Commit b33a79db authored by Penom Nom's avatar Penom Nom
Browse files

Increase documentation.

parent 1b38b183
......@@ -31,8 +31,9 @@ import jflow.seqio as seqio
class Flash (Analysis):
def _get_length_table(self, input_file):
"""
@param input_file : the fastq file path
@return : [nb_seq, {size: nb, size:...}]
@param input_file : [str] the fastq file path
@return : [list] the number of sequences and the number of fragment by size.
Format : [nb_seq, {size_x: nb_fragment, size_j:...}]
"""
nb_seq = 0
reader = seqio.SequenceReader(input_file)
......@@ -48,17 +49,17 @@ class Flash (Analysis):
def define_parameters(self, read1_files, read2_files, mismatch_ratio=None, min_overlap=None, max_overlap=None, avg_reads_length=None, avg_fragment_length=None,
standard_deviation=None, phred_offset=None, nb_thread=1, archive_name=None):
"""
@param read1_files : paths to reads 1
@param read2_files : paths to reads 2
@param mismatch_ratio : maximum allowed ratio between the number of mismatched base pairs and the overlap length. Two reads will not be combined with a given overlap if that overlap results in a mismatched base density higher than this value
@param min_overlap : the minimum required overlap length between two reads to provide a confident overlap
@param max_overlap : maximum overlap length expected in approximately 90% of read pairs
@param avg_reads_length : average read length
@param avg_fragment_length : average fragment length
@param standard_deviation : average fragment standard deviation
@param phred_offset : the smallest ASCII value of the characters used to represent quality values of bases in FASTQ files
@param nb_thread : set the number of worker threads
@param archive_name : name for the output archive
@param read1_files : [list] paths to reads 1
@param read2_files : [list] paths to reads 2
@param mismatch_ratio : [float] maximum allowed ratio between the number of mismatched base pairs and the overlap length. Two reads will not be combined with a given overlap if that overlap results in a mismatched base density higher than this value
@param min_overlap : [int] the minimum required overlap length between two reads to provide a confident overlap
@param max_overlap : [int] maximum overlap length expected in approximately 90% of read pairs
@param avg_reads_length : [int] average read length
@param avg_fragment_length : [int] average fragment length
@param standard_deviation : [int] average fragment standard deviation
@param phred_offset : [int] the smallest ASCII value of the characters used to represent quality values of bases in FASTQ files
@param nb_thread : [int] set the number of worker threads
@param archive_name : [str] name for the output archive
"""
self.read1_files = InputFileList(read1_files)#, Formats.FASTQ)
self.read2_files = InputFileList(read2_files)#, Formats.FASTQ)
......
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