In [1]:
import sys
In [2]:
import re
In [3]:
import glob
In [4]:
sys.path.append('./support_files/')
In [5]:
import aggregate_mummer_results as amr
In [6]:
d = amr.load_one_mummer_result('./mummer_results/Methylotenera_mobilis-123/Methylotenera_mobilis-123_to_Methylotenera_mobilis-63.tsv')
d.head()
Out[6]:
TAGS (ref)
TAGS (query)
LEN 1
LEN 2
LEN R
LEN Q
COV R
COV Q
% IDY
mummer file
query name
ref name
ref id
query id
ref contig
query contig
0
Ga0081640_1009
Ga0081608_1011
99
99
10097
14044
0.98
0.70
98.99
Methylotenera_mobilis-123/Methylotenera_mobili...
Methylotenera_mobilis-123
Methylotenera_mobilis-63
Ga0081640
Ga0081608
1009
1011
1
Ga0081640_1009
Ga0081608_1231
8194
8194
10097
8194
81.15
100.00
98.74
Methylotenera_mobilis-123/Methylotenera_mobili...
Methylotenera_mobilis-123
Methylotenera_mobilis-63
Ga0081640
Ga0081608
1009
1231
2
Ga0081640_1010
Ga0081608_1194
2168
2168
11116
4579
19.50
47.35
99.54
Methylotenera_mobilis-123/Methylotenera_mobili...
Methylotenera_mobilis-123
Methylotenera_mobilis-63
Ga0081640
Ga0081608
1010
1194
3
Ga0081640_1010
Ga0081608_1203
6599
6599
11116
6599
59.36
100.00
97.95
Methylotenera_mobilis-123/Methylotenera_mobili...
Methylotenera_mobilis-123
Methylotenera_mobilis-63
Ga0081640
Ga0081608
1010
1203
4
Ga0081640_1014
Ga0081608_1233
99
99
8878
4749
1.12
2.08
100.00
Methylotenera_mobilis-123/Methylotenera_mobili...
Methylotenera_mobilis-123
Methylotenera_mobilis-63
Ga0081640
Ga0081608
1014
1233
In [7]:
d['mummer file'][0]
Out[7]:
'Methylotenera_mobilis-123/Methylotenera_mobilis-123_to_Methylotenera_mobilis-63.tsv'
In [8]:
amr.load_individual_bin_summaries().head()
Out[8]:
bin path
bp
category
contigs
id
name
0
/work/meta4_bins/data/bins/fauzi/bins/Methylob...
5336445
fauzi
126
Ga0081657
Methylobacter-98
1
/work/meta4_bins/data/bins/fauzi/bins/Methylop...
2920449
fauzi
17
Ga0081650
Methylophilus_methylotrophus-79
2
/work/meta4_bins/data/bins/fauzi/bins/Opitutae...
3988942
fauzi
24
Ga0081625
Opitutae-40
3
/work/meta4_bins/data/bins/fauzi/bins/Methylot...
2438723
fauzi
208
Ga0081647
Methylotenera_mobilis-76-1
4
/work/meta4_bins/data/bins/fauzi/bins/Methylot...
3001309
fauzi
409
Ga0081649
Methylotenera_mobilis-76-2
In [9]:
amr.prepare_result('./mummer_results/Methylotenera_mobilis-123/Methylotenera_mobilis-123_to_Methylotenera_mobilis-63.tsv')
Out[9]:
TAGS (ref)
TAGS (query)
LEN 1
LEN 2
LEN R
LEN Q
COV R
COV Q
% IDY
mummer file
...
ref id_x
query id_x
ref contig
query contig
query bp
query contigs
query id_y
ref bp
ref contigs
ref id_y
0
Ga0081640_1009
Ga0081608_1011
99
99
10097
14044
0.98
0.70
98.99
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1009
1011
2204204
300
Ga0081608
1645626
291
Ga0081640
1
Ga0081640_1009
Ga0081608_1011
99
99
10097
14044
0.98
0.70
98.99
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1009
1011
2204204
300
Ga0081608
1645626
291
Ga0081640
2
Ga0081640_1009
Ga0081608_1011
99
99
10097
14044
0.98
0.70
98.99
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1009
1011
2204204
300
Ga0081608
1645626
291
Ga0081640
3
Ga0081640_1009
Ga0081608_1011
99
99
10097
14044
0.98
0.70
98.99
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1009
1011
2204204
300
Ga0081608
1645626
291
Ga0081640
4
Ga0081640_1009
Ga0081608_1231
8194
8194
10097
8194
81.15
100.00
98.74
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1009
1231
2204204
300
Ga0081608
1645626
291
Ga0081640
5
Ga0081640_1009
Ga0081608_1231
8194
8194
10097
8194
81.15
100.00
98.74
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1009
1231
2204204
300
Ga0081608
1645626
291
Ga0081640
6
Ga0081640_1009
Ga0081608_1231
8194
8194
10097
8194
81.15
100.00
98.74
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1009
1231
2204204
300
Ga0081608
1645626
291
Ga0081640
7
Ga0081640_1009
Ga0081608_1231
8194
8194
10097
8194
81.15
100.00
98.74
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1009
1231
2204204
300
Ga0081608
1645626
291
Ga0081640
8
Ga0081640_1010
Ga0081608_1194
2168
2168
11116
4579
19.50
47.35
99.54
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1010
1194
2204204
300
Ga0081608
1645626
291
Ga0081640
9
Ga0081640_1010
Ga0081608_1194
2168
2168
11116
4579
19.50
47.35
99.54
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1010
1194
2204204
300
Ga0081608
1645626
291
Ga0081640
10
Ga0081640_1010
Ga0081608_1194
2168
2168
11116
4579
19.50
47.35
99.54
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1010
1194
2204204
300
Ga0081608
1645626
291
Ga0081640
11
Ga0081640_1010
Ga0081608_1194
2168
2168
11116
4579
19.50
47.35
99.54
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1010
1194
2204204
300
Ga0081608
1645626
291
Ga0081640
12
Ga0081640_1010
Ga0081608_1203
6599
6599
11116
6599
59.36
100.00
97.95
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1010
1203
2204204
300
Ga0081608
1645626
