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LBMC
RMI2
fexi_splitter
Commits
0fbd47e2
Verified
Commit
0fbd47e2
authored
6 years ago
by
Laurent Modolo
Browse files
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tests: replace SeqIO by the Reads class
parent
7e59ad40
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src/rmi_splitter/tests/data_test.py
+14
-0
14 additions, 0 deletions
src/rmi_splitter/tests/data_test.py
src/rmi_splitter/tests/rmi_splitter_test.py
+61
-39
61 additions, 39 deletions
src/rmi_splitter/tests/rmi_splitter_test.py
with
75 additions
and
39 deletions
src/rmi_splitter/tests/data_test.py
+
14
−
0
View file @
0fbd47e2
...
@@ -6,6 +6,7 @@ This module provides data for the unitary tests for the rmi_splitter project
...
@@ -6,6 +6,7 @@ This module provides data for the unitary tests for the rmi_splitter project
"""
"""
from
io
import
StringIO
from
io
import
StringIO
from
Bio
import
SeqIO
from
Bio
import
SeqIO
from
..
import
rmi_splitter
# code to create yaml toy
# code to create yaml toy
"""
"""
...
@@ -68,37 +69,44 @@ TCGCCGCTGGTGTAGTGGTATCATGCGAGAAGAGATG\n\
...
@@ -68,37 +69,44 @@ TCGCCGCTGGTGTAGTGGTATCATGCGAGAAGAGATG\n\
+
\n\
+
\n\
AFFJJJJJJJFFJJJJJJJJJJJJJJFJJJJFFFFJ-
"
AFFJJJJJJJFFJJJJJJJJJJJJJJFJJJJFFFFJ-
"
SeqIO_single
=
SeqIO
.
read
(
StringIO
(
read_single
),
"
fastq
"
)
SeqIO_single
=
SeqIO
.
read
(
StringIO
(
read_single
),
"
fastq
"
)
Reads_single
=
rmi_splitter
.
Reads
(
StringIO
(
read_single
))
SeqIO_trim_single
=
SeqIO
.
read
(
StringIO
(
read_trim_single
),
"
fastq
"
)
SeqIO_trim_single
=
SeqIO
.
read
(
StringIO
(
read_trim_single
),
"
fastq
"
)
Reads_trim_single
=
rmi_splitter
.
Reads
(
StringIO
(
read_trim_single
))
umi_readnoumi
=
"
@K00201:182:HM3TMBBXX:6:2228:17706:1226 1:N:0:NCAGTG
\n\
umi_readnoumi
=
"
@K00201:182:HM3TMBBXX:6:2228:17706:1226 1:N:0:NCAGTG
\n\
TAGTGCCTCGCCGCTGGTGTAGTGGTATCATGCGAGAAGAGATG
\n\
TAGTGCCTCGCCGCTGGTGTAGTGGTATCATGCGAGAAGAGATG
\n\
+
\n\
+
\n\
JJJJJAAAFFJJJJJJJFFJJJJJJJJJJJJJJFJJJJFFFFJ-
"
JJJJJAAAFFJJJJJJJFFJJJJJJJJJJJJJJFJJJJFFFFJ-
"
SeqIO_single_noumi
=
SeqIO
.
read
(
StringIO
(
umi_readnoumi
),
"
fastq
"
)
SeqIO_single_noumi
=
SeqIO
.
read
(
StringIO
(
umi_readnoumi
),
"
fastq
"
)
Reads_single_noumi
=
rmi_splitter
.
