pyfermi -- python interface to the Fermi assembler

pyfermi is an Python interface to Heng Li's Fermi assembler. Use it with caution, as it's experimental and in beta.

Example

import fermi
import random
random.seed(0)
def random_reads(seq, n, rlen=50):
    for i in range(n):
        pos = random.randint(0, len(seq)-rlen)
        yield seq[pos:(pos+rlen)]

seq = """AACAAGATGGCCCTCTACGAGCAGTTCAGCGTCCCCTCCCAGCGCTTCGCCGCCAACGCCGCCAACACCGCCCCAGCCGCCGCCCCCCGCCCCGCCGCCAGCTACGCCGCCGTCTCCTCCGCCTCCGCCGGACAGATTGGTGGGATCGACAGACCTCTCTTTCCATCATTTTGCGTGCCTTCAAATGAACCTGTGCGTTTGCCCGAACACATCAAGACCAACTCGAGTGGGCGGGATGGCCAGGCTATATCTGGGAGGCTTTCCACCCAGCTTAAGAGCAAGGACGCCTATGCTGCAGGATCGACTGCTGAGTGTAGTAGTTCACAGCGTAGAGACAACAACAACAATAGCATGAAGAATTCTTCTGGGAAGAAGTTGACTAACGATGATGATTTTACGGTTCCTTCTGTCTTCTGCTCTGGAGCGCGCCCTCGTTCCAACCATGAGGAAGTGAGGATCCAAGAGAATGCCACACCCTTCCCAGCTACAAGTCCGTATAAGAGTGGGCCTACGGTGTCCAAACCAACTGCAAAATTTCCCAACACCGACAAGAGGTACCTGGAAGGAAGGAACGCGTCGGACACGAGATCAAGGGACTCTCCAAGTATTATCAGGGACAAAGCACCAGCAAACACAACGACAAACTTTTTGGAAACTGAAGAGAGGACTTCATCGTTCCAATTTTCTGCAGAGAAGACAATGGGTAAAAGAGATGACAAAGGTTCTTCGTATAGTAGGGTAAAAGAGACGAGCAGTATAAATGTTTCTGATAAGCAACATTCCCGAAACGAGGGGCATCAGGC"""
fermi = Fermi()
for read in random_reads(seq, 50, 70):
    fermi.addseq(read)
fermi.correct()
tigs = fermi.assemble(do_clean=True)

Notes

ext.c contains some extra C functions needed to wrap fermi. In some cases, I need klib functions not packaged with fermi, for example ksprintf from kstring.c. I try to keep things separate so fermi can be updated without breaking anything.

Todo

• Unit tests.
• More with error correction.