Answered step by step
Verified Expert Solution
Question
1 Approved Answer
Stage 1 (max score 80): Write a python script that accepts two parameters on the command line. These will be two sequence similarity survey files
Stage 1 (max score 80): Write a python script that accepts two parameters on the command line. These will be two sequence similarity survey files comparing proteins from two organisms Survey 1: Organism 1 vs organism 2 Survey 2: Organism 2 vs organism 1 The script should read both survey files. From each, remove similarities that have an eval>0.01. Among the remaining similarities, select the ones with the lowest evalue for each query sequence- these are the best hits for each query sequence. Compare the best hits from each survey and find similarities where best hits are reciprocal. In other words, find best hits where the same proteins are the query and subject in one survey, and the subject and query in the other. Print out the pair of ids for each reciprocal best hit, one pair to a line, with organism 1 ids first and organism 2 ids second Examples (example outputs on compile, long commands are line wrapped, note the redirected output) Example 1 (H. pylori and E. coli): s python orthologs.py h pylori_vs_e_coli.tsv e_coli_vs_h_pylori.tsv> Example 2 (H. pylori and H. influenzae): orthologs_h_pylori_and_e_coli_stagel.txt python orthologs.py h_pylori_vs_h_influenzae.tsv h_influenzae_vs_h_pylori.tsv orthologs_h_pylori_and_h_influenzae_stagel.txt
Step by Step Solution
There are 3 Steps involved in it
Step: 1
Get Instant Access to Expert-Tailored Solutions
See step-by-step solutions with expert insights and AI powered tools for academic success
Step: 2
Step: 3
Ace Your Homework with AI
Get the answers you need in no time with our AI-driven, step-by-step assistance
Get Started