def test_kmers_next():
km = kmers.Kmers("tests/172.fa")
header, kmer = km.next()
assert header == ">gi|1062504329|gb|CP014670.1| Escherichia coli strain CFSAN004177, complete genome"
assert kmer == "TCGCTTTCGTT"
header, kmer = km.next()
assert header == ">gi|1062504329|gb|CP014670.1| Escherichia coli strain CFSAN004177, complete genome"
assert kmer == "CGCTTTCGTTC"
def test_kmers_index_end():
"""Checks end case.
"""
km = kmers.Kmers("tests/ECI-2866_lcl.fasta")
header, kmer = km.next()
while km.has_next:
header, kmer = km.next()
assert header == ">lcl|ECI-2866|NODE_22_length_88582_cov_33.0406_ID_43"
assert kmer == "TACGGATTCTT"
def test_kmers_index_diff():
"""Checks last of a contig before switching.
"""
km = kmers.Kmers("tests/GCA_900015695.1_ED647_contigs_genomic.fasta")
header, kmer = km.next()
assert header == ">FAVS01000269.1 Escherichia coli strain ED647 genome assembly, contig: out_269, whole genome shotgun sequence"
while km.contig_has_next:
header, kmer = km.next()
assert header == ">FAVS01000269.1 Escherichia coli strain ED647 genome assembly, contig: out_269, whole genome shotgun sequence"
assert kmer == "TACTGCTACTG"
def test_kmers_load():
km = kmers.Kmers("tests/ECI-2866_lcl.fasta")
assert len(km.headers) == 297
assert len(km.sequences) == 297
assert km.headers[
0] == ">lcl|ECI-2866|NODE_177_length_532_cov_12.8938_ID_353"
assert km.headers[
1] == ">lcl|ECI-2866|NODE_222_length_438_cov_0.710611_ID_443"
assert km.sequences[
0] == "AACGCGCACTGACGTGAGGCCAGCGTACAGGCCGGATTATCGACATATTTCTGACAGGTGCCGTTATCTGCGGACTGTGTGACATATTTATCCCGGTATGCCCAGCACGCCTGTGTGATGCTCCAGGGTTTACCTTCCATCACACCTGTTTTCGTCCCCCCCGGCTCTGAACACTCAGTACCTTTCAGCACGCCATCCGCTTTATTAAACGGACAACTCTCCACCCACTCCACCCGTGGAACCCATTCCTTATCACGGACCTTCATCCTGAGTTTCAGCGTAAAGGTGGAAGCACCACTGACAAGCGATTCATAGACCATCCTGTCACCATTCCCGTGCGGGAGGCAATTACCGTTTGCAGTACAGCCACTACCGATCAGAACCTGCCCCTGTGTGACAGAAAACCCGGAGGGCACAGGTATGGTGAAAGTCCCGCTCTGTCCTGTAACCAGTTGCACATTAAAGGCTGTGTTCATAAAGTCGTAACGGGAGTTAAGGAAATATAGCCCTGCATGAGCCGACAGCGAGGCAC"
assert km.sequences[
1] == "ACATCGTGCCGCATTGTTGGCAGAGGGAATTCCTTTTCATTGCTTTTATTATCCCTGTGTTAGTGAAATACTACGTTAGGGTTTGGAACACGTAAGAAAAATGGCGTTGTCAATGGGATTGTTTTTTTTTTATGCCGGTCAGATCTCAAAAACTAGGCCAGAGATCAATTCTACTTGACCTCATGACAGTTTACTGCCGCTGCTGCCGGAATCCAAATCTCGTGGTATCCTAACTCAAGGAGTCGGCATGAAGTCCATCGAAGCATATTTTCTGTTCATCAGGTATTGACTAGTGACTCTGCAAGGACAAATCACCTTACTACATCCTGGTCCATGGTGAAGTCTAGCTTTGATACCTTGAGTTGTCCATTCCCGGAAATGCACCTCCGGGCCAGGGGTGCTCGCTCTGACCTTCGTGTCCCATGGAACTTCAGCCAG"
n = len(km.sequences[0])
assert n == 532
assert km.sequences[0][n - 1] == "C"
assert km.sequences[0][n - 2] == "A"
assert km.sequences[0][n - 3] == "C"
def km_short(request):
return kmers.Kmers(request.param)
def km(request):
return kmers.Kmers(request.param)
def test_kmers():
km = kmers.Kmers("tests/172.fa")
assert km.headers[
0] == ">gi|1062504329|gb|CP014670.1| Escherichia coli strain CFSAN004177, complete genome"
def test_kmers_unique():
"""Check that we are getting the correct number of unique kmers
"""
km = kmers.Kmers("tests/15.fa")
assert km.unique_kmers == 5