Commit fca6609a authored by Penom Nom's avatar Penom Nom
Browse files

Add comments.

parent ca7f74b7
......@@ -21,14 +21,16 @@ from weaver.abstraction import Map
from weaver.function import PythonFunction
from jflow.component import Component
from jflow.iotypes import OutputFileList, Formats
from jflow.iotypes import InputFileList, OutputFileList, Formats
def trim(input_file, output_file, start, end):
"""
@param input_file : path
@param output_file : path
@param start : index of the first nucleotide kept after trim (1 to N with included boundary)
@param end : index of the last nucleotide kept after trim (1 to N with included boundary)
Trim all sequences by start and end position.
@param input_file : [string] path
@param output_file : [string] path
@param start : [int] index of the first nucleotide kept after trim (1 to N with included boundary)
@param end : [int] index of the last nucleotide kept after trim (1 to N with included boundary)
"""
import jflow.seqio as seqio
reader = seqio.SequenceReader(input_file)
......@@ -57,15 +59,18 @@ def trim(input_file, output_file, start, end):
class Trimmer (Component):
"""
@summary : Trim all sequences by start and end position.
"""
def define_parameters(self, input_files, start=1, end=None):
"""
@param input_files : list of path
@param start : index of the first nucleotide kept after trim (1 to N with included boundary)
@param end : index of the last nucleotide kept after trim (1 to N with included boundary)
@param input_files : [list] list of path
@param start : [int] index of the first nucleotide kept after trim (1 to N with included boundary)
@param end : [int] index of the last nucleotide kept after trim (1 to N with included boundary)
"""
self.input_files = input_files
self.output_files = OutputFileList(self.get_outputs('{basename}', self.input_files))
self.input_files = InputFileList( input_files )
self.output_files = OutputFileList( self.get_outputs('{basename}', self.input_files) )
self.start = start
self.end = end
......
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