Skip to content

Repair canonical_transcripts #156

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
EFraim wants to merge 5 commits into
base: v0.11
Choose a base branch
from
Open

Repair canonical_transcripts #156

Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
62bc4ed
gffutils.feature expects Sequence objects from pyfaidx, not raw strings
Mar 2, 2020
ba2995f
Only take CDS length into account when it exists (otherwise uncompara…
Mar 2, 2020
87fa72a
key argument name must be explicitly specified in Python3.6+
Mar 2, 2020
5c78d2d
Use only CDS exons if CDS exists and don't assume sorting. Tested aga…
Mar 2, 2020
91fc6be
Merge branch 'github-actions' into efraim-master
daler Jan 25, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 5 additions & 5 deletions gffutils/helpers.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -434,7 +434,7 @@ def to_unicode(obj, encoding='utf-8'):

def canonical_transcripts(db, fasta_filename):
import pyfaidx
fasta = pyfaidx.Fasta(fasta_filename, as_raw=True)
fasta = pyfaidx.Fasta(fasta_filename, as_raw=False)
for gene in db.features_of_type('gene'):

# exons_list will contain (CDS_length, total_length, transcript, [exons]) tuples.
Expand All @@ -449,20 +449,20 @@ def canonical_transcripts(db, fasta_filename):
cds_len += exon_length
total_len += exon_length

exon_list.append((cds_len, total_len, transcript, exons))
exon_list.append((cds_len, total_len, transcript, exons if cds_len == 0 else [e for e in exons if e.featuretype in ['CDS', 'five_prime_UTR', 'three_prime_UTR']] ))

# If we have CDS, then use the longest coding transcript
if max(i[0] for i in exon_list) > 0:
best = sorted(exon_list)[0]
best = sorted(exon_list, key=lambda x: x[0], reverse=True)[0]
# Otherwise, just choose the longest
else:
best = sorted(exon_list, lambda x: x[1])[0]
best = sorted(exon_list, key=lambda x: x[1])[0]

print(best)

canonical_exons = best[-1]
transcript = best[-2]
seqs = [i.sequence(fasta) for i in canonical_exons]
seqs = [i.sequence(fasta) for i in sorted(canonical_exons, key=lambda x: x.start, reverse=transcript.strand != '+')]
yield transcript, ''.join(seqs)


Expand Down