convertΒΆ

$ micca convert --help
usage: micca convert [-h] -i FILE -o FILE [-q FILE] [-d DEFAULTQ]
                     [-f INPUT_FORMAT] [-F OUTPUT_FORMAT]

       micca convert converts between sequence file formats. See
       http://biopython.org/wiki/SeqIO#File_Formats for a comprehnsive list
       of the supported file formats.

       Supported input formats:
        * abi
* abi-trim
* ace
* embl
* embl-cds
* fasta
* fasta-qual
* fastq
* fastq-illumina
* fastq-sanger
* fastq-solexa
* gb
* genbank
* genbank-cds
* ig
* imgt
* pdb-atom
* pdb-seqres
* phd
* pir
* qual
* seqxml
* sff
* sff-trim
* swiss
* tab
* uniprot-xml

       Supported output formats:
        * embl
* fasta
* fastq
* fastq-illumina
* fastq-sanger
* fastq-solexa
* gb
* genbank
* imgt
* phd
* qual
* seqxml
* sff
* tab

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

arguments:
  -i FILE, --input FILE
                        input sequence file (required).
  -o FILE, --output FILE
                        output sequence file (required).
  -q FILE, --qual FILE  input quality file (required for 'fasta-qual' input
                        format.
  -d DEFAULTQ, --defaultq DEFAULTQ
                        default phred quality score for format-without-quality
                        to format-with-quality conversion (default 40).
  -f INPUT_FORMAT, --input-format INPUT_FORMAT
                        input file format (default fastq).
  -F OUTPUT_FORMAT, --output-format OUTPUT_FORMAT
                        input file format (default fasta).

Examples

Convert FASTA+QUAL files into a FASTQ (Sanger/Illumina 1.8+) file:

    micca convert -i input.fasta -q input.qual -o output.fastq \
    -f fasta-qual -F fastq

Convert a SFF file into a FASTQ (Sanger/Illumina 1.8+) file:

    micca convert -i input.sff -o output.fastq -f sff -F fastq