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when using vcf input, augur writes the file 'informative sites'

to the same directory in whcih the alignment is located. Improper
handling of the path resulted in augur trying to write to
'/informative_sites'. Fixed here using os.path.
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rneher committed Sep 9, 2019
1 parent 36d92a8 commit ffb929a51fca8c20046fc9ee0ecc088876089edc
Showing with 1 addition and 1 deletion.
  1. +1 −1 augur/tree.py
@@ -297,7 +297,7 @@ def write_out_informative_fasta(compress_seq, alignment, stripFile=None):
seqNamesCorr = list(reversed(seqNames))
toFasta = [ SeqRecord(id=seqNamesCorr[i], seq=Seq("".join(align[i])), description='') for i in range(len(sequences.keys()))]

fasta_file = '/'.join(alignment.split('/')[:-1]) + '/informative_sites.fasta'
fasta_file = os.path.join(os.path.dirname(alignment), 'informative_sites.fasta')

#now output this as fasta to read into raxml or iqtree
SeqIO.write(toFasta, fasta_file, 'fasta')

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