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import pkg_resources
import tempfile
import magic
def qc_fasta(sequence):
schema_resource = pkg_resources.resource_stream(__name__, "validation/formats")
with tempfile.NamedTemporaryFile() as tmp:
tmp.write(schema_resource.read())
tmp.flush()
val = magic.Magic(magic_file=tmp.name,
uncompress=False, mime=True)
seq_type = val.from_buffer(sequence.read(4096)).lower()
sequence.seek(0)
if seq_type == "text/fasta":
# ensure that contains only one entry
entries = 0
for line in sequence:
if line.startswith(">"):
entries += 1
if entries > 1:
raise ValueError("FASTA file contains multiple entries")
break
sequence.seek(0)
return "sequence.fasta"
elif seq_type == "text/fastq":
return "reads.fastq"
else:
raise ValueError("Sequence file does not look like FASTA or FASTQ")
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