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Godwin Ani 2024-01-12 11:07:31 -05:00 committed by GitHub
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Utilities/for_taxonomy/Query_SRA_egs.py
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'''
Modified by Elinor 2/13 to grab recent assemblies (since 2020) and GCA codes. Input is folder 'unique_taxon_lists' with files
of keywords by major clade (separated by new lines). Put -t (transcriptome, SRA db) or -g (genome, assembly db) in the command
line to specify data type
restrictions:
All data is since 2020
SRA excludes entries with 'Amplicon' in the description, and outputs the experiment and sequencing technology.
example command line: python Query_SRA_egs.py -t
Output: file of species, IDs, and GCA or SRR codes AND a file with uniquified codes. Updated 3.21.23 to output sequencing machine and type of experiment from SRA
#Author, date: Elinor Sterner, Feb 2023
#Intent: To grab recent assemblies (since 2020) and GCA codes.
#Dependencies: Python3, Biopython
#Inputs: Folder named 'unique_taxon_lists' with files of keywords by major clade (separated by new lines).
#Outputs: File of species, IDs, and GCA or SRR codes AND a file with uniquified codes.
#Example: python Query_SRA_egs.py -t (transcriptome, SRA db) or -g (genome, assembly db)
'''
from Bio import Entrez