Chapter 1: Python Code for An introduction to basic Ruffus syntax

See also

• Manual Table of Contents
• @transform syntax in detail
• Back to Chapter 1: An introduction to basic Ruffus syntax

Your first Ruffus script

::

#
#   The starting data files would normally exist beforehand!
#       We create some empty files for this example
#
starting_files = ["a.fasta", "b.fasta", "c.fasta"]

for ff in starting_files:
    open(ff, "w")


from ruffus import *

#
#   STAGE 1 fasta->sam
#
@transform(starting_files,                     # Input = starting files
            suffix(".fasta"),                  #         suffix = .fasta
            ".sam")                            # Output  suffix = .sam
def map_dna_sequence(input_file,
                    output_file):
    ii = open(input_file)
    oo = open(output_file, "w")

#
#   STAGE 2 sam->bam
#
@transform(map_dna_sequence,                   # Input = previous stage
            suffix(".sam"),                    #         suffix = .sam
            ".bam")                            # Output  suffix = .bam
def compress_sam_file(input_file,
                      output_file):
    ii = open(input_file)
    oo = open(output_file, "w")

#
#   STAGE 3 bam->statistics
#
@transform(compress_sam_file,                  # Input = previous stage
            suffix(".bam"),                    #         suffix = .bam
            ".statistics",                     # Output  suffix = .statistics
            "use_linear_model")                # Extra statistics parameter
def summarise_bam_file(input_file,
                       output_file,
                       extra_stats_parameter):
    """
    Sketch of real analysis function
    """
    ii = open(input_file)
    oo = open(output_file, "w")

pipeline_run()

Resulting Output

>>> pipeline_run()
    Job  = [a.fasta -> a.sam] completed
    Job  = [b.fasta -> b.sam] completed
    Job  = [c.fasta -> c.sam] completed
Completed Task = map_dna_sequence
    Job  = [a.sam -> a.bam] completed
    Job  = [b.sam -> b.bam] completed
    Job  = [c.sam -> c.bam] completed
Completed Task = compress_sam_file
    Job  = [a.bam -> a.statistics, use_linear_model] completed
    Job  = [b.bam -> b.statistics, use_linear_model] completed
    Job  = [c.bam -> c.statistics, use_linear_model] completed
Completed Task = summarise_bam_file