalization, spacing, and punctuation (as shown here using the real values for the first hit; study the file to understand exactly where these values came from):

Alignment #1: Accession = ref|XM_005094338.1| (Length = 2377, Score = 1098)

You must use regular expressions to pull out precisely the parts of the file that you want, which is the definition of parsing. Hint: you will very likely need to use parentheses to put some parts of those expressions into temporary memory (m.group(1), etc.) for later use.

Do not have your regular expression search for hardcoded values; your program should be able to read another BLASTN output file and run successfully, not just this specific one.

Pay careful attention to the exact appearance of the sample output, above. Although it is a good start to be able to, at a minimum, report the requested values, your program must also strive to match the formats specified.

Provide the complete source code AND the output of the program as it runs.