Download GFF files of the 120 UHGG C. scindens genomes

[breister2]

In order to download the GFF files using the ftp links provided, curl was used.

After obtaining the GFF files, they were converted to fasta files using the script /storage1/data19/Scripts/python_scripts/Convert_GFF_to_Fasta.py

import sys

input_gff_file = sys.argv[1]
output_fasta_file = input_gff_file.replace(".gff", ".fasta")
test = False

with open(input_gff_file, "r") as input, open(output_fasta_file, "w") as output:
    for line in input:
        if "##FASTA" not in line and test == False:
            continue
        elif "##FASTA" in line:
            test = True
            continue

        if test == True:
            output.write(line)

To confirm accuracy of the obtained fasta files, a custom python script was used to count the number of scaffolds and the number of nucleotides in the file.

[breister2]

The following genomes obtained from GFF files seemed to be incomplete when compared to the project metadata:

• MGYG000001303
• MGYG000091745
• MGYG000125324
• MGYG000225303