Example of using pbcore's FastaReader with generators in Python

el_pbcoreo.py

import os
import functools

import numpy as np

from pbcore.io import FastaReader, FastaRecord


def _to_records(func, file_name):
    with FastaReader(file_name) as f:
        for record in f:
            yield func(record)


def to_pbcore_record(r):
    """
    This is the identity operator.

    :type r: FastaRecord
    """
    return r

def to_my_record(r):
    """
    :type r: FastaRecord
    """
    return r.name, len(r.sequence)


def to_length(r):
    """
    :type r: FastaRecord
    """
    return len(r.sequence)


def to_movie_id(r):
    """
    header looks like:

    >m120201_042231_42129_c100275262550000001523007907041260_s1_p0/9/0_1756 [revcomp]
    """
    s = r.name.split(' ')[0].split('/')
    return s[0], s[1], s[2], len(r.sequence)


def to_pacbio_record_or_raise(r):
    if ":" in r.name:
        raise ValueError("Malformaed contig name '{n}'".format(n=r.name))
    return r.name, len(r.sequence)


def example_01(file_name):

    to_record = functools.partial(_to_records, to_my_record)

    for r in to_record(file_name):
        print r


def example_02(file_name):

    for r in _to_records(to_movie_id, file_name):
        print r


def example_03(file_name):
    for r in _to_records(to_pacbio_record_or_raise, file_name):
        print r


def example_04(file_name):
    """run all
    """
    funcs = [to_my_record, to_movie_id, to_pacbio_record_or_raise]
    for func in funcs:
        for r in _to_records(func, file_name):
            print r


def example_05(file_name):

    contig_lengths = np.fromiter(_to_records(to_length, file_name), dtype=np.int64, count=-1)
    print contig_lengths
    return contig_lengths


def run_examples():
    f = 'small.rc.fasta'
    examples = [example_01, example_02, example_03, example_04, example_05]
    for func in examples:
        func(f)

