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Issue 238 #239

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Jul 15, 2024
Merged

Issue 238 #239

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bfddf0c
closes #238
manulera Jul 9, 2024
ce62d6a
fix notebook
manulera Jul 9, 2024
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19 changes: 8 additions & 11 deletions src/pydna/dseqrecord.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -482,15 +482,12 @@ def format(self, f="gb"):

"""

s = super().format(f).strip()

if f in ("genbank", "gb"):
if self.circular:
return _pretty_str(s[:55] + "circular" + s[63:])
else:
return _pretty_str(s[:55] + "linear " + s[63:])
record = _copy.deepcopy(self)
if f in ("genbank", "gb") and self.circular:
record.annotations["topology"] = "circular"
else:
return _pretty_str(s).strip()
record.annotations["topology"] = "linear"
return _SeqRecord.format(record, f).strip()

def write(self, filename=None, f="gb"):
"""Writes the Dseqrecord to a file using the format f, which must
Expand Down Expand Up @@ -1114,7 +1111,7 @@ def orfs_to_features(self, minsize=300):
_SimpleLocation(x, y, strand=strand),
type="CDS",
qualifiers={
"note": f"{y-x}bp {(y-x)//3}aa",
"note": f"{y - x}bp {(y - x) // 3}aa",
"checksum": [orf.seguid() + " (DNA)", prt.seguid() + " (protein)"],
"codon_start": 1,
"transl_table": 11,
Expand Down Expand Up @@ -1153,8 +1150,8 @@ def figure(self, feature=0, highlight="\x1b[48;5;11m", plain="\x1b[0m"):

ovhg = self.seq.ovhg + len(self.seq.watson) - len(self.seq.crick)

w = f"{self.seq.ovhg*chr(32)}{self.seq.watson}{-ovhg*chr(32)}"
c = f"{-self.seq.ovhg*chr(32)}{self.seq.crick[::-1]}{ovhg*chr(32)}"
w = f"{self.seq.ovhg * chr(32)}{self.seq.watson}{-ovhg * chr(32)}"
c = f"{-self.seq.ovhg * chr(32)}{self.seq.crick[::-1]}{ovhg * chr(32)}"

if strand == 1:
s1, s2 = w, c
Expand Down
51 changes: 9 additions & 42 deletions tests/format_sequences.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": null,
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -14,7 +14,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -31,7 +31,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -41,7 +41,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -50,7 +50,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 5,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -85,18 +85,7 @@
{
"data": {
"text/plain": [
"LOCUS . 3 bp DNA linear UNK 20-DEC-2016\n",
"DEFINITION .\n",
"ACCESSION <unknown id>\n",
"VERSION <unknown id>\n",
"KEYWORDS .\n",
"SOURCE .\n",
" ORGANISM .\n",
" .\n",
"FEATURES Location/Qualifiers\n",
"ORIGIN\n",
" 1 aaa\n",
"//"
"'LOCUS . 3 bp DNA linear UNK 20-DEC-2016\\nDEFINITION .\\nACCESSION <unknown id>\\nVERSION <unknown id>\\nKEYWORDS .\\nSOURCE .\\n ORGANISM .\\n .\\nFEATURES Location/Qualifiers\\nORIGIN\\n 1 aaa\\n//'"
]
},
"execution_count": 6,
Expand All @@ -118,18 +107,7 @@
{
"data": {
"text/plain": [
"LOCUS name 3 bp DNA linear UNK 20-DEC-2016\n",
"DEFINITION description.\n",
"ACCESSION id\n",
"VERSION id\n",
"KEYWORDS .\n",
"SOURCE .\n",
" ORGANISM .\n",
" .\n",
"FEATURES Location/Qualifiers\n",
"ORIGIN\n",
" 1 aaa\n",
"//"
"'LOCUS name 3 bp DNA linear UNK 20-DEC-2016\\nDEFINITION description.\\nACCESSION id\\nVERSION id\\nKEYWORDS .\\nSOURCE .\\n ORGANISM .\\n .\\nFEATURES Location/Qualifiers\\nORIGIN\\n 1 aaa\\n//'"
]
},
"execution_count": 7,
Expand All @@ -151,18 +129,7 @@
{
"data": {
"text/plain": [
"LOCUS abc 3 bp DNA linear UNK 20-DEC-2016\n",
"DEFINITION abc.\n",
"ACCESSION abc\n",
"VERSION abc\n",
"KEYWORDS .\n",
"SOURCE .\n",
" ORGANISM .\n",
" .\n",
"FEATURES Location/Qualifiers\n",
"ORIGIN\n",
" 1 aaa\n",
"//"
"'LOCUS abc 3 bp DNA linear UNK 20-DEC-2016\\nDEFINITION abc.\\nACCESSION abc\\nVERSION abc\\nKEYWORDS .\\nSOURCE .\\n ORGANISM .\\n .\\nFEATURES Location/Qualifiers\\nORIGIN\\n 1 aaa\\n//'"
]
},
"execution_count": 8,
Expand Down Expand Up @@ -214,7 +181,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.8"
"version": "3.12.3"
}
},
"nbformat": 4,
Expand Down
56 changes: 34 additions & 22 deletions tests/test_module_dseqrecord.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@ def test_orfs():
for orf, ln in zip(s.orfs(1002), lens):
assert len(orf) == ln


