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.. include:: ../../global.inc
.. include:: manual_chapter_numbers.inc
.. _new_manual.introduction.code:
##############################################################################################################
|new_manual.introduction.chapter_num|: Python Code for An introduction to basic Ruffus syntax
##############################################################################################################
.. seealso::
* :ref:`Manual Table of Contents <new_manual.table_of_contents>`
* :ref:`@transform syntax in detail <decorators.transform>`
* Back to |new_manual.introduction.chapter_num|: :ref:`An introduction to basic Ruffus syntax <new_manual.introduction>`
*******************************************
Your first Ruffus script
*******************************************
.. code-block:: python
::
#
# 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
|