291
Ga0081640
13
Ga0081640_1010
Ga0081608_1203
6599
6599
11116
6599
59.36
100.00
97.95
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1010
1203
2204204
300
Ga0081608
1645626
291
Ga0081640
14
Ga0081640_1010
Ga0081608_1203
6599
6599
11116
6599
59.36
100.00
97.95
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1010
1203
2204204
300
Ga0081608
1645626
291
Ga0081640
15
Ga0081640_1010
Ga0081608_1203
6599
6599
11116
6599
59.36
100.00
97.95
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1010
1203
2204204
300
Ga0081608
1645626
291
Ga0081640
16
Ga0081640_1014
Ga0081608_1233
99
99
8878
4749
1.12
2.08
100.00
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1014
1233
2204204
300
Ga0081608
1645626
291
Ga0081640
17
Ga0081640_1014
Ga0081608_1233
99
99
8878
4749
1.12
2.08
100.00
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1014
1233
2204204
300
Ga0081608
1645626
291
Ga0081640
18
Ga0081640_1014
Ga0081608_1233
99
99
8878
4749
1.12
2.08
100.00
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1014
1233
2204204
300
Ga0081608
1645626
291
Ga0081640
19
Ga0081640_1014
Ga0081608_1233
99
99
8878
4749
1.12
2.08
100.00
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1014
1233
2204204
300
Ga0081608
1645626
291
Ga0081640
20
Ga0081640_1014
Ga0081608_1266
100
100
8878
3830
1.13
2.61
100.00
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1014
1266
2204204
300
Ga0081608
1645626
291
Ga0081640
21
Ga0081640_1014
Ga0081608_1266
100
100
8878
3830
1.13
2.61
100.00
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1014
1266
2204204
300
Ga0081608
1645626
291
Ga0081640
22
Ga0081640_1014
Ga0081608_1266
100
100
8878
3830
1.13
2.61
100.00
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1014
1266
2204204
300
Ga0081608
1645626
291
Ga0081640
23
Ga0081640_1014
Ga0081608_1266
100
100
8878
3830
1.13
2.61
100.00
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1014
1266
2204204
300
Ga0081608
1645626
291
Ga0081640
24
Ga0081640_1016
Ga0081608_1049
2510
2510
2510
6305
100.00
39.81
98.05
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1016
1049
2204204
300
Ga0081608
1645626
291
Ga0081640
25
Ga0081640_1016
Ga0081608_1049
2510
2510
2510
6305
100.00
39.81
98.05
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1016
1049
2204204
300
Ga0081608
1645626
291
Ga0081640
26
Ga0081640_1016
Ga0081608_1049
2510
2510
2510
6305
100.00
39.81
98.05
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1016
1049
2204204
300
Ga0081608
1645626
291
Ga0081640
27
Ga0081640_1016
Ga0081608_1049
2510
2510
2510
6305
100.00
39.81
98.05
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1016
1049
2204204
300
Ga0081608
1645626
291
Ga0081640
28
Ga0081640_1017
Ga0081608_1213
2520
2520
2520
5573
100.00
45.22
99.76
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1017
1213
2204204
300
Ga0081608
1645626
291
Ga0081640
29
Ga0081640_1017
Ga0081608_1213
2520
2520
2520
5573
100.00
45.22
99.76
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1017
1213
2204204
300
Ga0081608
1645626
291
Ga0081640
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
1574
Ga0081640_1286
Ga0081608_1107
2222
2221
4083
5756
54.42
38.59
99.46
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1286
1107
2204204
300
Ga0081608
1645626
291
Ga0081640
1575
Ga0081640_1286
Ga0081608_1107
2222
2221
4083
5756
54.42
38.59
99.46
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1286
1107
2204204
300
Ga0081608
1645626
291
Ga0081640
1576
Ga0081640_1287
Ga0081608_1220
4807
4807
7291
6337
65.93
75.86
99.25
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1287
1220
2204204
300
Ga0081608
1645626
291
Ga0081640
1577
Ga0081640_1287
Ga0081608_1220
4807
4807
7291
6337
65.93
75.86
99.25
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1287
1220
2204204
300
Ga0081608
1645626
291
Ga0081640
1578
Ga0081640_1287
Ga0081608_1220
4807
4807
7291
6337
65.93
75.86
99.25
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1287
1220
2204204
300
Ga0081608
1645626
291
Ga0081640
1579
Ga0081640_1287
Ga0081608_1220
4807
4807
7291
6337
65.93
75.86
99.25
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1287
1220
2204204
300
Ga0081608
1645626
291
Ga0081640
1580
Ga0081640_1287
Ga0081608_1120
2503
2508
7291
7263
34.33
34.53
98.33
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1287
1120
2204204
300
Ga0081608
1645626
291
Ga0081640
1581
Ga0081640_1287
Ga0081608_1120
2503
2508
7291
7263
34.33
34.53
98.33
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1287
1120
2204204
300
Ga0081608
1645626
291
Ga0081640
1582
Ga0081640_1287
Ga0081608_1120
2503
2508
7291
7263
34.33
34.53
98.33
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1287
1120
2204204
300
Ga0081608
1645626
291
Ga0081640
1583
Ga0081640_1287
Ga0081608_1120
2503
2508
7291
7263
34.33
34.53
98.33