def test_cas9():
from pydna.dseqrecord import Dseqrecord

Expand Down Expand Up @@ -434,6 +435,15 @@ def test_format():
s = Dseqrecord("GGATCC", circular=False)
s.format("fasta")

# A long sequence name is properly handled
s.name = "A" * 45
genbank_str = s.format("genbank")
locus_line = genbank_str.split("\n")[0]
assert (
locus_line
== "LOCUS AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6 bp DNA linear UNK 01-JAN-1980"
)


def test_write():
from unittest.mock import patch
Expand Down Expand Up @@ -673,7 +683,9 @@ def test_cut_add():

a = Dseqrecord("GGATCCtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtGGATCC").seq
b = a.cut(BamHI)[1]
c = Dseqrecord("nCTGCAGtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtGAATTCn").seq
c = Dseqrecord(
"nCTGCAGtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtGAATTCn"
).seq
f, d, l = c.cut((EcoRI, PstI))

pUC19 = read("pUC19.gb")
Expand Down Expand Up @@ -808,9 +820,9 @@ def test_Dseqrecord_cutting_adding_2():
for enz in enzymes:
for f in a:
b, c, d = f.cut(enz)
#print(b.seq.__repr__())
#print(c.seq.__repr__())
#print(d.seq.__repr__())
# print(b.seq.__repr__())
# print(c.seq.__repr__())
# print(d.seq.__repr__())
e = b + c + d
assert str(e.seq).lower() == str(f.seq).lower()

