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jwaageSnippets/gist:4224188

Created December 6, 2012 12:40
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Convert bed with sequences to fasta
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gistfile1.sh
# substitute cut -f 20 with column containing sequence. Sed bit removes last line
cat file_with_sequences.bed | cut -f 20 | awk '{print; if (FNR % 1 == 0 ) printf ">" NR "\n";}' | sed -n '$!p' > sequences.fasta
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