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1287
1120
2204204
300
Ga0081608
1645626
291
Ga0081640
1584
Ga0081640_1288
Ga0081608_1074
3672
3672
3672
10004
100.00
36.71
98.26
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1288
1074
2204204
300
Ga0081608
1645626
291
Ga0081640
1585
Ga0081640_1288
Ga0081608_1074
3672
3672
3672
10004
100.00
36.71
98.26
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1288
1074
2204204
300
Ga0081608
1645626
291
Ga0081640
1586
Ga0081640_1288
Ga0081608_1074
3672
3672
3672
10004
100.00
36.71
98.26
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1288
1074
2204204
300
Ga0081608
1645626
291
Ga0081640
1587
Ga0081640_1288
Ga0081608_1074
3672
3672
3672
10004
100.00
36.71
98.26
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1288
1074
2204204
300
Ga0081608
1645626
291
Ga0081640
1588
Ga0081640_1289
Ga0081608_1061
2871
2871
2871
24297
100.00
11.82
98.68
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1289
1061
2204204
300
Ga0081608
1645626
291
Ga0081640
1589
Ga0081640_1289
Ga0081608_1061
2871
2871
2871
24297
100.00
11.82
98.68
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1289
1061
2204204
300
Ga0081608
1645626
291
Ga0081640
1590
Ga0081640_1289
Ga0081608_1061
2871
2871
2871
24297
100.00
11.82
98.68
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1289
1061
2204204
300
Ga0081608
1645626
291
Ga0081640
1591
Ga0081640_1289
Ga0081608_1061
2871
2871
2871
24297
100.00
11.82
98.68
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1289
1061
2204204
300
Ga0081608
1645626
291
Ga0081640
1592
Ga0081640_1290
Ga0081608_1297
12653
12653
24502
18693
51.64
67.69
98.67
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1290
1297
2204204
300
Ga0081608
1645626
291
Ga0081640
1593
Ga0081640_1290
Ga0081608_1297
12653
12653
24502
18693
51.64
67.69
98.67
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1290
1297
2204204
300
Ga0081608
1645626
291
Ga0081640
1594
Ga0081640_1290
Ga0081608_1297
12653
12653
24502
18693
51.64
67.69
98.67
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1290
1297
2204204
300
Ga0081608
1645626
291
Ga0081640
1595
Ga0081640_1290
Ga0081608_1297
12653
12653
24502
18693
51.64
67.69
98.67
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1290
1297
2204204
300
Ga0081608
1645626
291
Ga0081640
1596
Ga0081640_1290
Ga0081608_1117
3185
3185
24502
3185
13.00
100.00
99.34
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1290
1117
2204204
300
Ga0081608
1645626
291
Ga0081640
1597
Ga0081640_1290
Ga0081608_1117
3185
3185
24502
3185
13.00
100.00
99.34
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1290
1117
2204204
300
Ga0081608
1645626
291
Ga0081640
1598
Ga0081640_1290
Ga0081608_1117
3185
3185
24502
3185
13.00
100.00
99.34
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1290
1117
2204204
300
Ga0081608
1645626
291
Ga0081640
1599
Ga0081640_1290
Ga0081608_1117
3185
3185
24502
3185
13.00
100.00
99.34
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1290
1117
2204204
300
Ga0081608
1645626
291
Ga0081640
1600
Ga0081640_1290
Ga0081608_1112
3227
3227
24502
3227
13.17
100.00
99.13
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1290
1112
2204204
300
Ga0081608
1645626
291
Ga0081640
1601
Ga0081640_1290
Ga0081608_1112
3227
3227
24502
3227
13.17
100.00
99.13
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1290
1112
2204204
300
Ga0081608
1645626
291
Ga0081640
1602
Ga0081640_1290
Ga0081608_1112
3227
3227
24502
3227
13.17
100.00
99.13
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1290
1112
2204204
300
Ga0081608
1645626
291
Ga0081640
1603
Ga0081640_1290
Ga0081608_1112
3227
3227
24502
3227
13.17
100.00
99.13
Methylotenera_mobilis-123/Methylotenera_mobili...
...
Ga0081640
Ga0081608
1290
1112
2204204
300
Ga0081608
1645626
291
Ga0081640
1604 rows × 22 columns
In [10]:
sample = amr.prepare_result('./mummer_results/Methylotenera_mobilis-123/Methylotenera_mobilis-123_to_Methylotenera_mobilis-63.tsv')
sample_longest = amr.keep_longest_query_match(sample)
In [11]:
sample.columns
Out[11]:
Index(['TAGS (ref)', 'TAGS (query)', 'LEN 1', 'LEN 2', 'LEN R', 'LEN Q',
'COV R', 'COV Q', '% IDY', 'mummer file', 'query name', 'ref name',
'ref id_x', 'query id_x', 'ref contig', 'query contig', 'query bp',
'query contigs', 'query id_y', 'ref bp', 'ref contigs', 'ref id_y'],
dtype='object')
In [12]:
print(sample.shape)
print(sample_longest.shape)
(1604, 22)
(984, 22)
In [13]:
amr.summarize('./mummer_results/Methylotenera_mobilis-123/Methylotenera_mobilis-123_to_Methylotenera_mobilis-63.tsv')
Out[13]:
mummer file
query name
ref name
ref id_x
query id_x
query bp
query contigs
query id_y
ref bp
ref contigs
ref id_y
% identity
query alignment length total
number alignments aggregated
frac of query aligned
estimated % identity
0
Methylotenera_mobilis-123/Methylotenera_mobili...
