Last active
August 29, 2015 14:16
-
-
Save kallam/6594cd58faef0cdd1f84 to your computer and use it in GitHub Desktop.
Parse fasta file
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| sequences = [] | |
| sequence = {} | |
| text = "" | |
| f = open("in.txt", "r") | |
| for line in f: | |
| if line[0] == '>': | |
| if text != "": | |
| sequence["text"] = text | |
| sequences.append(sequence) | |
| sequence = {} | |
| text = "" | |
| sequence["meta"] = line[1:-1] | |
| elif line == "\n": | |
| if text != "": | |
| sequence["text"] = text | |
| sequences.append(sequence) | |
| sequence = {} | |
| text = "" | |
| else: | |
| text = text + line[:-1] | |
| f.close() | |
| # GBA, strain, name, na, date, host, country = sequence["meta"].split("|") |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment