def test_get_sequence():
file = pdbx.PDBxFile.read(join(data_dir("structure"), "5ugo.cif"))
sequences = pdbx.get_sequence(file)
file = pdbx.PDBxFile.read(join(data_dir("structure"), "4gxy.cif"))
sequences += pdbx.get_sequence(file)
assert str(sequences[0]) == "CCGACGGCGCATCAGC"
assert type(sequences[0]) is seq.NucleotideSequence
assert str(sequences[1]) == "GCTGATGCGCC"
assert type(sequences[1]) is seq.NucleotideSequence
assert str(sequences[2]) == "GTCGG"
assert type(sequences[2]) is seq.NucleotideSequence
assert (str(sequences[3]) == "MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYN"
"AYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQD"
"DTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGD"
"FEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPS"
"FTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHR"
"RIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVA"
"GEPLPVDSEKDIFDYIQWKYREPKDRSE")
assert type(sequences[3]) is seq.ProteinSequence
assert (str(sequences[4]) == "GGCGGCAGGTGCTCCCGACCCTGCGGTCGGGAGTTAA"
"AAGGGAAGCCGGTGCAAGTCCGGCACGGTCCCGCCACTGTGACGGGGAGTCGCC"
"CCTCGGGATGTGCCACTGGCCCGAAGGCCGGGAAGGCGGAGGGGCGGCGAGGAT"
"CCGGAGTCAGGAAACCTGCCTGCCGTC")
assert type(sequences[4]) is seq.NucleotideSequence
def test_search_sequence():
IDENTIY_CUTOFF = 0.9
pdbx_file = pdbx.PDBxFile.read(join(data_dir("structure"), "1l2y.cif"))
ref_sequence = pdbx.get_sequence(pdbx_file)[0]
query = rcsb.SequenceQuery(ref_sequence,
"protein",
min_identity=IDENTIY_CUTOFF)
test_ids = rcsb.search(query)
for id in test_ids:
fasta_file = fasta.FastaFile.read(rcsb.fetch(id, "fasta"))
test_sequence = fasta.get_sequence(fasta_file)
matrix = align.SubstitutionMatrix.std_protein_matrix()
alignment = align.align_optimal(ref_sequence,
test_sequence,
matrix,
terminal_penalty=False)[0]
identity = align.get_sequence_identity(alignment, mode="shortest")
assert identity >= IDENTIY_CUTOFF
import matplotlib.colors as colors
import biotite
import biotite.structure as struc
import biotite.structure.io.pdbx as pdbx
import biotite.sequence as seq
import biotite.sequence.io.fasta as fasta
import biotite.sequence.align as align
import biotite.sequence.graphics as graphics
import biotite.application.blast as blast
import biotite.application.clustalo as clustalo
import biotite.database.rcsb as rcsb
import biotite.database.entrez as entrez
# Get structure and sequence
pdbx_file = pdbx.PDBxFile.read(rcsb.fetch("1GUU", "mmcif"))
sequence = pdbx.get_sequence(pdbx_file)[0]
# 'use_author_fields' is set to false,
# to ensure that values in the 'res_id' annotation point to the sequence
structure = pdbx.get_structure(pdbx_file, model=1, use_author_fields=False)
structure = structure[struc.filter_amino_acids(structure)]
# Identity threshold for a sequence to be counted as homologous sequence
IDENTITY_THESHOLD = 0.4
# Find homologous proteins in SwissProt via BLAST
app = blast.BlastWebApp("blastp", sequence, database="swissprot")
app.start()
app.join()
alignments = app.get_alignments()
hit_seqs = [sequence]
hit_ids = ["Query"]
hit_starts = [1]