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blt fastx2tsv(1) General Commands Manual blt fastx2tsv(1) NAME blt fastx2tsv - Convert FASTA and FASTQ streams to TSV format SYNOPSIS blt fastx2tsv < file.fastq > file.tsv blt fastx2tsv < file.fasta > file.tsv DESCRIPTION blt fastx2tsv converts a FASTA or FASTQ stream, possibly containing wrapped sequences and phred scores, into tab-separated data (TSV) for easier pro- cessing using standard tools such as awk, cut, etc. The TSV output of pro- cessing can be converted back to FASTA or FASTQ format using awk as fol- lows: awk -F '\t' '{ printf("%s\n%s\n", $1, $2); }' \ file.tsv > file.fasta awk -F '\t' '{ printf("%s\n%s\n%s\n%s\n", $1, $2, $3, $4); }' \ file.tsv > file.fastq EXAMPLES # Filter a FASTA file for sequences containing a pattern blt fastx2tsv < file.fasta | \ awk -F '\t' '$2 ~ "ATTACGTAAC" { printf("%s\n%s\n", $1, $2); }' \ > filtered.fasta SEE ALSO blt-fastx-derep(1), blt-fastq-derep.sh(1) AUTHOR J. Bacon blt fastx2tsv(1)
NAME | SYNOPSIS | DESCRIPTION | EXAMPLES | SEE ALSO | AUTHOR
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