Methylotenera_mobilis-123
Methylotenera_mobilis-63
Ga0081640
Ga0081608
2204204
300
Ga0081608
1645626
291
Ga0081640
98.306833
3496000
984
1.58606
155.920545
In [14]:
m = re.search('/([\w-]+)_to_([\w-]+).tsv',
'Methylotenera_mobilis-123/Methylotenera_mobilis-123_to_Methylotenera_mobilis-63.tsv')
In [15]:
m.group()
Out[15]:
'/Methylotenera_mobilis-123_to_Methylotenera_mobilis-63.tsv'
In [16]:
m.group(1)
Out[16]:
'Methylotenera_mobilis-123'
In [17]:
m.group(2)
Out[17]:
'Methylotenera_mobilis-63'
In [18]:
d['mummer file'][0].split(sep='_to_')
Out[18]:
['Methylotenera_mobilis-123/Methylotenera_mobilis-123',
'Methylotenera_mobilis-63.tsv']
In [19]:
summary_tsv_paths = glob.glob('./mummer_results/*/*.tsv')
In [20]:
len(summary_tsv_paths)
Out[20]:
27036
In [21]:
amr.load_one_mummer_result('./mummer_results/elviz-contigs-1056229.Burkholderiales-1/elviz-contigs-1056229.Burkholderiales-1_to_elviz-contigs-1056013.Comamonadaceae-1.tsv')
Out[21]:
TAGS (ref)
TAGS (query)
LEN 1
LEN 2
LEN R
LEN Q
COV R
COV Q
% IDY
mummer file
query name
ref name
ref id
query id
ref contig
query contig
0
Ga0066401_1002015
Ga0066473_129705
434
434
2718
434
15.97
100.00
93.78
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1002015
129705
1
Ga0066401_1002591
Ga0066473_130841
425
425
2458
425
17.29
100.00
97.18
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1002591
130841
2
Ga0066401_1002591
Ga0066473_143339
159
159
2458
344
6.47
46.22
87.42
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1002591
143339
3
Ga0066401_1003446
Ga0066473_113765
602
602
2193
672
27.45
89.58
83.97
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1003446
113765
4
Ga0066401_1004073
Ga0066473_105303
381
381
2046
1115
18.62
34.17
84.02
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1004073
105303
5
Ga0066401_1005420
Ga0066473_105968
740
740
1822
1050
40.61
70.48
99.59
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1005420
105968
6
Ga0066401_1005879
Ga0066473_105068
749
749
1764
1144
42.46
65.47
86.00
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1005879
105068
7
Ga0066401_1006082
Ga0066473_104726
443
443
1739
1189
25.47
37.26
87.36
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1006082
104726
8
Ga0066401_1007403
Ga0066473_115747
560
563
1608
626
34.83
89.94
80.64
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1007403
115747
9
Ga0066401_1008325
Ga0066473_108653
858
858
1533
860
55.97
99.77
99.53
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1008325
108653
10
Ga0066401_1008857
Ga0066473_107625
714
714
1493
919
47.82
77.69
85.89
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1008857
107625
11
Ga0066401_1009178
Ga0066473_110813
363
363
1472
766
24.66
47.39
97.25
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1009178
110813
12
Ga0066401_1009399
Ga0066473_132051
227
227
1458
415
15.57
54.70
85.90
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1009399
132051
13
Ga0066401_1009730
Ga0066473_148871
254
254
1435
318
17.70
79.87
85.43
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1009730
148871
14
Ga0066401_1010390
Ga0066473_121209
264
264
1398
529
18.88
49.91
80.08
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1010390
121209
15
Ga0066401_1010411
Ga0066473_128485
204
216
1397
445
14.60
48.54
84.79
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1010411
128485
16
Ga0066401_1010435
Ga0066473_124476
252
252
1396
487
18.05
51.75
83.79
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1010435
124476
17
Ga0066401_1011844
Ga0066473_111029
757
757
1322
757
57.26
100.00
93.79
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1011844
111029
18
Ga0066401_1012310
Ga0066473_119069
561
561
1301
561
43.12
100.00
98.40
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1012310
119069
19
Ga0066401_1013819
Ga0066473_114361
279
279
1241
657
22.48
42.47
84.40
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1013819
114361
20
Ga0066401_1013845
Ga0066473_105170
321
324
1240
1129
25.89
28.70
83.44
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1013845
105170
21
Ga0066401_1014968
Ga0066473_133893
294
297
1200
401
24.50
74.06
81.94
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1014968
133893
22
Ga0066401_1015056
Ga0066473_117636
587
587
1197
587
49.04
100.00
98.30
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1015056
117636
23
Ga0066401_1015056
Ga0066473_126045
469
469
1197
469
39.18
100.00
97.65
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1015056
126045
24
Ga0066401_1015537
Ga0066473_116615
287
287
1181
607
24.30
47.28
97.92
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1015537
116615
25
Ga0066401_1015719
Ga0066473_116061
532
532
1176
619
45.24
85.95
92.11
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1015719
116061
26
Ga0066401_1015936
Ga0066473_104903
622
622
1169
1165
53.21
53.39
80.93
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1015936
104903
27
Ga0066401_1016462
Ga0066473_136001
248
248
1152
386
21.53
64.25
86.29
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1016462
136001
28
Ga0066401_1016462
Ga0066473_124649
355
355
1152
485
30.82
