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Repair canonical_transcripts #156

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Repair canonical_transcripts #156

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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
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10 changes: 5 additions & 5 deletions gffutils/helpers.py
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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)


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