def sniffer(filename):
try:
if is_sam(filename): return "SAM"
except:
pass
try:
if is_bam(filename): return "BAM"
except:
pass
try:
if is_cram(filename): return "CRAM"
except:
pass
try:
if is_fastq(filename): return "FASTQ"
except:
pass
try:
if is_fasta(filename): return "FASTA"
except:
pass
def sniffer(filename):
try:
if is_sam(filename): return "SAM"
except:
pass
try:
if is_bam(filename): return "BAM"
except:
pass
try:
if is_cram(filename): return "CRAM"
except:
pass
try:
if is_fastq(filename): return "FASTQ"
except:
pass
try:
if is_fasta(filename): return "FASTA"
except:
pass
def test_others():
filename = sequana_data("test_fasta.fasta")
ff = FastA(filename)
assert len(ff) == 16
assert len(ff.comments) == 16
assert len(ff.names) == 16
assert len(ff.sequences) == 16
assert is_fasta(filename) == True
ff.get_lengths_as_dict()
with TempFile(suffix='.fasta') as fh:
ff.select_random_reads(4, output_filename=fh.name)
ff.select_random_reads([1, 2, 3], output_filename=fh.name)
ff.select_random_reads({1, 2, 3}, output_filename=fh.name)
assert ff.get_stats()['N'] == 16
assert ff.get_stats()['mean_length'] > 454
with TempFile(suffix='.fasta') as fh:
ff.reverse_and_save(fh.name)
ff.to_fasta(fh.name)
ff.to_igv_chrom_size(fh.name)