Reads
(
StringIO
(
umi_readnoumi
))
umi_readnoRT
=
"
@K00201:182:HM3TMBBXX:6:2228:17706:1226 1:N:0:NCAGTG
\n\
umi_readnoRT
=
"
@K00201:182:HM3TMBBXX:6:2228:17706:1226 1:N:0:NCAGTG
\n\
NTTCTCTCGCCGCTGGTGTAGTGGTATCATGCGAGAAGAGATG
\n\
NTTCTCTCGCCGCTGGTGTAGTGGTATCATGCGAGAAGAGATG
\n\
+
\n\
+
\n\
#AAFFJAFFJJJJJJJFFJJJJJJJJJJJJJJFJJJJFFFFJ-
"
#AAFFJAFFJJJJJJJFFJJJJJJJJJJJJJJFJJJJFFFFJ-
"
SeqIO_single_noRT
=
SeqIO
.
read
(
StringIO
(
umi_readnoRT
),
"
fastq
"
)
SeqIO_single_noRT
=
SeqIO
.
read
(
StringIO
(
umi_readnoRT
),
"
fastq
"
)
Reads_single_noRT
=
rmi_splitter
.
Reads
(
StringIO
(
umi_readnoRT
))
umi_read
=
"
@K00201:182:HM3TMBBXX:6:2228:17706:1226_NTTCTC 1:N:0:NCAGTG
\n\
umi_read
=
"
@K00201:182:HM3TMBBXX:6:2228:17706:1226_NTTCTC 1:N:0:NCAGTG
\n\
NTTCTCTAGTGCCTCGCCGCTGGTGTAGTGGTATCATGCGAGAAGAGATG
\n\
NTTCTCTAGTGCCTCGCCGCTGGTGTAGTGGTATCATGCGAGAAGAGATG
\n\
+
\n\
+
\n\
#AAFFJJJJJJAAAFFJJJJJJJFFJJJJJJJJJJJJJJFJJJJFFFFJ-
"
#AAFFJJJJJJAAAFFJJJJJJJFFJJJJJJJJJJJJJJFJJJJFFFFJ-
"
SeqIO_umi_single
=
SeqIO
.
read
(
StringIO
(
umi_read
),
"
fastq
"
)
SeqIO_umi_single
=
SeqIO
.
read
(
StringIO
(
umi_read
),
"
fastq
"
)
Reads_umi_single
=
rmi_splitter
.
Reads
(
StringIO
(
umi_read
))
umi_readnoumi
=
"
@K00201:182:HM3TMBBXX:6:2228:17706:1226_NTTCTC 1:N:0:NCAGTG
\n\
umi_readnoumi
=
"
@K00201:182:HM3TMBBXX:6:2228:17706:1226_NTTCTC 1:N:0:NCAGTG
\n\
TAGTGCCTCGCCGCTGGTGTAGTGGTATCATGCGAGAAGAGATG
\n\
TAGTGCCTCGCCGCTGGTGTAGTGGTATCATGCGAGAAGAGATG
\n\
+
\n\
+
\n\
JJJJJAAAFFJJJJJJJFFJJJJJJJJJJJJJJFJJJJFFFFJ-
"
JJJJJAAAFFJJJJJJJFFJJJJJJJJJJJJJJFJJJJFFFFJ-
"
SeqIO_umi_single_noumi
=
SeqIO
.
read
(
StringIO
(
umi_readnoumi
),
"
fastq
"
)
SeqIO_umi_single_noumi
=
SeqIO
.
read
(
StringIO
(
umi_readnoumi
),
"
fastq
"
)
Reads_umi_single_noumi
=
rmi_splitter
.
Reads
(
StringIO
(
umi_readnoumi
))
umi_readnoRT
=
"
@K00201:182:HM3TMBBXX:6:2228:17706:1226_NTTCTC 1:N:0:NCAGTG
\n\
umi_readnoRT
=
"
@K00201:182:HM3TMBBXX:6:2228:17706:1226_NTTCTC 1:N:0:NCAGTG
\n\
NTTCTCTCGCCGCTGGTGTAGTGGTATCATGCGAGAAGAGATG
\n\
NTTCTCTCGCCGCTGGTGTAGTGGTATCATGCGAGAAGAGATG
\n\
+
\n\
+
\n\
#AAFFJAFFJJJJJJJFFJJJJJJJJJJJJJJFJJJJFFFFJ-
"
#AAFFJAFFJJJJJJJFFJJJJJJJJJJJJJJFJJJJFFFFJ-
"
SeqIO_umi_single_noRT
=
SeqIO
.
read
(
StringIO
(
umi_readnoRT
),
"
fastq
"
)
SeqIO_umi_single_noRT
=
SeqIO
.
read
(
StringIO
(
umi_readnoRT
),
"
fastq
"
)
Reads_umi_single_noRT
=
rmi_splitter
.