Expand Down Expand Up @@ -2264,26 +2276,26 @@ def find_feature_by_id(f: Dseqrecord, id: str) -> SeqFeature:
# Single cut case, check that features are transmitted correctly.
for strand in [1, -1, None]:
seq = Dseqrecord("acgtATGaatt", circular=True)
seq.features.append(SeqFeature(SimpleLocation(4, 7, strand), id='full_overlap'))
seq.features.append(SeqFeature(SimpleLocation(3, 7, strand), id='left_side'))
seq.features.append(SeqFeature(SimpleLocation(4, 8, strand), id='right_side'))
seq.features.append(SeqFeature(SimpleLocation(3, 10, strand), id='throughout'))
seq.features.append(SeqFeature(SimpleLocation(4, 7, strand), id="full_overlap"))
seq.features.append(SeqFeature(SimpleLocation(3, 7, strand), id="left_side"))
seq.features.append(SeqFeature(SimpleLocation(4, 8, strand), id="right_side"))
seq.features.append(SeqFeature(SimpleLocation(3, 10, strand), id="throughout"))
for shift in range(len(seq)):
seq_shifted = seq.shifted(shift)
cut_feature = find_feature_by_id(seq_shifted, 'full_overlap')
cut_feature = find_feature_by_id(seq_shifted, "full_overlap")
start, end = _location_boundaries(cut_feature.location)
# Cut leaving + and - overhangs in the feature full_overlap
for dummy_cut in (((start, -3), None), ((end, 3), None)):
open_seq = seq_shifted.apply_cut(dummy_cut, dummy_cut)
assert len(open_seq.features) == 4
new_locs = sorted(str(f.location) for f in open_seq.features)
assert str(open_seq.seq) == 'ATGaattacgtATG'
assert str(open_seq.seq) == "ATGaattacgtATG"
if strand == 1:
assert new_locs == sorted(['[0:3](+)', '[0:4](+)', '[11:14](+)', '[10:14](+)'])
assert new_locs == sorted(["[0:3](+)", "[0:4](+)", "[11:14](+)", "[10:14](+)"])
elif strand == -1:
assert new_locs == sorted(['[0:3](-)', '[0:4](-)', '[11:14](-)', '[10:14](-)'])
assert new_locs == sorted(["[0:3](-)", "[0:4](-)", "[11:14](-)", "[10:14](-)"])
if strand == None:
assert new_locs == sorted(['[0:3]', '[0:4]', '[11:14]', '[10:14]'])
assert new_locs == sorted(["[0:3]", "[0:4]", "[11:14]", "[10:14]"])


def test_apply_cut():
Expand All @@ -2298,26 +2310,26 @@ def find_feature_by_id(f: Dseqrecord, id: str) -> SeqFeature:
# Single cut case, check that features are transmitted correctly.
for strand in [1, -1, None]:
seq = Dseqrecord("acgtATGaatt", circular=True)
seq.features.append(SeqFeature(SimpleLocation(4, 7, strand), id='full_overlap'))
seq.features.append(SeqFeature(SimpleLocation(3, 7, strand), id='left_side'))
seq.features.append(SeqFeature(SimpleLocation(4, 8, strand), id='right_side'))
seq.features.append(SeqFeature(SimpleLocation(3, 10, strand), id='throughout'))
seq.features.append(SeqFeature(SimpleLocation(4, 7, strand), id="full_overlap"))
seq.features.append(SeqFeature(SimpleLocation(3, 7, strand), id="left_side"))
seq.features.append(SeqFeature(SimpleLocation(4, 8, strand), id="right_side"))
seq.features.append(SeqFeature(SimpleLocation(3, 10, strand), id="throughout"))
for shift in range(len(seq)):
seq_shifted = seq.shifted(shift)
cut_feature = find_feature_by_id(seq_shifted, 'full_overlap')
cut_feature = find_feature_by_id(seq_shifted, "full_overlap")
start, end = _location_boundaries(cut_feature.location)
# Cut leaving + and - overhangs in the feature full_overlap
for dummy_cut in (((start, -3), None), ((end, 3), None)):
open_seq = seq_shifted.apply_cut(dummy_cut, dummy_cut)
assert len(open_seq.features) == 4
new_locs = sorted(str(f.location) for f in open_seq.features)
assert str(open_seq.seq) == 'ATGaattacgtATG'
assert str(open_seq.seq) == "ATGaattacgtATG"
if strand == 1:
assert new_locs == sorted(['[0:3](+)', '[0:4](+)', '[11:14](+)', '[10:14](+)'])
assert new_locs == sorted(["[0:3](+)", "[0:4](+)", "[11:14](+)", "[10:14](+)"])
elif strand == -1:
assert new_locs == sorted(['[0:3](-)', '[0:4](-)', '[11:14](-)', '[10:14](-)'])
assert new_locs == sorted(["[0:3](-)", "[0:4](-)", "[11:14](-)", "[10:14](-)"])
if strand == None:
assert new_locs == sorted(['[0:3]', '[0:4]', '[11:14]', '[10:14]'])
assert new_locs == sorted(["[0:3]", "[0:4]", "[11:14]", "[10:14]"])


if __name__ == "__main__":
Expand Down
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