73.20
84.92
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1016462
124649
29
Ga0066401_1017723
Ga0066473_133000
161
161
1116
408
14.43
39.46
82.72
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1017723
133000
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
64
Ga0066401_1033773
Ga0066473_103004
169
169
848
1557
19.93
10.85
86.39
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1033773
103004
65
Ga0066401_1034155
Ga0066473_123538
323
323
844
499
38.27
64.73
84.88
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1034155
123538
66
Ga0066401_1034237
Ga0066473_133384
310
310
843
405
36.77
76.54
86.45
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1034237
133384
67
Ga0066401_1034720
Ga0066473_112075
520
520
838
722
62.05
72.02
84.48
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1034720
112075
68
Ga0066401_1035681
Ga0066473_139414
103
103
828
365
12.44
28.22
96.12
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1035681
139414
69
Ga0066401_1035707
Ga0066473_112711
382
382
828
702
46.14
54.42
86.65
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1035707
112711
70
Ga0066401_1036526
Ga0066473_131869
220
220
820
416
26.83
52.88
100.00
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1036526
131869
71
Ga0066401_1036716
Ga0066473_133514
219
219
818
404
26.77
54.21
97.26
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1036716
133514
72
Ga0066401_1036947
Ga0066473_140307
360
360
816
360
44.12
100.00
98.89
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1036947
140307
73
Ga0066401_1037188
Ga0066473_114394
124
124
814
656
15.23
18.90
85.48
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1037188
114394
74
Ga0066401_1037617
Ga0066473_115605
544
544
810
629
67.16
86.49
84.10
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1037617
115605
75
Ga0066401_1038504
Ga0066473_119931
237
231
802
547
29.55
42.23
91.56
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1038504
119931
76
Ga0066401_1038646
Ga0066473_105016
303
303
800
1150
37.88
26.35
82.51
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1038646
105016
77
Ga0066401_1039239
Ga0066473_106732
279
276
795
981
35.09
28.13
83.57
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1039239
106732
78
Ga0066401_1039271
Ga0066473_107144
375
375
795
953
47.17
39.35
85.60
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1039271
107144
79
Ga0066401_1040291
Ga0066473_120292
390
390
786
541
49.62
72.09
85.93
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1040291
120292
80
Ga0066401_1040922
Ga0066473_143663
281
281
781
342
35.98
82.16
94.66
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1040922
143663
81
Ga0066401_1041381
Ga0066473_119335
209
209
777
557
26.90
37.52
87.62
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1041381
119335
82
Ga0066401_1042431
Ga0066473_141629
167
167
769
353
21.72
47.31
95.21
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1042431
141629
83
Ga0066401_1042555
Ga0066473_134525
321
368
768
396
41.80
92.93
82.61
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1042555
134525
84
Ga0066401_1043642
Ga0066473_108250
666
666
759
882
87.75
75.51
97.60
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1043642
108250
85
Ga0066401_1043829
Ga0066473_122019
399
399
758
518
52.64
77.03
80.55
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1043829
122019
86
Ga0066401_1044283
Ga0066473_123553
276
276
754
499
36.60
55.31
98.55
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1044283
123553
87
Ga0066401_1044283
Ga0066473_121139
185
185
754
530
24.54
34.91
99.46
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1044283
121139
88
Ga0066401_1044922
Ga0066473_128142
170
170
750
449
22.67
37.86
99.41
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1044922
128142
89
Ga0066401_1045870
Ga0066473_114854
272
271
743
647
36.61
41.89
88.24
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1045870
114854
90
Ga0066401_1046069
Ga0066473_109580
589
588
741
816
79.49
72.06
82.06
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1046069
109580
91
Ga0066401_1047914
Ga0066473_125323
292
292
728
478
40.11
61.09
84.12
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1047914
125323
92
Ga0066401_1047919
Ga0066473_133145
168
168
728
407
23.08
41.28
96.43
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1047919
133145
93
Ga0066401_1049786
Ga0066473_118681
259
259
716
568
36.17
45.60
96.54
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
1049786
118681
94 rows × 16 columns
In [22]:
import name_extractions
In [23]:
name_extractions.query_and_ref_names_from_path('elviz-contigs-1056229.Burkholderiales-1/elviz-contigs-1056229.Burkholderiales-1_to_elviz-contigs-1056013.Comamonadaceae-1.tsv')
Out[23]:
{'query': 'elviz-contigs-1056229.Burkholderiales-1',
'ref': 'elviz-contigs-1056013.Comamonadaceae-1'}
In [24]:
amr.prepare_result('./mummer_results/elviz-contigs-1056229.Burkholderiales-1/elviz-contigs-1056229.Burkholderiales-1_to_elviz-contigs-1056013.Comamonadaceae-1.tsv')
Out[24]:
TAGS (ref)
TAGS (query)
LEN 1
LEN 2
LEN R
LEN Q
COV R
COV Q
% IDY
mummer file
...
