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Fix formatting
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lauraluebbert committed May 25, 2024
1 parent ea509c8 commit f37c12d
Showing 1 changed file with 8 additions and 4 deletions.
12 changes: 8 additions & 4 deletions gget/gget_ref.py
Original file line number Diff line number Diff line change
Expand Up @@ -210,9 +210,13 @@ def ref(
if not grch37:
## Raise error if species not found (both FASTA and GTF have to be available)
# Find all available species for genome FASTAs for this Ensembl release
species_list_dna = ref_species_options("dna", database=database, release=ENS_rel)
species_list_dna = ref_species_options(
"dna", database=database, release=ENS_rel
)
# Find all available species for GTFs for this Ensembl release
species_list_gtf = ref_species_options("gtf", database=database, release=ENS_rel)
species_list_gtf = ref_species_options(
"gtf", database=database, release=ENS_rel
)
# Find intersection of the two lists
# (Only species which have GTF and FASTAs available can continue)
species_list = list(set(species_list_gtf) & set(species_list_dna))
Expand All @@ -237,9 +241,9 @@ def ref(
gtf_search_url = database + f"release-{ENS_rel}/gtf/{species}/"

if grch37:
link_substring="GRCh37.87.gtf.gz"
link_substring = "GRCh37.87.gtf.gz"
else:
link_substring=f"{ENS_rel}.gtf.gz"
link_substring = f"{ENS_rel}.gtf.gz"

# Get link, release date and dataset size
gtf_str, gtf_date, gtf_size = find_FTP_link(
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