ammaraziz
/ parseSNPs.py
Created
November 18, 2020 13:59
— forked from peterk87/parseSNPs.py
Python: Parse SNPs from one or more multiple sequence alignments in multifasta format and output a concatenated SNP fasta, a basic SNP report, and/or [binarized] SNP table.
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| import argparse | |
| import textwrap | |
| import os | |
| import sys | |
| from datetime import timedelta, datetime | |
| # function for reading a multifasta file | |
| # returns a dictionary with sequence headers and nucleotide sequences | |
| def get_seqs_from_fasta(filepath): |
ammaraziz
/ flumart.py
Created
July 5, 2022 06:17
— forked from gfairchild/flumart.py
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| """ | |
| This code pulls data from the WHO's influenza surveillance database: | |
| https://apps.who.int/flumart/Default?ReportNo=12 | |
| This website is pretty tricky to parse; you must pass realistic headers to the POST requests, and you must also | |
| issue 3 total requests: 1) a GET request, 2) a POST request, and 3) another POST request. All 3 of these requests, | |
| in order, are required to actually collect the underlying data that's displayed in the table. See `get_table_data` | |
| for more documentation on this process. |