def test_sequentual_phy__different_length_names_2():
msa = MSA([
FASTA("Burchelli_4", None, "ACGTTGATAACCAGG"),
FASTA("Donkey", None, "TGCAGAGTACGACGT")
])
expected = \
"""2 15
Burchelli_4 ACGTTGATAA CCAGG
Donkey TGCAGAGTAC GACGT"""
print interleaved_phy(msa), expected
assert_equal(interleaved_phy(msa), expected)
def test_sequentual_phy__different_length_names_1():
msa = MSA([
FASTA("A_short_name", None, "ACGTTGATAACCAGG"),
FASTA("Another_really_long_sequence_name_that_is_too_long", None,
"TGCAGAGTACGACGT")
])
expected = \
"""2 15
A_short_name ACGTTGATAA CCAGG
Another_really_long_sequence_n TGCAGAGTAC GACGT"""
print interleaved_phy(msa), expected
assert_equal(interleaved_phy(msa), expected)
from nose.tools import assert_equal
from pypeline.common.formats.phylip import \
sequential_phy, \
interleaved_phy
from pypeline.common.formats.msa import \
MSA
from pypeline.common.formats.fasta import \
FASTA
_MSA_SHORT_SEQUENCES = \
MSA([FASTA("seq1", None, "ACGTTGATAACCAGG"),
FASTA("seq2", None, "TGCAGAGTACGACGT")])
_MSA_MEDIUM_SEQUENCES = \
MSA([FASTA("seq1", None, "ACGTTGATAACCAGGAGGGATTCGCGATTGGTGGTAACGTAGCC"),
FASTA("seq2", None, "TGCAGAGTACGACGTCTCCTAGATCCTGGACAATTTAAACCGAA")])
_MSA_LONG_SEQUENCES = \
MSA([FASTA("seq1", None, "CGGATCTGCTCCTCCACTGGCCACGTTTACTGTCCCCCAACCGTT" \
"CGTCCCGACCTAGTTATACTTCTTAGCAAGGTGTAAAACCAGAGATTGAGGTTATAACG" \
"TTCCTAATCAGTTATTAAATTACCGCGCCCCGACAG"),
FASTA("seq2", None, "AGTTGAAGAGGCGGAACGTTTGTAAACCGCGCTAACGTAGTTCTA" \
"CAACCAGCCACCCGGTTCGAAGGAACAACTGGTCGCCATAATTAGGCGAAACGATAGTG" \
"CACTAAGGTCAGGTGCGCCCCTGTAAATAATTAGAT")])
_MSA_MEDIUM_NAMES = \
MSA([FASTA("A_really_long_sequence", None, "ACGTTGATAACCAGG"),
FASTA("Another_real_long_one!", None, "TGCAGAGTACGACGT")])
_MSA_LONG_NAMES = \
