flowcraft.templates.integrity_coverage module

Purpose

This module receives paired FastQ files, a genome size estimate and a minimum coverage threshold and has three purposes while iterating over the FastQ files:

• Checks the integrity of FastQ files (corrupted files).
• Guesses the encoding of FastQ files (this can be turned off in the opts argument).
• Estimates the coverage for each sample.

Expected input

The following variables are expected whether using NextFlow or the main() executor.

• sample_id : Sample Identification string

  • e.g.: 'SampleA'

• fastq_pair : Pair of FastQ file paths

  • e.g.: 'SampleA_1.fastq.gz SampleA_2.fastq.gz'

• gsize : Expected genome size

  • e.g.: '2.5'

• cov : Minimum coverage threshold

  • e.g.: '15'

• opts : Specify additional arguments for executing integrity_coverage. The arguments should be a string of command line arguments, such as ‘-e’. The accepted arguments are:

  • '-e' : Skip encoding guess.

Generated output

The generated output are output files that contain an object, usually a string. (Values within ${} are substituted by the corresponding variable.)

• ${sample_id}_encoding : Stores the encoding for the sample FastQ. If no encoding could be guessed, write ‘None’ to file.

  • e.g.: 'Illumina-1.8' or 'None'

• ${sample_id}_phred : Stores the phred value for the sample FastQ. If no phred could be guessed, write ‘None’ to file.

  • '33' or 'None'

• ${sample_id}_coverage : Stores the expected coverage of the samples, based on a given genome size.

  • '112' or 'fail'

• ${sample_id}_report : Stores the report on the expected coverage estimation. This string written in this file will appear in the coverage report.

  • '${sample_id}, 112, PASS'

• ${sample_id}_max_len : Stores the maximum read length for the current sample.

  • '152'

Notes

In case of a corrupted sample, all expected output files should have 'corrupt' written.

Code documentation

flowcraft.templates.integrity_coverage.RANGES = {'Illumina-1.3': [64, (64, 104)], 'Illumina-1.5': [64, (66, 105)], 'Illumina-1.8': [33, (33, 74)], 'Sanger': [33, (33, 73)], 'Solexa': [64, (59, 104)]}

dict: Dictionary containing the encoding values for several fastq formats. The key contains the format and the value contains a list with the corresponding phred score and a list with the range of encodings.

flowcraft.templates.integrity_coverage.MAGIC_DICT = {b'\\x1f\\x8b\\x08': 'gz', b'\\x42\\x5a\\x68': 'bz2', b'\\x50\\x4b\\x03\\x04': 'zip'}

dict: Dictionary containing the binary signatures for three compression formats (gzip, bzip2 and zip).

flowcraft.templates.integrity_coverage.guess_file_compression(file_path, magic_dict=None)

Guesses the compression of an input file.

This function guesses the compression of a given file by checking for a binary signature at the beginning of the file. These signatures are stored in the MAGIC_DICT dictionary. The supported compression formats are gzip, bzip2 and zip. If none of the signatures in this dictionary are found at the beginning of the file, it returns None.

Parameters:

file_path : str

Path to input file.

magic_dict : dict, optional

Dictionary containing the signatures of the compression types. The key should be the binary signature and the value should be the compression format. If left None, it falls back to MAGIC_DICT.

Returns:

file_type : str or None

If a compression type is detected, returns a string with the format. If not, returns None.

flowcraft.templates.integrity_coverage.get_qual_range(qual_str)

Get range of the Unicode encode range for a given string of characters.

The encoding is determined from the result of the ord() built-in.

Parameters:

qual_str : str

Arbitrary string.

Returns:

x : tuple

(Minimum Unicode code, Maximum Unicode code).

flowcraft.templates.integrity_coverage.get_encodings_in_range(rmin, rmax)

Returns the valid encodings for a given encoding range.

The encoding ranges are stored in the RANGES dictionary, with the encoding name as a string and a list as a value containing the phred score and a tuple with the encoding range. For a given encoding range provided via the two first arguments, this function will return all possible encodings and phred scores.

Parameters:

rmin : int

Minimum Unicode code in range.

rmax : int

Maximum Unicode code in range.

Returns:

valid_encodings : list

List of all possible encodings for the provided range.

valid_phred : list

List of all possible phred scores.