Crate fasten_convert

Convert between different sequence formats

Examples

Simple conversion

cat file.fastq | fasten_convert -i fastq -o fasta > out.fasta

Convert to sam and then to bam

cat file.fastq | fasten_convert -i fastq -o sam   | samtools view -bS > file.bam

Convert to fastq and then clean

cat file.fasta | fasten_convert -i fasta -o fastq | fasten_clean > cleaned.fastq

Usage

Usage: fasten_convert [-h] [-n INT] [-p] [-v] [-i FORMAT] [-o FORMAT]

Options:
    -h, --help          Print this help menu.
    -n, --numcpus INT   Number of CPUs (default: 1)
    -p, --paired-end    The input reads are interleaved paired-end
    -v, --verbose       Print more status messages
    -i, --in-format FORMAT
                        The input format for stdin
    -o, --out-format FORMAT
                        The output format for stdin
  FORMAT can be: fastq, fasta, sam

Structs

FastenSeq

Struct that can handle paired end reads

Functions

main

read_fasta

Read fasta from stdin and transmit it to a channel

read_fastq

Read fastq from stdin and transmit it to a channel

read_sam

Read sam from stdin and transmit it to a channel

write_fasta

Read from a channel and print as fasta

write_fastq

Read from a channel and print as fastq

write_sam

Read from a channel and print as sam