ydeng/splitmsa
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Completed translation mechanism

Browse Source
This commit is contained in:
Harrison Deng 2023-03-28 15:56:50 -05:00
parent 03d87a670f
commit 0c5f188b80
2 changed files with 34641 additions and 4 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

11
msa_splitter.py
View File

@ -196,14 +196,17 @@ def trim(
) )
if perform_translation: if perform_translation:
aa_sequence = Seq(nt_sequence.replace("-", "n")).translate() aa_sequence = (
s_record.seq[tru_start + start_shift - 1 : end + end_shift]
.replace("-", "n")
.translate()
)
aa_sequence_records.append( aa_sequence_records.append(
SeqRecord.SeqRecord(aa_sequence, *record_metadata) SeqRecord.SeqRecord(aa_sequence, *record_metadata)
) )
if gen_cut_stop_codon: if gen_cut_stop_codon:
aa_no_stop_sequence = Seq( aa_no_stop_sequence = aa_sequence[:-1]
nt_no_stop_sequence.replace("-", "n")
).translate()
aa_no_stop_sequence_records.append( aa_no_stop_sequence_records.append(
SeqRecord.SeqRecord(aa_no_stop_sequence, *record_metadata) SeqRecord.SeqRecord(aa_no_stop_sequence, *record_metadata)
) )

34634
tests/resources/test_msa_transl.aln Normal file
View File

File diff suppressed because it is too large Load Diff