ref id_x
query id_x
ref contig
query contig
query bp
query contigs
query id_y
ref bp
ref contigs
ref id_y
0
Ga0066401_1002015
Ga0066473_129705
434
434
2718
434
15.97
100.00
93.78
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1002015
129705
2738909
4662
Ga0066473
2022224
1990
Ga0066401
1
Ga0066401_1002591
Ga0066473_130841
425
425
2458
425
17.29
100.00
97.18
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1002591
130841
2738909
4662
Ga0066473
2022224
1990
Ga0066401
2
Ga0066401_1002591
Ga0066473_143339
159
159
2458
344
6.47
46.22
87.42
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1002591
143339
2738909
4662
Ga0066473
2022224
1990
Ga0066401
3
Ga0066401_1003446
Ga0066473_113765
602
602
2193
672
27.45
89.58
83.97
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1003446
113765
2738909
4662
Ga0066473
2022224
1990
Ga0066401
4
Ga0066401_1004073
Ga0066473_105303
381
381
2046
1115
18.62
34.17
84.02
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1004073
105303
2738909
4662
Ga0066473
2022224
1990
Ga0066401
5
Ga0066401_1005420
Ga0066473_105968
740
740
1822
1050
40.61
70.48
99.59
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1005420
105968
2738909
4662
Ga0066473
2022224
1990
Ga0066401
6
Ga0066401_1005879
Ga0066473_105068
749
749
1764
1144
42.46
65.47
86.00
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1005879
105068
2738909
4662
Ga0066473
2022224
1990
Ga0066401
7
Ga0066401_1006082
Ga0066473_104726
443
443
1739
1189
25.47
37.26
87.36
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1006082
104726
2738909
4662
Ga0066473
2022224
1990
Ga0066401
8
Ga0066401_1007403
Ga0066473_115747
560
563
1608
626
34.83
89.94
80.64
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1007403
115747
2738909
4662
Ga0066473
2022224
1990
Ga0066401
9
Ga0066401_1008325
Ga0066473_108653
858
858
1533
860
55.97
99.77
99.53
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1008325
108653
2738909
4662
Ga0066473
2022224
1990
Ga0066401
10
Ga0066401_1008857
Ga0066473_107625
714
714
1493
919
47.82
77.69
85.89
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1008857
107625
2738909
4662
Ga0066473
2022224
1990
Ga0066401
11
Ga0066401_1009178
Ga0066473_110813
363
363
1472
766
24.66
47.39
97.25
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1009178
110813
2738909
4662
Ga0066473
2022224
1990
Ga0066401
12
Ga0066401_1009399
Ga0066473_132051
227
227
1458
415
15.57
54.70
85.90
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1009399
132051
2738909
4662
Ga0066473
2022224
1990
Ga0066401
13
Ga0066401_1009730
Ga0066473_148871
254
254
1435
318
17.70
79.87
85.43
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1009730
148871
2738909
4662
Ga0066473
2022224
1990
Ga0066401
14
Ga0066401_1010390
Ga0066473_121209
264
264
1398
529
18.88
49.91
80.08
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1010390
121209
2738909
4662
Ga0066473
2022224
1990
Ga0066401
15
Ga0066401_1010411
Ga0066473_128485
204
216
1397
445
14.60
48.54
84.79
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1010411
128485
2738909
4662
Ga0066473
2022224
1990
Ga0066401
16
Ga0066401_1010435
Ga0066473_124476
252
252
1396
487
18.05
51.75
83.79
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1010435
124476
2738909
4662
Ga0066473
2022224
1990
Ga0066401
17
Ga0066401_1011844
Ga0066473_111029
757
757
1322
757
57.26
100.00
93.79
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1011844
111029
2738909
4662
Ga0066473
2022224
1990
Ga0066401
18
Ga0066401_1012310
Ga0066473_119069
561
561
1301
561
43.12
100.00
98.40
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1012310
119069
2738909
4662
Ga0066473
2022224
1990
Ga0066401
19
Ga0066401_1013819
Ga0066473_114361
279
279
1241
657
22.48
42.47
84.40
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1013819
114361
2738909
4662
Ga0066473
2022224
1990
Ga0066401
20
Ga0066401_1013845
Ga0066473_105170
321
324
1240
1129
25.89
28.70
83.44
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1013845
105170
2738909
4662
Ga0066473
2022224
1990
Ga0066401
21
Ga0066401_1014968
Ga0066473_133893
294
297
1200
401
24.50
74.06
81.94
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1014968
133893
2738909
4662
Ga0066473
2022224
1990
Ga0066401
22
Ga0066401_1015056
Ga0066473_117636
587
587
1197
587
49.04
100.00
98.30
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1015056
117636
2738909
4662
Ga0066473
2022224
1990
Ga0066401
23
Ga0066401_1015056
Ga0066473_126045
469
469
1197
469
39.18
100.00
97.65
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1015056
126045
2738909
4662
Ga0066473
2022224
1990
Ga0066401
24
Ga0066401_1015537
Ga0066473_116615
287
287
1181
607
24.30
47.28
97.92
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1015537
116615
2738909
4662
Ga0066473
2022224
1990
Ga0066401
25
Ga0066401_1015719
Ga0066473_116061
532
532
1176
619
45.24
85.95
92.11
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1015719
116061
2738909
4662
Ga0066473
2022224
1990
Ga0066401
26
Ga0066401_1015936
Ga0066473_104903
622
622
1169
1165
53.21
53.39
80.93
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1015936
104903
2738909
4662
Ga0066473
2022224
1990
Ga0066401
27
Ga0066401_1016462
Ga0066473_136001
248
248
1152
386
21.53
64.25
86.29
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1016462
136001
2738909
4662
Ga0066473
2022224
1990
Ga0066401
28
Ga0066401_1016462
Ga0066473_124649
355
355
1152
485
30.82
73.20
84.92
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1016462
124649
2738909
4662
Ga0066473
2022224
1990
Ga0066401
29
Ga0066401_1017723
Ga0066473_133000
161
161
1116
408
14.43
39.46
82.72
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1017723
