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Fix/alignment length #59

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merged 3 commits into from
Mar 20, 2024
Merged

Fix/alignment length #59

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6a375f3
fix: inconsistent tabs/spaces
rneher Mar 20, 2024
8b4bd8c
fix: pick feature to insert in the same way the reference was extract…
rneher Mar 20, 2024
4cf1cd4
fix: derive insert length from inserted alignment, not the annotation
rneher Mar 20, 2024
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fix: derive insert length from inserted alignment, not the annotation
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@rneher
rneher committed Mar 20, 2024
commit 4cf1cd472087814dccc724aa6d4388b8a058394b
10 changes: 6 additions & 4 deletions scripts/align_for_tree.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
from Bio import SeqIO
from Bio import SeqIO, AlignIO
from Bio.SeqRecord import SeqRecord
import shutil
import argparse
Expand All @@ -8,10 +8,12 @@ def alignfortree(realign, align, reference, newoutput, build):
if build != "genome":
shutil.copy(realign, newoutput)
else:
realigned = {s.id:s for s in SeqIO.parse(realign, "fasta")}
realigned_aln = AlignIO.read(realign, 'fasta')
insert_length = realigned_aln.get_alignment_length()
realigned = {s.id:s for s in realigned_aln}
original = SeqIO.parse(align, "fasta")
ref = SeqIO.read(reference, "genbank")

for feature in ref.features:
if feature.type =='gene' or feature.type=='CDS':
a =str((list(feature.qualifiers.items())[0])[-1])[2:-2]
Expand All @@ -22,7 +24,7 @@ def alignfortree(realign, align, reference, newoutput, build):
for record_original in original:
sequence_to_insert = realigned.get(record_original.id, None)
if sequence_to_insert is None:
sequence_to_insert = '-' * (endofgene - startofgene)
sequence_to_insert = '-' * insert_length
else:
sequence_to_insert = sequence_to_insert.seq

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