small.rc.fasta

>m120201_042231_42129_c100275262550000001523007907041260_s1_p0/9/0_1756 [revcomp]
TCGCCTTCCGTGTCGCTTACGCGAAATTGAGAAGAACTGAATGCAGTGATGCCGTACCGAACCGGCGTAC
GCTCGCATGAAGCAGGCATAAATATCCATCTGATGGAAATGCCGGGGCTGAACTCGGTATATCTCTGTAT
AACCGTGGGCGAAAACACCACTCGATGCACGTGAAAGTTCGCCAGGCTCTGACCTACGCGTTGAACAAAG
ACGGATCATCAAAGCCGGTTTTATCAGGCGGCGGCGTCATCGCGAAAAACTGATCCCGCCACCATGTGGG
GCTATCACGACGACGTTTCAGGACTACACCTCGATCCTGAAAAGCGGAAGCCTTGGCTGAAGAAGAGGGT
CTGGAAAAAGGTCTCCCATCGGACCTGTGGGCGATGCCGGTACAAATTCCGTTATAACCCGAACGGCTCG
GCCGCATGGCGGAGTTATGATTCAGGGCAGACCTGGCGAAAGGTCGGCGTGCAGGCAAATTGTCACCTAC
GATGGTGGTGAGTACCTCAAGCGTGCGAAAGATGGCGAGCACCAGACCGGTAATGATGGGCTGGACTGGC
GTACGGGGATCCGGTATCTTCGCCACCCTGTTCAGTCTGCGCCGCCTTGAACAAGGCTCCAAACTACTCA
AAATGGTGCTACAAAACGTTTGAAGATCTGATCTTCACCCGGCGCGTGCTACGACGACATCCAATAACGC
GTGACTGACAACAGCGCAGGTGGTTGATGCACGACATCAGGCTCCGGCACTGATTCATCGCTCACTCACC
GTGTTGGAACCGGTACGTAAAGAAGTTAAAGGCTATGTGGTTGATTCCATTAGGCAACATCACTTCGAAA
CGTCTCTATCGATAATTAAAAGGCCATACAAGACTGATGCAAAGGCAAAAATGCCTGGATGCGCTCCGCC
CTTATCAGGCCTACGAATTCTGCAATGTATAATTTGCACGATTTTGTAGGCCGGATAAGCGGTTAACGCC
GCCATCGGCTATACCAAAGCGCACTTGTCACAATCTTATACCGTGGCCGCTGTGCTCTGCGGCAGCGCCA
TCGGCAGCATACTTCTCCCTGTCGATAAGGGCGGGAATGATTTGTGGGCAATACGACACGCAGTTCCAGG
CTGCGGGTCACTACTAGAGAATCCCGGGTGGGGGGGTTATGTTTGCAGTTTATTTTCTCGACGTTTGCGG
ATTCGTCATCCCCACGTTAATCGGTATTCCCTTCTCACATTTGCCTTTGTCCACATGATCCGGGCGATCC
GGTGTATGATCATGGCGGGATGGGCGAACCGTGGGATTCTCCCAGAGCGTCAACGCGCAGCTGCTGGCTG
GAACTCGGCTTAGATAAAACCGATGTGGCACAGTTATCTCCATTACATTGGCGTTATGCATGGCGAATCT
AGGACATTCAATGAAAAGCGCCATCCCGGTTTGGGAAGAGTTCGTGCGCGCTTCCAGGGCCACGCTGGAA
CTGGCGTCTGCGCATGATTTTTGGCTACGGCAGTCGTATTCCGGTCGGCGTGGCTGGCGGCGGGTAAACG
CTGTTCCTTTCGATCCACCAGCGGTTGCTGGCGCTGACAGGTTATTCAATGCCTTATTTCGGTGGGCATG
ATGCTGATCATGCTGTCGGTGCACTGGAACCTGGACGCCCGTTCCGTGCTGGAGGATATCGGTTGTTCCT
CGATGACTCCAATCGTAACCGTGTTTATGCTATCGACACCGCCATCTGGGTGGAAGACGGAACCTTTCGA
TGGCCG
>m120201_042231_42129_c100275262550000001523007907041260_s1_p0/11/1513_4949 [revcomp]
TTTAATGTCAGCGGTATTGCTTTTGCAGGGCACTATAAAGCGTGACGTTTTGCCGCTGCGGCTAGGGCCA
GTTACCAGCACGTCCTGTGGTTGTTGCTCAAAGGCATTGAGAAAGTCGACCCAGTTGTAACGGTGGCATT
CCAGCGTGGTGCATCCAGTGCCTGACCACCTTGCTGTAACCACCTTAATACCCTTTTTTCACCCCGACAT
GGTAGGTCGCATACGAAACTGAGACGGCGTTTTCCTGCAGTTCGACAGTGAATTGCCCGCTCCTGCGGCC
GGCGATGTTCCGCAATATCAGGTTTCCCAGCACTTTTAATCTGGCGGTTTAATTGCGACTCCGCGCATCC
GGTGAACATCCGGTAAAAGGATGCAATACGCGCGTCGATACGCAGCGGGATGCGGTGGCATTGTCCGCTG
GGTTCGAGTTGATATCGAGCGCGGTTGTTTCGCGCAGATTGTAACGTTCGAGTTAGCAACTCTGCTTTGG
TGATGACTTCTCAACTGACAGCTACGGCGCAATGTTGTTGGTGTGCGGGCTGGCGTGACTCCATTTGTTG
GCGCCCGTCCAGCAGGTGATCATCATACGTTTGGTAGGTAGCGAAATAGCAAATGCGTCCAGTCGGCTCA
TGCGAATGGTGCAATCGACTACCGCCAACATGAACCACCTTCTTTCGCTGGCTCAGCAAGACTCCATGAT
AACGCAGACCACAGGCAGTGAGCCTGTGGAATATTCATTGCCGCTCCTTCGTGGGCGTCAATCAGCGGAA
GACATTTCGCAGGTTGCTGCAATGCAGCTGTCACTTTGGATTATTGCAGTTGCGCTGTTCCAGCCGGTGA
ACGCCGGTTTGCGTTATCCAACCCGGTGTCTGGACGACGCTTAGGCCATTGGCCTTTCCTTGCCGGTCAG
CGACACCACGCCCTTTGCCACACTCATGGCTGAACATGCGGGTGCGTGGTAGGCGAGGGAATGCCATTGC
TGCCACCGTCGCAGGTATCCTAATCATCCATGTTCCAGCGACGGCACAACTATCGGCGGTACGGTAAGCG
