mergeΒΆ

$ micca merge --help
usage: micca merge [-h] -i FILE [FILE ...] -o FILE [-s SEP] [-f {fastq,fasta}]

micca merge merges several FASTQ or FASTA files in a single file.
Different samples will be merged in a single file and sample names
will be appended to the sequence identifier
(e.g. >SEQID;sample=SAMPLENAME). Sample names are defined as the
leftmost part of the file name splitted by the first occurence of '.'
(-s/--sep option). Whitespace characters in names will be replaced
with a single character underscore ('_').

optional arguments:
  -h, --help            show this help message and exit

arguments:
  -i FILE [FILE ...], --input FILE [FILE ...]
                        input FASTQ/FASTA file(s) (required).
  -o FILE, --output FILE
                        output FASTQ/FASTA file (required).
  -s SEP, --sep SEP     Sample names are defined as the leftmost part of the
                        file name splitted by the first occurence of 'SEP'
                        (default .)
  -f {fastq,fasta}, --format {fastq,fasta}
                        file format (default fastq).

Examples

Merge files in FASTA format:

    micca merge -i in1.fasta in2.fasta in3.fasta -o merged.fasta \
    -f fasta