133000
2738909
4662
Ga0066473
2022224
1990
Ga0066401
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
64
Ga0066401_1033773
Ga0066473_103004
169
169
848
1557
19.93
10.85
86.39
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1033773
103004
2738909
4662
Ga0066473
2022224
1990
Ga0066401
65
Ga0066401_1034155
Ga0066473_123538
323
323
844
499
38.27
64.73
84.88
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1034155
123538
2738909
4662
Ga0066473
2022224
1990
Ga0066401
66
Ga0066401_1034237
Ga0066473_133384
310
310
843
405
36.77
76.54
86.45
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1034237
133384
2738909
4662
Ga0066473
2022224
1990
Ga0066401
67
Ga0066401_1034720
Ga0066473_112075
520
520
838
722
62.05
72.02
84.48
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1034720
112075
2738909
4662
Ga0066473
2022224
1990
Ga0066401
68
Ga0066401_1035681
Ga0066473_139414
103
103
828
365
12.44
28.22
96.12
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1035681
139414
2738909
4662
Ga0066473
2022224
1990
Ga0066401
69
Ga0066401_1035707
Ga0066473_112711
382
382
828
702
46.14
54.42
86.65
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1035707
112711
2738909
4662
Ga0066473
2022224
1990
Ga0066401
70
Ga0066401_1036526
Ga0066473_131869
220
220
820
416
26.83
52.88
100.00
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1036526
131869
2738909
4662
Ga0066473
2022224
1990
Ga0066401
71
Ga0066401_1036716
Ga0066473_133514
219
219
818
404
26.77
54.21
97.26
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1036716
133514
2738909
4662
Ga0066473
2022224
1990
Ga0066401
72
Ga0066401_1036947
Ga0066473_140307
360
360
816
360
44.12
100.00
98.89
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1036947
140307
2738909
4662
Ga0066473
2022224
1990
Ga0066401
73
Ga0066401_1037188
Ga0066473_114394
124
124
814
656
15.23
18.90
85.48
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1037188
114394
2738909
4662
Ga0066473
2022224
1990
Ga0066401
74
Ga0066401_1037617
Ga0066473_115605
544
544
810
629
67.16
86.49
84.10
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1037617
115605
2738909
4662
Ga0066473
2022224
1990
Ga0066401
75
Ga0066401_1038504
Ga0066473_119931
237
231
802
547
29.55
42.23
91.56
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1038504
119931
2738909
4662
Ga0066473
2022224
1990
Ga0066401
76
Ga0066401_1038646
Ga0066473_105016
303
303
800
1150
37.88
26.35
82.51
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1038646
105016
2738909
4662
Ga0066473
2022224
1990
Ga0066401
77
Ga0066401_1039239
Ga0066473_106732
279
276
795
981
35.09
28.13
83.57
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1039239
106732
2738909
4662
Ga0066473
2022224
1990
Ga0066401
78
Ga0066401_1039271
Ga0066473_107144
375
375
795
953
47.17
39.35
85.60
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1039271
107144
2738909
4662
Ga0066473
2022224
1990
Ga0066401
79
Ga0066401_1040291
Ga0066473_120292
390
390
786
541
49.62
72.09
85.93
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1040291
120292
2738909
4662
Ga0066473
2022224
1990
Ga0066401
80
Ga0066401_1040922
Ga0066473_143663
281
281
781
342
35.98
82.16
94.66
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1040922
143663
2738909
4662
Ga0066473
2022224
1990
Ga0066401
81
Ga0066401_1041381
Ga0066473_119335
209
209
777
557
26.90
37.52
87.62
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1041381
119335
2738909
4662
Ga0066473
2022224
1990
Ga0066401
82
Ga0066401_1042431
Ga0066473_141629
167
167
769
353
21.72
47.31
95.21
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1042431
141629
2738909
4662
Ga0066473
2022224
1990
Ga0066401
83
Ga0066401_1042555
Ga0066473_134525
321
368
768
396
41.80
92.93
82.61
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1042555
134525
2738909
4662
Ga0066473
2022224
1990
Ga0066401
84
Ga0066401_1043642
Ga0066473_108250
666
666
759
882
87.75
75.51
97.60
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1043642
108250
2738909
4662
Ga0066473
2022224
1990
Ga0066401
85
Ga0066401_1043829
Ga0066473_122019
399
399
758
518
52.64
77.03
80.55
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1043829
122019
2738909
4662
Ga0066473
2022224
1990
Ga0066401
86
Ga0066401_1044283
Ga0066473_123553
276
276
754
499
36.60
55.31
98.55
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1044283
123553
2738909
4662
Ga0066473
2022224
1990
Ga0066401
87
Ga0066401_1044283
Ga0066473_121139
185
185
754
530
24.54
34.91
99.46
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1044283
121139
2738909
4662
Ga0066473
2022224
1990
Ga0066401
88
Ga0066401_1044922
Ga0066473_128142
170
170
750
449
22.67
37.86
99.41
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1044922
128142
2738909
4662
Ga0066473
2022224
1990
Ga0066401
89
Ga0066401_1045870
Ga0066473_114854
272
271
743
647
36.61
41.89
88.24
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1045870
114854
2738909
4662
Ga0066473
2022224
1990
Ga0066401
90
Ga0066401_1046069
Ga0066473_109580
589
588
741
816
79.49
72.06
82.06
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1046069
109580
2738909
4662
Ga0066473
2022224
1990
Ga0066401
91
Ga0066401_1047914
Ga0066473_125323
292
292
728
478
40.11
61.09
84.12
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1047914
125323
2738909
4662
Ga0066473
2022224
1990
Ga0066401
92
Ga0066401_1047919
Ga0066473_133145
168
168
728
407
23.08
41.28
96.43
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1047919
133145
2738909
4662
Ga0066473
2022224
1990
Ga0066401
93
Ga0066401_1049786
Ga0066473_118681
259
259
716
568
36.17
45.60
96.54
elviz-contigs-1056229.Burkholderiales-1/elviz-...
...
