def as_fasta(record):
"""Turn a SeqRecord into a FASTA formated string.
This is used internally by the SeqRecord's .format("fasta")
method and by the SeqIO.write(..., ..., "fasta") function.
"""
id = _clean(record.id)
description = _clean(record.description)
if description and description.split(None, 1)[0] == id:
# The description includes the id at the start
title = description
elif description:
title = "%s %s" % (id, description)
else:
title = id
assert "\n" not in title
assert "\r" not in title
lines = [">%s\n" % title]
data = _get_seq_string(record) # Catches sequence being None
assert "\n" not in data
assert "\r" not in data
for i in range(0, len(data), 60):
lines.append(data[i : i + 60] + "\n")
return "".join(lines)
def as_fasta(record):
"""Turn a SeqRecord into a FASTA formated string.
This is used internally by the SeqRecord's .format("fasta")
method and by the SeqIO.write(..., ..., "fasta") function.
"""
id = _clean(record.id)
description = _clean(record.description)
if description and description.split(None, 1)[0] == id:
# The description includes the id at the start
title = description
elif description:
title = "%s %s" % (id, description)
else:
title = id
assert "\n" not in title
assert "\r" not in title
lines = [">%s\n" % title]
data = _get_seq_string(record) # Catches sequence being None
assert "\n" not in data
assert "\r" not in data
for i in range(0, len(data), 60):
lines.append(data[i:i + 60] + "\n")
return "".join(lines)
def as_tab(record):
title = _clean(record.id)
seq = _get_seq_string(record) # Catches sequence being None
assert "\t" not in title
assert "\n" not in title
assert "\r" not in title
assert "\t" not in seq
assert "\n" not in seq
assert "\r" not in seq
return "%s\t%s\n" % (title, seq)
def as_tab(record):
"""Return record as tab separated (id(tab)seq) string."""
title = _clean(record.id)
seq = _get_seq_string(record) # Catches sequence being None
assert "\t" not in title
assert "\n" not in title
assert "\r" not in title
assert "\t" not in seq
assert "\n" not in seq
assert "\r" not in seq
return "%s\t%s\n" % (title, seq)
def as_tab(record):
"""Return record as tab separated (id(tab)seq) string."""
title = _clean(record.id)
seq = _get_seq_string(record) # Catches sequence being None
assert "\t" not in title
assert "\n" not in title
assert "\r" not in title
assert "\t" not in seq
assert "\n" not in seq
assert "\r" not in seq
return "%s\t%s\n" % (title, seq)
def as_fasta_2line(record):
"""Turn a SeqRecord into a two-line FASTA formated string.
This is used internally by the SeqRecord's .format("fasta-2line")
method and by the SeqIO.write(..., ..., "fasta-2line") function.
"""
id = _clean(record.id)
description = _clean(record.description)
if description and description.split(None, 1)[0] == id:
# The description includes the id at the start
title = description
elif description:
title = "%s %s" % (id, description)
else:
title = id
assert "\n" not in title
assert "\r" not in title
data = _get_seq_string(record) # Catches sequence being None
assert "\n" not in data
assert "\r" not in data
return ">%s\n%s\n" % (title, data)
def as_fasta_2line(record):
"""Turn a SeqRecord into a two-line FASTA formated string.
This is used internally by the SeqRecord's .format("fasta-2line")
method and by the SeqIO.write(..., ..., "fasta-2line") function.
"""
id = _clean(record.id)
description = _clean(record.description)
if description and description.split(None, 1)[0] == id:
# The description includes the id at the start
title = description
elif description:
title = "%s %s" % (id, description)
else:
title = id
assert "\n" not in title
assert "\r" not in title
data = _get_seq_string(record) # Catches sequence being None
assert "\n" not in data
assert "\r" not in data
return ">%s\n%s\n" % (title, data)