Reads
(
StringIO
(
umi_readnoRT
))
"""
"""
paired-end
paired-end
...
@@ -166,6 +174,9 @@ NCAACA\n\
...
@@ -166,6 +174,9 @@ NCAACA\n\
SeqIO_paired_1
=
SeqIO
.
read
(
StringIO
(
read_paired_1
),
"
fastq
"
)
SeqIO_paired_1
=
SeqIO
.
read
(
StringIO
(
read_paired_1
),
"
fastq
"
)
SeqIO_paired_2
=
SeqIO
.
read
(
StringIO
(
read_paired_2
),
"
fastq
"
)
SeqIO_paired_2
=
SeqIO
.
read
(
StringIO
(
read_paired_2
),
"
fastq
"
)
SeqIO_paired_3
=
SeqIO
.
read
(
StringIO
(
read_paired_3
),
"
fastq
"
)
SeqIO_paired_3
=
SeqIO
.
read
(
StringIO
(
read_paired_3
),
"
fastq
"
)
Reads_paired_1
=
rmi_splitter
.
Reads
(
StringIO
(
read_paired_1
))
Reads_paired_2
=
rmi_splitter
.
Reads
(
StringIO
(
read_paired_2
))
Reads_paired_3
=
rmi_splitter
.
Reads
(
StringIO
(
read_paired_3
))
RT_barcode_paired
=
'
TAGTGCC
'
RT_barcode_paired
=
'
TAGTGCC
'
PCR_barcode_paired
=
'
NCAACA
'
PCR_barcode_paired
=
'
NCAACA
'
...
@@ -186,3 +197,6 @@ results_read_paired_3 = "@GWNJ-0842:360:GW1809071399:6:1101:18243:1625 2:N:0:1\n
...
@@ -186,3 +197,6 @@ results_read_paired_3 = "@GWNJ-0842:360:GW1809071399:6:1101:18243:1625 2:N:0:1\n
SeqIO_results_paired_1
=
SeqIO
.
read
(
StringIO
(
read_paired_1
),
"
fastq
"
)
SeqIO_results_paired_1
=
SeqIO
.
read
(
StringIO
(
read_paired_1
),
"
fastq
"
)
SeqIO_results_paired_2
=
SeqIO
.
read
(
StringIO
(
read_paired_2
),
"
fastq
"
)
SeqIO_results_paired_2
=
SeqIO
.
read
(
StringIO
(
read_paired_2
),
"
fastq
"
)
SeqIO_results_paired_3
=
SeqIO
.
read
(
StringIO
(
read_paired_3
),
"
fastq
"
)
SeqIO_results_paired_3
=
SeqIO
.
read
(
StringIO
(
read_paired_3
),
"
fastq
"
)
Reads_results_paired_1
=
rmi_splitter
.
Reads
(
StringIO
(
read_paired_1
))
Reads_results_paired_2
=
rmi_splitter
.
Reads
(
StringIO
(
read_paired_2
))
Reads_results_paired_3
=
rmi_splitter
.
Reads
(
StringIO
(
read_paired_3
))
This diff is collapsed.
Click to expand it.
src/rmi_splitter/tests/rmi_splitter_test.py
+
61
−
39
View file @
0fbd47e2
...
@@ -197,9 +197,10 @@ class ReadsReadTest(unittest.TestCase):
...
@@ -197,9 +197,10 @@ class ReadsReadTest(unittest.TestCase):
"""
"""
test extraction of umi
test extraction of umi
"""
"""
reads_test
=
copy
.
deepcopy
(
data_test
.