CACAAGGTTTGTAGCATGTCGGTGGTGCGGCTTTGCGCAGGTAGTTTTGATAAGCGGGTCCAATGGCGCT
TAAAATGGCATGAATGCAATAACCACTCAGTTCGATAGTGTAAAACCGCGTTGTTGGTCCATCTGTTCGC
TCCTTGATTTGCGTTGGCGCTACCTTTGGCAAACGCCCTCAGCACAGCGTAGGGGCAAAAACGAAACGGG
GAAAGCGATTCCCGAGGTTTTTATTTCGTTGCAGCGAAAGACAAGAAATTTGCGGGCGTTACGAAGAAAG
TTGGGGGAGGGGAGATTATCCGCCCGCGATCGAGCGGATAAATCTGTAATATTGCGAAAACGGCATTGAG
GTCGGAGTGCTTGTACGTGTTTAGTTAGCGCACGACGTCTTTGAGATAAAGTCCACGGCCCGTTCGCGCA
ATTCACGCAGTGTTTTGTCGTGGACGTTGCCGACATTCCGTAGCGCCTTGCCGTTGGTGGTTTTGACGGC
TTCGCGCATCTGTTCTGTTTCGGCTTATCCCAGCATGATGCTATCGGCTCCTGCTTTTTCAGGGCTTCAT
CAAGTTCTTCCAGATTCTCTCTTTCGATGTTCTGCGCATCCGGGTGCAGCCAGGCGCTTTTTTCGACCCG
CCTGGCGCCTGAGCCCGGAGGGCAAATAATATGGTTTTCTTTGTATCAGGAAGGCATCAGAAGCCCCGGA
CGTTGATTCGCTCCGCCGCCGCAAAGTCGCGTTTTCAGAAGCTGAACGCAGGCCGGGTAAGGTTTTGCGC
GTATCCAACAACTGGCGTGTTGGTGCCTTCCAGCATTCGACACTAGGTGGTACCTTACTGGCCAACTCCT
GAAAGGGTTTGCACAAATTAAGCGCATGCGTTCGCCCGTACGCACGCGGGATGGGGCCTTCAAGTTCGAA
CAAGGATGATTGGCATTGATTGCTCGCCGTTCACATGCCAGATTATGGGTGACATCGTCGCCTGCCAGTT
GAAAACACTCTTAACCGCGTTTGCGCAAAGACGCCATTCTCGCGCAAGGTGATAACCGTGGCATGAGAGC
GACTGAACTTTTCGGTAAGTTTTGCGTAATATCATTGTTGGCATCGACTGTTTCCGCCTAATCTTCCCGC
TCGCTTGGGCCACCGCGCCGGGATATCGAGCATTAAATTGCGTTCAAGCAGTCGTGCACGTCGGTGTCAG
GTATACGGCGGGAGCGGCATGTTAAACTCCAGACGTAGCTAACGAATCATAAGGTAGAACATGCTTACTC
TGAACCGGGTACTTGCACACAATTAAGGTCTGCATGTTGTTAGAACAGGGGTGGCTGGTTGGCGCGCGCG
CGCGTTTCCTACCACATTACGTTGGCGCCCCGCCCCCGATGCGGACACGCCCGGCTGTGAGGTGCACAAT
ATTAGCCTGCCGCAGGCGGTTTGGCGGTCCGTGGATCGGACGGCATTATTCACTGGAACTATTTATTCCG
CAGGCCATCTTTCTTTGCTGAGATCGCCATTTAGCGCGTCTCCGTCACTGTTTGATTCGCTGATGGTGAA
ATAGTCCAGTATGTTCCTTTCGTAAACGTTGCATGGCATGCGGGAGTCTCTCAGTATCAGGGGCGGCGAC
GCTGCAATGATTTTTCTATTGGGATTGAGCTTGAAGGCACGATACGCTGGCGTATTACGATGCGCGTATT
CAACAGTGGTGTCGTTGTGGCCATCCTGGGCGGATTGTTACCTGTGGTGTGCTCATACATATTTTTGTAA
TGTAGCTCTGCAGTGTGTCACGCGATATTCCGCTTGTCACCTGGAACGTGCCGGCGCATATTTCGTAGGA
TTGTAGCGTCGGCAGCCCATTCACGTCGGAAATTTTCCCGACATAGCATGCAGGAGGTCCATGCTATGTG
TAACTGTTATATGTGCTGGGGGCGCGAACGGTCGTGTCTGTGCTGTGTCTCGCTTGGCAATCGGATGTTA
CTAATGTCGACGCTAGTCCTCTCTCGGCAATACGACCTCGTATCACATGTGTGTATTCAGTTCTGGGGCG
TCTGTATTATAGTAGAGTGCTGTGAGCGATGTGGCAGCTATGGTATCATCTGTCACTGTTGTAAAGCTGT
CTGTGGTCTTCGGACGCAGCTCGTTTACGCCCTTCAGGTGTGCGGGCGATAAAACATTTTGATCCGTGTT
TTTTAAATACCAGCGTCAACTCGTTAGCATTAACCATCATCTGATTTTTTCTTTGGCTGGAATGGCCGGA
ACATTAATGTAGAACAGCGACTTTTTATTTTCAGGCAGGTTATCAGCTGTTTTATAATTCGCCAGGGATG
AGTCATCGCCAGCCTCAAGCGAAAATAGCGGTGGGGTTATAATAAATGCGGGCACGGCTTTTACCATCTA
TATTAT
>m120201_042231_42129_c100275262550000001523007907041260_s1_p0/13/0_68 [revcomp]
GCTGACTGAGGGTTGTGCACTTCACTTCGAACAGATGCTTGCCGTAGACTAGGCTCGCGTGTCGAGGC
>m120201_042231_42129_c100275262550000001523007907041260_s1_p0/13/117_519 [revcomp]
CATTTTTTTCTTTGGGTTGGTGGGAAAGCGTGTGGTTGGAGGACGGGCCGACATACTGGCCCGTTACTAT
GTCGACGCGGTGCGTGAATATTGTATGCTTGTGTGGCAACTAGCTGAGGGATTGAGTCATTCGCCTTGCG
CGTATTGCTTGTTGAAGTTGGCGGGGCCGGCCTGTTATTAGCGGGGGTCATCGCCACTGCGCGGCATGGT
GGAAGGGGCTTTGAGTAGGGTTTCGCCGAGCTCTTCAGCATCGCGTCTTTCGGTGAAAGCGGGCGCAATG
GCGACAGCTGTGTGTGTGATCCTACGCCGCGAATCGACGTGTCCGAAAATAGTAACTGTACGGCATGACT
TCGGCCGTGATGCTTCGGTGTTTAGAGCTTGTTGAAGTTGGGAGTCATGTCG