Crate fasten

Perform random operations on fastq files, using unix streaming. Secure your analysis with Fasten!

Synopsis

read metrics

 
$ cat testdata/R1.fastq testdata/R2.fastq | \
    fasten_shuffle | fasten_metrics | column -t
totalLength  numReads  avgReadLength  avgQual
800          8         100            19.53875

read cleaning

$ cat testdata/R1.fastq testdata/R2.fastq | \
    fasten_shuffle | \
    fasten_clean --paired-end --min-length 2 | \
    gzip -c > cleaned.shuffled.fastq.gz
 
$ zcat cleaned.shuffled.fastq.gz | fasten_metrics | column -t
totalLength  numReads  avgReadLength  avgQual
800          8         100            19.53875

NOTE: No reads were actually filtered with cleaning, with –min-length=2

Kmer counting

$ cat testdata/R1.fastq | \
  fasten_kmer -k 21 > 21mers.tsv

Read sampling

$ cat testdata/R1.fastq testdata/R2.fastq | \
    fasten_shuffle | \
    fasten_sample --paired-end --frequency 0.1 > 10percent.fastq

Advanced

Set of downsampled reads

Create a set of downsampled reads for a titration experiment and clean them

for frequency in 0.1 0.2 0.3 0.4 0.5; do
  cat testdata/R1.fastq testdata/R2.fastq | \
    fasten_shuffle | \
    fasten_clean --paired-end --min-length 50 --min-trim-quality 25
    fasten_sample --paired-end --frequency $frequency > cleaned.$frequency.fastq
done

Validate a whole directory of fastq reads

\ls *_1.fastq.gz | xargs -n 1 -P 4 bash -c '
  echo -n "." >&2 # progress bar
  R1=$0
  R2=${0/_1.fastq.gz/_2.fastq.gz}
  zcat $R1 $R2 | fasten_shuffle | fasten_validate --paired-end
'

Modules

io

input/output methods

Macros

print

Rewrite print!() so that it doesn’t panic on broken pipe.

Functions

eexit

Propagate an error by printing invalid read(s)

fasten_base_options

a function that reads an options object and adds fasten default options.

fasten_base_options_matches

a function that processes the options on the command line The brief is a str that describes the program without using the program name, e.g., “counts kmers” for fasten_kmer. This function also takes care of –version. If –help is invoked, then the program name, the brief, and the usage() are all printed to stdout and then the program exits with 0.

logmsg

Print a formatted message to stderr

reverse_complement

Reverse complement a DNA sequence. Take into account lowercase vs uppercase. Ambiguity codes are also handled.