FastQ input/output commands for the App::RecordStream (recs) system
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README.md
recs-fromfastq
recs-tofastq

README.md

FastQ input and output commands for recs

fromfastq

usage: recs-fromfastq [-h] [-Q] [--fk FIELD] [input.fastq [input.fastq ...]]

Each sequence in the FastQ input files (or stdin) produces an
output record with the keys name, sequence, and quality.

This command is part of the App::RecordStream (recs) system.
See https://recs.pl for more information.

positional arguments:
  input.fastq           FastQ input files (default: None)

optional arguments:
  -h, --help            show this help message and exit
  -Q, --decode-quality  Decode Phred+33 quality string into integer scores
                        (default: False)
  --fk FIELD, --filename-key FIELD
                        Add a key FIELD set to the source filename (if no
                        filename is applicable will put NONE) (default: None)

tofastq

usage: recs-tofastq [-h] [-Q] [file [file ...]]

Outputs a FastQ sequence for each record using the fields name,
sequence, and quality.  These match the fields produced by
fromfastq.

This command is part of the App::RecordStream (recs) system.
See https://recs.pl for more information.

positional arguments:
  file                  record stream input files (default: None)

optional arguments:
  -h, --help            show this help message and exit
  -Q, --encode-quality  Encode a Phred+33 quality string from integer scores
                        in the quality field (default: False)

What's recs?

"A set of programs for creating, manipulating, and outputing a stream of Records, or JSON hashes."

For other bioinformatics-related recs commands, see App::RecordStream::Bio.

Installation

recs-fastq requires Python 2.7 and BioPython. You can install BioPython by running pip install biopython.

Install fromfastq and tofastq into /usr/local/bin with:

make install

or $HOME/bin with:

make install prefix=$HOME

Uninstall using:

make uninstall