Ga0066401
Ga0066473
1049786
118681
2738909
4662
Ga0066473
2022224
1990
Ga0066401
94 rows × 22 columns
In [25]:
amr.summarize('./mummer_results/elviz-contigs-1056229.Burkholderiales-1/elviz-contigs-1056229.Burkholderiales-1_to_elviz-contigs-1056013.Comamonadaceae-1.tsv')
Out[25]:
mummer file
query name
ref name
ref id_x
query id_x
query bp
query contigs
query id_y
ref bp
ref contigs
ref id_y
% identity
query alignment length total
number alignments aggregated
frac of query aligned
estimated % identity
0
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
2738909
4662
Ga0066473
2022224
1990
Ga0066401
89.51239
33702
94
0.012305
1.101441
In [26]:
z = amr.percent_idty_all_results(summary_tsv_paths[1:10])
summarize ./mummer_results/elviz-contigs-1056229.Burkholderiales-1/elviz-contigs-1056229.Burkholderiales-1_to_elviz-contigs-1056013.Comamonadaceae-1.tsv
--> ./mummer_results/elviz-contigs-1056229.Burkholderiales-1/elviz-contigs-1056229.Burkholderiales-1_to_elviz-contigs-1056013.Comamonadaceae-1.tsv:
summarize ./mummer_results/elviz-contigs-1056229.Burkholderiales-1/elviz-contigs-1056229.Burkholderiales-1_to_elviz-contigs-1056247.Burkholderiales-1.tsv
--> ./mummer_results/elviz-contigs-1056229.Burkholderiales-1/elviz-contigs-1056229.Burkholderiales-1_to_elviz-contigs-1056247.Burkholderiales-1.tsv:
summarize ./mummer_results/elviz-contigs-1056229.Burkholderiales-1/elviz-contigs-1056229.Burkholderiales-1_to_elviz-contigs-1056055.Methylosarcina-1.tsv
no rows for ./mummer_results/elviz-contigs-1056229.Burkholderiales-1/elviz-contigs-1056229.Burkholderiales-1_to_elviz-contigs-1056055.Methylosarcina-1.tsv; assume zero similarity
summarize ./mummer_results/elviz-contigs-1056229.Burkholderiales-1/elviz-contigs-1056229.Burkholderiales-1_to_elviz-contigs-1056121.Comamonadaceae-2.tsv
--> ./mummer_results/elviz-contigs-1056229.Burkholderiales-1/elviz-contigs-1056229.Burkholderiales-1_to_elviz-contigs-1056121.Comamonadaceae-2.tsv:
summarize ./mummer_results/elviz-contigs-1056229.Burkholderiales-1/elviz-contigs-1056229.Burkholderiales-1_to_elviz-contigs-1056124.Methylophilus-1.tsv
--> ./mummer_results/elviz-contigs-1056229.Burkholderiales-1/elviz-contigs-1056229.Burkholderiales-1_to_elviz-contigs-1056124.Methylophilus-1.tsv:
summarize ./mummer_results/elviz-contigs-1056229.Burkholderiales-1/elviz-contigs-1056229.Burkholderiales-1_to_Acidovorax-69.tsv
--> ./mummer_results/elviz-contigs-1056229.Burkholderiales-1/elviz-contigs-1056229.Burkholderiales-1_to_Acidovorax-69.tsv:
summarize ./mummer_results/elviz-contigs-1056229.Burkholderiales-1/elviz-contigs-1056229.Burkholderiales-1_to_elviz-contigs-1056226.Burkholderiales-1.tsv
--> ./mummer_results/elviz-contigs-1056229.Burkholderiales-1/elviz-contigs-1056229.Burkholderiales-1_to_elviz-contigs-1056226.Burkholderiales-1.tsv:
summarize ./mummer_results/elviz-contigs-1056229.Burkholderiales-1/elviz-contigs-1056229.Burkholderiales-1_to_elviz-contigs-1056229.Flavobacterium-1.tsv
no rows for ./mummer_results/elviz-contigs-1056229.Burkholderiales-1/elviz-contigs-1056229.Burkholderiales-1_to_elviz-contigs-1056229.Flavobacterium-1.tsv; assume zero similarity
summarize ./mummer_results/elviz-contigs-1056229.Burkholderiales-1/elviz-contigs-1056229.Burkholderiales-1_to_elviz-contigs-1056019.Flavobacterium-1.tsv
no rows for ./mummer_results/elviz-contigs-1056229.Burkholderiales-1/elviz-contigs-1056229.Burkholderiales-1_to_elviz-contigs-1056019.Flavobacterium-1.tsv; assume zero similarity
number of empty and filled files: 3, 6
In [27]:
z.head()
Out[27]:
mummer file
query name
ref name
ref id_x
query id_x
query bp
query contigs
query id_y
ref bp
ref contigs
ref id_y
% identity
query alignment length total
number alignments aggregated
frac of query aligned
estimated % identity
0
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056013.Comamonadaceae-1
Ga0066401
Ga0066473
2738909
4662
Ga0066473
2022224
1990
Ga0066401
89.512390
33702
94
0.012305
1.101441
0
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056247.Burkholderiales-1
Ga0066479
Ga0066473
2738909
4662
Ga0066473
4860710
5582
Ga0066479
90.094688
282160
799
0.103019
9.281476
0
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056121.Comamonadaceae-2
Ga0066437
Ga0066473
2738909
4662
Ga0066473
2881263
2858
Ga0066437
91.209037
110727
280
0.040427
3.687345
0
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
elviz-contigs-1056124.Methylophilus-1
Ga0066438
Ga0066473
2738909
4662
Ga0066473
2904105
102
Ga0066438
100.000000
158
1
0.000058
0.005769
0
elviz-contigs-1056229.Burkholderiales-1/elviz-...
elviz-contigs-1056229.Burkholderiales-1
Acidovorax-69
Ga0081644
Ga0066473
2738909
4662
Ga0066473
3012106
445
Ga0081644
93.064607
160753
270
0.058692
5.462180
In [ ]:
Content source: JanetMatsen/meta4_bins_janalysis
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