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# -*- coding: utf-8 -*-
from pairtools.lib import headerops
import pytest
def test_make_standard_header():
header = headerops.make_standard_pairsheader()
assert any([l.startswith("## pairs format") for l in header])
assert any([l.startswith("#shape") for l in header])
assert any([l.startswith("#columns") for l in header])
header = headerops.make_standard_pairsheader(
chromsizes=[("b", 100), ("c", 100), ("a", 100)]
)
assert sum([l.startswith("#chromsize") for l in header]) == 3
def test_samheaderops():
header = headerops.make_standard_pairsheader()
samheader = [
"@SQ\tSN:chr1\tLN:100",
"@SQ\tSN:chr2\tLN:100",
"@SQ\tSN:chr3\tLN:100",
"@PG\tID:bwa\tPN:bwa\tCL:bwa",
"@PG\tID:bwa-2\tPN:bwa\tCL:bwa\tPP:bwa",
]
header_with_sam = headerops.insert_samheader(header, samheader)
assert len(header_with_sam) == len(header) + len(samheader)
for l in samheader:
assert any([l2.startswith("#samheader") and l in l2 for l2 in header_with_sam])
# test adding new programs to the PG chain
header_extra_pg = headerops.append_new_pg(header_with_sam, ID="test", PN="test")
# test if all lines got transferred
assert all([(old_l in header_extra_pg) for old_l in header_with_sam])
# test if one PG got added
assert len(header_extra_pg) == len(header_with_sam) + 1
# test if the new PG has PP matching the ID of one of already existing PGs
new_l = [l for l in header_extra_pg if l not in header_with_sam][0]
pp = [f[3:] for f in new_l.split("\t") if f.startswith("PP:")][0]
assert (
len(
[
l
for l in header_extra_pg
if l.startswith("#samheader") and ("\tID:{}\t".format(pp) in l)
]
)
== 1
)
def test_merge_pairheaders():
headers = [["## pairs format v1.0"], ["## pairs format v1.0"]]
merged_header = headerops._merge_pairheaders(headers)
assert merged_header == headers[0]
headers = [["## pairs format v1.0", "#a"], ["## pairs format v1.0", "#b"]]
merged_header = headerops._merge_pairheaders(headers)
assert merged_header == ["## pairs format v1.0", "#a", "#b"]
headers = [
["## pairs format v1.0", "#chromsize: chr1 100", "#chromsize: chr2 200"],
["## pairs format v1.0", "#chromsize: chr1 100", "#chromsize: chr2 200"],
]
merged_header = headerops._merge_pairheaders(headers)
assert merged_header == headers[0]
def test_merge_different_pairheaders():
with pytest.raises(Exception):
headers = [["## pairs format v1.0"], ["## pairs format v1.1"]]
merged_header = headerops._merge_pairheaders(headers)
def test_force_merge_pairheaders():
headers = [
["## pairs format v1.0", "#chromsize: chr1 100"],
["## pairs format v1.0", "#chromsize: chr2 200"],
]
merged_header = headerops._merge_pairheaders(headers, force=True)
assert merged_header == [
"## pairs format v1.0",
"#chromsize: chr1 100",
"#chromsize: chr2 200",
]
def test_merge_samheaders():
headers = [
["@HD\tVN:1"],
["@HD\tVN:1"],
]
merged_header = headerops._merge_samheaders(headers)
assert merged_header == headers[0]
headers = [
[
"@HD\tVN:1",
"@SQ\tSN:chr1\tLN:100",
"@SQ\tSN:chr2\tLN:100",
],
[
"@HD\tVN:1",
"@SQ\tSN:chr1\tLN:100",
"@SQ\tSN:chr2\tLN:100",
],
]
merged_header = headerops._merge_samheaders(headers)
assert merged_header == headers[0]
headers = [
[
"@HD\tVN:1",
"@PG\tID:bwa\tPN:bwa\tPP:cat",
],
[
"@HD\tVN:1",
"@PG\tID:bwa\tPN:bwa\tPP:cat",
],
]
merged_header = headerops._merge_samheaders(headers)
print(merged_header)
assert merged_header == [
"@HD\tVN:1",
"@PG\tID:bwa-1\tPN:bwa\tPP:cat-1",
"@PG\tID:bwa-2\tPN:bwa\tPP:cat-2",
]
def test_merge_headers():
headers = [
[
"## pairs format v1.0",
"#samheader: @HD\tVN:1",
"#samheader: @SQ\tSN:chr1\tLN:100",
"#samheader: @SQ\tSN:chr2\tLN:100",
]
] * 2
merged_header = headerops.merge_headers(headers)
assert merged_header == headers[0]
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