Reads_single
)
self
.
assertEqual
(
self
.
assertEqual
(
rmi_splitter
.
extract_barcode_pos
(
rmi_splitter
.
extract_barcode_pos
(
read
=
data_test
.
SeqIO_single
,
read
s
=
reads_test
,
start
=
0
,
start
=
0
,
stop
=
5
,
stop
=
5
,
header
=
False
)[
'
seq
'
],
header
=
False
)[
'
seq
'
],
...
@@ -210,9 +211,10 @@ class ReadsReadTest(unittest.TestCase):
...
@@ -210,9 +211,10 @@ class ReadsReadTest(unittest.TestCase):
"""
"""
test extraction of umi
test extraction of umi
"""
"""
reads_test
=
copy
.
deepcopy
(
data_test
.
Reads_single
)
self
.
assertEqual
(
self
.
assertEqual
(
rmi_splitter
.
extract_barcode_pos
(
rmi_splitter
.
extract_barcode_pos
(
read
=
data_test
.
SeqIO_single
,
read
s
=
reads_test
,
start
=
1
,
start
=
1
,
stop
=
3
,
stop
=
3
,
header
=
True
)[
'
seq
'
],
header
=
True
)[
'
seq
'
],
...
@@ -223,9 +225,10 @@ class ReadsReadTest(unittest.TestCase):
...
@@ -223,9 +225,10 @@ class ReadsReadTest(unittest.TestCase):
"""
"""
test extraction of RT barcode from position
test extraction of RT barcode from position
"""
"""
reads_test
=
copy
.
deepcopy
(
data_test
.
Reads_single
)
self
.
assertEqual
(
self
.
assertEqual
(
rmi_splitter
.
extract_barcode_pos
(
rmi_splitter
.
extract_barcode_pos
(
read
=
data_test
.
SeqIO_single
,
read
s
=
reads_test
,
start
=
6
,
start
=
6
,
stop
=
13
,
stop
=
13
,
header
=
False
)[
'
seq
'
],
header
=
False
)[
'
seq
'
],
...
@@ -236,8 +239,9 @@ class ReadsReadTest(unittest.TestCase):
...
@@ -236,8 +239,9 @@ class ReadsReadTest(unittest.TestCase):
"""
"""
test extraction of PCR barcode from position
test extraction of PCR barcode from position
"""
"""
reads_test
=
copy
.
deepcopy
(
data_test
.
Reads_single
)
self
.
assertEqual
(
self
.
assertEqual
(
rmi_splitter
.
extract_barcode_pos
(
data_test
.
SeqIO_single
,
rmi_splitter
.
extract_barcode_pos
(
reads_test
,
0
,
0
,
5
,
5
,
True
)[
'
seq
'
],
True
)[
'
seq
'
],
...
@@ -248,9 +252,10 @@ class ReadsReadTest(unittest.TestCase):
...
@@ -248,9 +252,10 @@ class ReadsReadTest(unittest.TestCase):
"""
"""
test extraction of RT barcode from config
test extraction of RT barcode from config
"""
"""
reads_test
=
copy
.
deepcopy
(
data_test
.
Reads_single
)
self
.
assertEqual
(
self
.
assertEqual
(
rmi_splitter
.
extract_barcode
(
rmi_splitter
.
extract_barcode
(
data_test
.
SeqIO_single
,
reads_test
,
rmi_splitter
.
load_yaml
(
rmi_splitter
.
load_yaml
(
path
=
"
rmi_splitter/tests/data/toy_file.yaml
"
),
path
=
"
rmi_splitter/tests/data/toy_file.yaml
"
),
"
RT
"
,
verbose
=
True
)[
'
seq
'
],
"
RT
"
,
verbose
=
True
)[
'
seq
'
],
...
@@ -261,9 +266,10 @@ class ReadsReadTest(unittest.TestCase):
...
