def it_raises_on_bad_fasta():
fasta_str = """
MKSGSGGGSPTSLWGLLFLSAALSLWPTSGEICGPGIDIRNDYQQLKRLENCTVIEGYLH
"""
with zest.raises(ValueError) as e:
uniprot.fasta_split(fasta_str)
assert "data before the header" in str(e.exception)
def protein_fasta(fasta_str, override_name=None):
"""
Parse fasta format as defined by Uniprot.
https://www.uniprot.org/help/fasta-headers
Arguments:
fasta_str: The string (not the file path!) of the fasta
override_name: If non-None will replace the found protein name
Returns:
List(Dict(id, seqstr))
"""
seqs = uniprot.fasta_split(fasta_str)
ret = []
for header, seqstr in seqs:
header = header.split(" ")[0]
parts = header.split("|")
if len(parts) >= 2:
id = parts[1]
else:
id = parts[0]
if override_name is not None:
id = override_name
assert len(seqs) == 1
ret += [dict(id=id, seqstr=seqstr)]
return ret
def it_returns_multiple_lines_and_headers():
fasta_str = """
>sp|P08069|IGF1R_HUMAN Insulin-like growth factor 1 receptor OS=H**o sapiens OX=9606 GN=IGF1R PE=1 SV=1
MKSGSGGGSPTSLWGLLFLSAALSLWPTSGEICGPGIDIRNDYQQLKRLENCTVIEGYLH
ILLISKAEDYRSYRFPKLTVITEYLLLFRVAGLESLGDLFPNLTVIRGWKLFYNYALVIF
>sp|P1010|IGF1R_HUMAN something else OS=H**o sapiens OX=9606 GN=IGF1R PE=1 SV=1
ZZZZZZZ
AAAAAAA
"""
groups = uniprot.fasta_split(fasta_str)
assert groups == [
(
"sp|P08069|IGF1R_HUMAN Insulin-like growth factor 1 receptor OS=H**o sapiens OX=9606 GN=IGF1R PE=1 SV=1",
"MKSGSGGGSPTSLWGLLFLSAALSLWPTSGEICGPGIDIRNDYQQLKRLENCTVIEGYLHILLISKAEDYRSYRFPKLTVITEYLLLFRVAGLESLGDLFPNLTVIRGWKLFYNYALVIF",
),
(
"sp|P1010|IGF1R_HUMAN something else OS=H**o sapiens OX=9606 GN=IGF1R PE=1 SV=1",
"ZZZZZZZAAAAAAA",
),
]
def it_returns_on_none():
groups = uniprot.fasta_split(None)
assert groups == []
def it_returns_empty():
groups = uniprot.fasta_split("")
assert groups == []