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fastx_getseqs command
Commands > FASTA/Q files

See also
 
fastx_getseq

  fastx_getsubseq

Extract sequences from a FASTA or FASTQ file by matching sequence labels.

The -label option specifies a string to match the label.

The -labels option specifies the name of a text file. Each line of the text file contains a string to match the label.

The -label_word option specifies a word which must match the label. The match must be to a whole word.

The -label_words option specifies a text file. Each line of the text file contains a word to match the label.

Matches specified by -label and -labels are case-insensitive.

Matches specified by -label_word and -label_words are case-sensitive.

The -label_field option specifies the name of a name=xxx; style annotation in the label. Word matches by -label_word or -label_words is then performed on the xxx string, not the full label.

The -label_substr_match option specifies that matches to a string given by -label or -labels may be to a substring of the label. Otherwise the strings must be identical.

Sequence with labels that match are written to filenames given by -fastaout (FASTA) and/or -fastqout (FASTQ).

Sequences which do not match are written to filename given by -notmatched (FASTA) or -notmatchedfq (FASTQ).

Example

usearch -fastx_getseqs seqs.fa -labels labels.txt -fastaout subset.fa