@@ -261,9 +266,10 @@ class ReadsReadTest(unittest.TestCase):
"""
"""
test extraction of PCR barcode from config
test extraction of PCR barcode from config
"""
"""
reads_test
=
copy
.
deepcopy
(
data_test
.
Reads_single
)
self
.
assertEqual
(
self
.
assertEqual
(
rmi_splitter
.
extract_barcode
(
rmi_splitter
.
extract_barcode
(
data_test
.
SeqIO_single
,
reads_test
,
rmi_splitter
.
load_yaml
(
rmi_splitter
.
load_yaml
(
path
=
"
rmi_splitter/tests/data/toy_file.yaml
"
),
path
=
"
rmi_splitter/tests/data/toy_file.yaml
"
),
"
PCR
"
)[
'
seq
'
],
"
PCR
"
)[
'
seq
'
],
...
@@ -292,90 +298,98 @@ class ModifyReadTest(unittest.TestCase):
...
@@ -292,90 +298,98 @@ class ModifyReadTest(unittest.TestCase):
"""
"""
test writting umi in header
test writting umi in header
"""
"""
reads_test
=
copy
.
deepcopy
(
data_test
.
Reads_single
)
self
.
assertEqual
(
self
.
assertEqual
(
rmi_splitter
.
write_umi_in_header
(
rmi_splitter
.
write_umi_in_header
(
data_test
.
SeqIO_single
,
data_test
.
CONFIG_TOY
,
'
UMI
'
).
id
,
reads_test
,
data_test
.
CONFIG_TOY
,
'
UMI
'
).
header
,
data_test
.
SeqIO
_umi_single
.
id
data_test
.
Reads
_umi_single
.
header
)
)
def
test_remove_barcode_umi_pos
(
self
):
def
test_remove_barcode_umi_pos
(
self
):
"""
"""
test removing umi with pos
test removing umi with pos
"""
"""
reads_test
=
copy
.
deepcopy
(
data_test
.
Reads_single
)
reads_test2
=
copy
.
deepcopy
(
data_test
.
Reads_single
)
reads_test3
=
copy
.
deepcopy
(
data_test
.
Reads_single
)
self
.
assertEqual
(
self
.
assertEqual
(
rmi_splitter
.
remove_barcode_pos
(
rmi_splitter
.
remove_barcode_pos
(
seq
=
data_test
.
SeqIO_single
,
reads
=
reads_test
,
start
=
0
,
start
=
0
,
stop
=
5
,
stop
=
5
,
header
=
False
).
seq
,
header
=
False
).
seq
,
data_test
.
SeqIO
_single_noumi
.
seq
data_test
.
Reads
_single_noumi
.
seq
)
)
self
.
assertEqual
(
self
.
assertEqual
(
rmi_splitter
.
remove_barcode_pos
(
rmi_splitter
.
remove_barcode_pos
(
seq
=
data_test
.
SeqIO_single
,
reads
=
reads_test2
,
start
=
0
,
start
=
0
,
stop
=
5
,
stop
=
5
,
header
=
False
).
description
,
header
=
False
).
header
,
data_test
.
SeqIO
_single_noumi
.
description
data_test
.
Reads
_single_noumi
.
header
)
)
self
.
assertEqual
(
self
.
assertEqual
(
rmi_splitter
.
remove_barcode_pos
(
rmi_splitter
.
remove_barcode_pos
(
seq
=
data_test
.
SeqIO_single
,
reads
=
reads_test3
,
start
=
0
,
start
=
0
,
stop
=
5
,
stop
=
5
,
header
=
False
).
letter_annotations
[
'
phred_quality
'
]
,
header
=
False
).
qual
,
data_test
.
SeqIO
_single_noumi
.
letter_annotations
[
'
phred_quality
'
]
data_test
.
Reads
_single_noumi
.
qual
)
)
def
test_remove_barcode_rt_pos_seq
(
self
):
def
test_remove_barcode_rt_pos_seq
(
self
):
"""
"""
test removing rt with pos
test removing rt with pos
"""
"""
reads_test
=
copy
.
deepcopy
(
data_test
.
