Methods

Methods are invoked using an object-oriented syntax. For example:

mapped = select(mapped) using |mr|:
    mr = mr.pe_filter()

They can also take arguments

mapped = select(mapped) using |mr|:
    mr = mr.filter(min_match_size=30)

Short reads

Short reads have the following methods:

• avg_quality(): the average quality (as a double)
• fraction_at_least(q): the fraction of bases of quality greater or equal to q
• n_to_zero_quality(): transform the quality scores so that any N (or n) bases in the sequence get a quality of zero.

Mapped reads

Mapped reads contain several methods. None of these methods changes its argument, they return new values. The typical approach is to reassign the result to the same variable as before (see examples above).

• pe_filter: only matches where both mates match are kept.
• flag: Takes one of {mapped} or {unmapped} and returns true if the reads were mapped (in a paired-end setting, a read is considered mapped if at least one of the mates mapped).
• some_match: Takes a reference name and returns True if the read mapped to that reference name.
• allbest: eliminates matches that are not as good as the best. For NGLess, the number of errors (given by the NM field) divided by the length of the longest match is the fractional distance of a match. Thus, a match with 3 errors over 100 bp is considered better than a match with 0 errors over 90bps.

filter

filter takes a mapped read and returns a mapped read according to several criteria:

• min_match_size: minimum match size
• min_identity_pc: minimum percent identity (considered over the matching location, trimming on the left and right are excluded).
• max_trim: maximum number of bases trimmed off the ends. Use 0 to specify only global matches.

If more than one test is specified, then they are combined with the AND operation (i.e., all conditions have to be fulfilled for the test to be true).

The default is to discard mappings that do not pass the test, but it can be changed with the action argument, which must be one of {drop} (default: the read is excluded from the output), or {unmatch} (the read is changed so that it no longer reports matching).

You can pass the flag reverse (i.e., reverse=True) to reverse the sign of the test.