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