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