Reads_single
)
self
.
assertEqual
(
self
.
assertEqual
(
rmi_splitter
.
remove_barcode_pos
(
rmi_splitter
.
remove_barcode_pos
(
seq
=
data_test
.
SeqIO_single
,
reads
=
reads_test
,
start
=
6
,
start
=
6
,
stop
=
13
,
stop
=
13
,
header
=
False
).
seq
,
header
=
False
).
seq
,
data_test
.
SeqIO
_single_noRT
.
seq
data_test
.
Reads
_single_noRT
.
seq
)
)
def
test_remove_barcode_rt_pos_description
(
self
):
def
test_remove_barcode_rt_pos_description
(
self
):
"""
"""
test removing rt with pos
test removing rt with pos
"""
"""
reads_test
=
copy
.
deepcopy
(
data_test
.
Reads_single
)
self
.
assertEqual
(
self
.
assertEqual
(
rmi_splitter
.
remove_barcode_pos
(
rmi_splitter
.
remove_barcode_pos
(
seq
=
data_test
.
SeqIO_single
,
reads
=
reads_test
,
start
=
6
,
start
=
6
,
stop
=
13
,
stop
=
13
,
header
=
False
).
description
,
header
=
False
).
header
,
data_test
.
SeqIO
_single_noRT
.
description
data_test
.
Reads
_single_noRT
.
header
)
)
def
test_remove_barcode_rt_pos_qual
(
self
):
def
test_remove_barcode_rt_pos_qual
(
self
):
"""
"""
test removing rt with pos
test removing rt with pos
"""
"""
reads_test
=
copy
.
deepcopy
(
data_test
.
Reads_single
)
self
.
assertEqual
(
self
.
assertEqual
(
rmi_splitter
.
remove_barcode_pos
(
rmi_splitter
.
remove_barcode_pos
(
seq
=
data_test
.
SeqIO_single
,
reads
=
reads_test
,
start
=
6
,
start
=
6
,
stop
=
13
,
stop
=
13
,
header
=
False
).
letter_annotations
[
'
phred_quality
'
]
,
header
=
False
).
qual
,
data_test
.
SeqIO
_single_noRT
.
letter_annotations
[
'
phred_quality
'
]
data_test
.
Reads
_single_noRT
.
qual
)
)
def
test_remove_barcode_pos_header
(
self
):
def
test_remove_barcode_pos_header
(
self
):
"""
"""
test remove of umi
test remove of umi
"""
"""
reads_test
=
copy
.
deepcopy
(
data_test
.
Reads_single
)
self
.
assertEqual
(
self
.
assertEqual
(
rmi_splitter
.
remove_barcode_pos
(
rmi_splitter
.
remove_barcode_pos
(
seq
=
data_test
.
SeqIO_single
,
reads
=
reads_test
,
start
=
1
,
start
=
1
,
stop
=
3
,
stop
=
3
,
header
=
True
).
description
,
header
=
True
).
header
,
"
K00201:182:HM3TMBBXX:6:2228:17706:1226 1:N:0:NCG
"
"
K00201:182:HM3TMBBXX:6:2228:17706:1226 1:N:0:NCG
"
)
)
...
@@ -383,13 +397,14 @@ class ModifyReadTest(unittest.TestCase):
...
@@ -383,13 +397,14 @@ class ModifyReadTest(unittest.TestCase):
"""
"""
test removing rt with config
test removing rt with config
"""
"""
reads_test
=
copy
.
deepcopy
(
data_test
.
Reads_single
)
self
.
assertEqual
(
self
.
assertEqual
(
rmi_splitter
.
remove_barcode
(
rmi_splitter
.
remove_barcode
(
data_test
.
SeqIO_single
,
reads_test
,
data_test
.
CONFIG_TOY
,
data_test
.
CONFIG_TOY
,
"
RT
"
"
RT
"
).
seq
,
).
seq
,
data_test
.
