Iterators¶
Introduction¶
The bio_utils’ iterators subpackage contains numerous iterators for a variety of biology-relevant file types. The contained iterators share numerous features listed in the next section. The subsequent sections detail iterator-specific elements. Each iterator returns file-specific Python classes. This page only details how to use the iterators not the instances they return, see Classes for details on each class in bio_utils.
Common Features¶
Abilities shared by all iterators in this package include:
- Return file-specific instances, see Classes for more details
- Support the
next()and__next__()methods - Usable in for loops
- Accept any iterator:
iter()objects, file handles, memory files, etc. - Begin iteration at arbitrary lines using start_line or header argument
All iterators in this package are quite fast; the following table compares SCREED’s, Biopython’s, and bio_utils’ FASTA iteration speed in seconds on a 3.2 GB FASTA file containing 1,614,108 sequence entries averaging 158 bases each.
| FASTA File Iteration Speed for Different Libraries (seconds) | ||||||
|---|---|---|---|---|---|---|
| Library | Trial#1 | Trial#2 | Trial#3 | Trial#4 | Trial#5 | Average |
| SCREED | 974.812 | 971.185 | 953.027 | 961.247 | 971.924 | 966.439 |
| Biopython | 581.148 | 575.677 | 585.322 | 548.876 | 516.235 | 561.452 |
| bio_utils | 290.876 | 298.047 | 291.625 | 291.966 | 289.635 | 292.430 |
b6_iter¶
Iterates over B6 alignment files and returns each line as an instance of B6Entry. This iterator does not support arbitrary table modifications as does BLAST+.
fasta_iter¶
Iterates over a FASTA file and returns each entry as an instance of FastaEntry. This iterator can handle sequences spanning multiple lines.
fastq_iter¶
Iterates over a FASTQ file and returns each entry as an instance of FastqEntry. This iterator can handle sequences and quality score spanning multiple lines.