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Use bases for gaps for internal nodes after fastml #70

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Mar 15, 2013
Merged

Use bases for gaps for internal nodes after fastml #70

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7456f54
data file for tests
andrewjpage Mar 15, 2013
8d4d413
use base from gaps for internal nodes
andrewjpage Mar 15, 2013
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12 changes: 9 additions & 3 deletions run_gubbins.py
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Original file line number Diff line number Diff line change
Expand Up @@ -324,19 +324,25 @@ def reinsert_gaps_into_fasta_file(input_fasta_filename, input_vcf_file, output_f

sample_names = []
gap_position = []
gap_alt_base = []

for vcf_line in vcf_file:
if re.match('^#CHROM', vcf_line) != None :
sample_names = vcf_line.split('\t' )[9:-1]
elif re.match('^\d', vcf_line) != None :
# If the alternate is only a gap it wont have a base in this column
if re.match('^([^\t]+\t){4}([^ACGTacgt])\t', vcf_line) != None:
if re.match('^([^\t]+\t){3}([ACGTacgt])\t([^ACGTacgt])\t', vcf_line) != None:
m = re.match('^([^\t]+\t){3}([ACGTacgt])\t([^ACGTacgt])\t', vcf_line)
gap_position.append(1)
gap_alt_base.append(m.group(2))
elif re.match('^([^\t]+\t){3}([^ACGTacgt])\t([ACGTacgt])\t', vcf_line) != None:
# sometimes the ref can be a gap only
m = re.match('^([^\t]+\t){3}([^ACGTacgt])\t([ACGTacgt])\t', vcf_line)
gap_position.append(1)
gap_alt_base.append(m.group(3))
else:
gap_position.append(0)
gap_alt_base.append('-')

gapped_alignments = []
# interleave gap only and snp bases
Expand All @@ -350,14 +356,14 @@ def reinsert_gaps_into_fasta_file(input_fasta_filename, input_vcf_file, output_f
gap_index = 0
for input_base in record.seq:
while gap_index < len(gap_position) and gap_position[gap_index] == 1:
inserted_gaps.append('-')
inserted_gaps.append(gap_alt_base[gap_index])
gap_index+=1
if gap_index < len(gap_position):
inserted_gaps.append(input_base)
gap_index+=1

while gap_index < len(gap_position):
inserted_gaps.append('-')
inserted_gaps.append(gap_alt_base[gap_index])
gap_index+=1

record.seq = Seq(''.join(inserted_gaps))
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6 changes: 6 additions & 0 deletions tests/data/alignment_with_gap_in_parent.aln
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Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
>child_1
AC--
>child2
ACNA
>parent
----