SeqIO
_single_noRT
.
seq
data_test
.
Reads
_single_noRT
.
seq
)
)
def
test_update_config
(
self
):
def
test_update_config
(
self
):
...
@@ -411,9 +426,11 @@ class ModifyReadTest(unittest.TestCase):
...
@@ -411,9 +426,11 @@ class ModifyReadTest(unittest.TestCase):
barcode_dic
=
rmi_splitter
.
create_barcode_dictionaries
(
barcode_dic
=
rmi_splitter
.
create_barcode_dictionaries
(
config
=
config
config
=
config
)
)
reads_test
=
copy
.
deepcopy
(
data_test
.
Reads_single
)
reads_test2
=
copy
.
deepcopy
(
data_test
.
Reads_single
)
self
.
assertEqual
(
self
.
assertEqual
(
rmi_splitter
.
match_barcode
(
rmi_splitter
.
match_barcode
(
read
=
data_test
.
SeqIO_single
,
read
s
=
reads_test
,
config
=
rmi_splitter
.
update_positions
(
config
=
rmi_splitter
.
update_positions
(
config
=
data_test
.
CONFIG_TOY
,
config
=
data_test
.
CONFIG_TOY
,
adaptator
=
"
UMI
"
adaptator
=
"
UMI
"
...
@@ -422,7 +439,7 @@ class ModifyReadTest(unittest.TestCase):
...
@@ -422,7 +439,7 @@ class ModifyReadTest(unittest.TestCase):
barcode_dictionary
=
barcode_dic
barcode_dictionary
=
barcode_dic
),
),
rmi_splitter
.
match_barcode
(
rmi_splitter
.
match_barcode
(
read
=
data_test
.
SeqIO_single
,
read
s
=
reads_test2
,
config
=
data_test
.
CONFIG_TOY
,
config
=
data_test
.
CONFIG_TOY
,
adaptator
=
"
PCR
"
,
adaptator
=
"
PCR
"
,
barcode_dictionary
=
barcode_dic
barcode_dictionary
=
barcode_dic
...
@@ -433,12 +450,13 @@ class ModifyReadTest(unittest.TestCase):
...
@@ -433,12 +450,13 @@ class ModifyReadTest(unittest.TestCase):
"""
"""
test removing rt with config
test removing rt with config
"""
"""
reads_test
=
copy
.
deepcopy
(
data_test
.
Reads_single
)
self
.
assertEqual
(
self
.
assertEqual
(
rmi_splitter
.
remove_barcodes
(
rmi_splitter
.
remove_barcodes
(
data_test
.
SeqIO_single
,
reads_test
,
data_test
.
CONFIG_TOY
,
data_test
.
CONFIG_TOY
,
).
seq
,
).
seq
,
data_test
.
SeqIO
_trim_single
.
seq
data_test
.
Reads
_trim_single
.
seq
)
)
...
@@ -455,9 +473,10 @@ class SeachBarcodeTest(unittest.TestCase):
...
@@ -455,9 +473,10 @@ class SeachBarcodeTest(unittest.TestCase):
barcode_dic
=
rmi_splitter
.
create_barcode_dictionaries
(
barcode_dic
=
rmi_splitter
.
create_barcode_dictionaries
(
config
=
config
config
=
config
)
)
reads_test
=
copy
.
deepcopy
(
data_test
.
Reads_single
)
self
.
assertEqual
(
self
.
assertEqual
(
rmi_splitter
.
match_barcode
(
rmi_splitter
.
match_barcode
(
read
=
data_test
.
SeqIO_single
,
read
s
=
reads_test
,
config
=
config
,
config
=
config
,
adaptator
=
"
PCR
"
,
adaptator
=
"
PCR
"
,
barcode_dictionary
=
barcode_dic
barcode_dictionary
=
barcode_dic
...
@@ -474,9 +493,10 @@ class SeachBarcodeTest(unittest.TestCase):
...
