Fastq utility functions
Trys to guess the type of quality string used in a Fastq file
Parameters: qualities (str) – string with the quality scores as in the Fastq file Return str: a string with the guessed quality score
Possible values are the following, classified but the values usually used in other softwares:
- ASCII33: sanger, illumina-1.8
- ASCII64: illumina-1.3, illumina-1.5, solexa-old
Return the guessed compiled regular expression :param str seq_id: sequence header to test
Returns: compiled regular expression object or None if no match found
Convert old seq_id format for Illumina reads to the new found in Casava 1.8+
Parameters: seq_id (str) – seq_id of the sequence (stripped of ‘@’) Return str: the new format seq_id
Example from Wikipedia:
old casava seq_id: @HWUSI-EAS100R:6:73:941:1973#0/1 new casava seq_id: @EAS139:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCAC
Deprecated since version 0.3.3.
Convert old seq_id format for Illumina reads to the new found in Casava until 1.8, which marks the new format.
Parameters: Return str:
the new format seq_id
New in version 0.3.1.
Loads a fastq file and returns a generator of tuples in which the first element is the name of the sequence, the second the sequence and the third the quality scores (converted in a numpy array if num_qual is True).
this is a simple parser that assumes each sequence is on 4 lines, 1st and 3rd for the headers, 2nd for the sequence and 4th the quality scores
file_handle (str, file) – fastq file to open, can be a file name or a file handle
tuple – first element is the sequence name/header, the second element is the sequence, the third is the quality score. The quality scores are kept as a string if num_qual is False (default) and converted to a numpy array with correct values (0-41) if num_qual is True
load_fastq_rename(file_handle, num_qual=False, name_func=None)¶
New in version 0.3.3.
Mirrors the same functionality in
mgkit.io.fasta.load_fasta_rename(). Renames the header of the sequences using name_func, which is called on each header. By default, the behaviour is to keep the header to the left of the first space (BLAST behaviour).
write_fastq_sequence(file_handle, name, seq, qual, write_mode='a')¶
Changed in version 0.3.3: if qual is not a string it’s converted to chars (phred33)
Write a fastq sequence to file. If the file_handle is a string, the file will be opened using write_mode.