@@ -474,9 +493,10 @@ class SeachBarcodeTest(unittest.TestCase):
barcode_dic
=
rmi_splitter
.
create_barcode_dictionaries
(
barcode_dic
=
rmi_splitter
.
create_barcode_dictionaries
(
config
=
config
config
=
config
)
)
reads_test
=
copy
.
deepcopy
(
data_test
.
Reads_single
)
try
:
try
:
rmi_splitter
.
match_barcode
(
rmi_splitter
.
match_barcode
(
read
=
data_test
.
SeqIO_single
,
read
s
=
reads_test
,
config
=
config
,
config
=
config
,
adaptator
=
"
PCT
"
,
adaptator
=
"
PCT
"
,
barcode_dictionary
=
barcode_dic
,
barcode_dictionary
=
barcode_dic
,
...
@@ -496,9 +516,10 @@ class SeachBarcodeTest(unittest.TestCase):
...
@@ -496,9 +516,10 @@ class SeachBarcodeTest(unittest.TestCase):
barcode_dic
=
rmi_splitter
.
create_barcode_dictionaries
(
barcode_dic
=
rmi_splitter
.
create_barcode_dictionaries
(
config
=
config
config
=
config
)
)
reads_test
=
copy
.
deepcopy
(
data_test
.
Reads_single
)
self
.
assertEqual
(
self
.
assertEqual
(
rmi_splitter
.
match_barcodes
(
rmi_splitter
.
match_barcodes
(
read
=
data_test
.
SeqIO_single
,
read
s
=
reads_test
,
config
=
config
,
config
=
config
,
barcode_dictionary
=
barcode_dic
barcode_dictionary
=
barcode_dic
),
),
...
@@ -558,9 +579,10 @@ class HandleFastqTest(unittest.TestCase):
...
@@ -558,9 +579,10 @@ class HandleFastqTest(unittest.TestCase):
config
=
rmi_splitter
.
load_yaml
(
config
=
rmi_splitter
.
load_yaml
(
path
=
"
rmi_splitter/tests/data/toy_file.yaml
"
)
path
=
"
rmi_splitter/tests/data/toy_file.yaml
"
)
)
)
reads_test
=
copy
.
deepcopy
(
data_test
.
Reads_single
)
self
.
assertEqual
(
self
.
assertEqual
(
rmi_splitter
.
assign_reads
(
rmi_splitter
.
assign_reads
(
reads_list
=
[
data_test
.
SeqIO_single
],
reads_list
=
[
reads_test
],
config
=
rmi_splitter
.
load_yaml
(
config
=
rmi_splitter
.
load_yaml
(
path
=
"
rmi_splitter/tests/data/toy_file.yaml
"
),
path
=
"
rmi_splitter/tests/data/toy_file.yaml
"
),
barcode_dictionary
=
barcode_dic
,
barcode_dictionary
=
barcode_dic
,
...
@@ -579,9 +601,9 @@ class HandleFastqTest(unittest.TestCase):
...
@@ -579,9 +601,9 @@ class HandleFastqTest(unittest.TestCase):
)
)
self
.
assertEqual
(
self
.
assertEqual
(
rmi_splitter
.
assign_reads
(
rmi_splitter
.
assign_reads
(
reads_list
=
[
data_test
.
SeqIO
_paired_1
,
reads_list
=
[
data_test
.
Reads
_paired_1
,
data_test
.
SeqIO
_paired_2
,
data_test
.
Reads
_paired_2
,
data_test
.
SeqIO
_paired_3
],
data_test
.
Reads
_paired_3
],
config
=
rmi_splitter
.
load_yaml
(
config
=
rmi_splitter
.
load_yaml
(
path
=
"
rmi_splitter/tests/data/toy_file_paired.yaml
"
),
path
=
"
rmi_splitter/tests/data/toy_file_paired.yaml
"
),
barcode_dictionary
=
barcode_dic
,
barcode_dictionary
=
barcode_dic
,
...
...
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