In [1]:

    

from __future__ import division
import sys
import petl.interactive as etl
import petlx.all
sys.path.insert(0, '/home/aliman/src/github/alimanfoo/veff')
%reload_ext autoreload
%autoreload 1
%aimport veff


    

In [2]:

    

fasta_fn = '../../../data/genome/sanger/version3/September_2012/Pf3D7_v3.fa'
gff3_fn = '../../../data/genome/sanger/version3/September_2012/Pf3D7_v3.gff'
genome = veff.Genome(fasta_fn, gff3_fn, seqid=None)


    

In [12]:

    

vcf_fn = '../../../data/public/20141022/3d7_hb3.combined.final.vcf.gz'
tbl = (etl
    .fromvcf(vcf_fn, samples=None)
#     .eq('CHROM', 'Pf3D7_01_v3')
    .unpackinfo('EFF')
    .addfield('veff', lambda row: list(veff.get_effects(genome, row.CHROM, row.POS, row.REF, row.ALT[0])))
    .convert(['EFF', 'veff'], lambda v: v[0] if v else None)
    .addfield('strand', lambda row: row.veff.gene_strand)
    .addfield('snpeff_effect', lambda row: row.EFF.split('(')[0] if row.EFF is not None else None)
    .addfield('veff_effect', lambda row: row.veff.effect if row.veff is not None else None)
    .addfield('snpeff_codon_change', lambda row: row.EFF.split('|')[2] if row.EFF is not None else None)
    .addfield('veff_codon_change', lambda row: row.veff.codon_change if row.veff is not None else None)
    .addfield('snpeff_aa_change', lambda row: row.EFF.split('|')[3] if row.EFF is not None else None)
    .addfield('veff_aa_change', lambda row: row.veff.aa_change if row.veff is not None else None)
    .addfield('veff_ref_aa', lambda row: row.veff.ref_aa if row.veff is not None else None)
    .addfield('veff_alt_aa', lambda row: row.veff.alt_aa if row.veff is not None else None)
    .addfield('vlen', lambda row: row.veff.vlen if row.veff is not None else None)
    .cutout('REF', 'ALT')
    .cutout('veff', 'EFF')
    .cutout('ID', 'FILTER', 'QUAL')
#     .selectnotin('eff_effect', ['INTERGENIC', 'INTRON'])
)
tbl.select(lambda row: row.snpeff_effect != row.veff_effect).display(40)


    

    








CHROM
POS
strand
snpeff_effect
veff_effect
snpeff_codon_change
veff_codon_change
snpeff_aa_change
veff_aa_change
veff_ref_aa
veff_alt_aa
vlen




Pf3D7_01_v3
127692
-
CODON_CHANGE_PLUS_CODON_INSERTION
CODON_INSERTION
aac/aTAATAAac
aaC/aaTAATAAC
N150IIN
N150NNN
N
NNN
6


Pf3D7_01_v3
135874
-
CODON_CHANGE_PLUS_CODON_DELETION
CODON_DELETION
aaggaaaaggaaaat/aat
aaGGAAAAGGAAAAT/aaT
KEKEN1124N
KEKEN1124N
KEKEN
N
-12


Pf3D7_01_v3
137201
-
CODON_CHANGE_PLUS_CODON_DELETION
CODON_DELETION
aatata/ata
aATATa/aTa
NI685I
NI685I
NI
I
-3


Pf3D7_01_v3
146124
-
CODON_CHANGE_PLUS_CODON_DELETION
CODON_DELETION
aataaa/aaa
aaTAAA/aaA
NK90K
NK90K
NK
K
-3


Pf3D7_01_v3
148768
-
CODON_CHANGE_PLUS_CODON_DELETION
CODON_DELETION
ggtgataatttccaccgtgat/gat
gGTGATAATTTCCACCGTGAt/gAt
GDNFHRD1331D
GDNFHRD1331D
GDNFHRD
D
-18


Pf3D7_01_v3
233811
-
NON_SYNONYMOUS_CODING
SYNONYMOUS_CODING
tCa/tTa
atC/atT
S134L
I245I
I
I
0


Pf3D7_01_v3
257826
-
CODON_CHANGE_PLUS_CODON_INSERTION
CODON_INSERTION
aat/aaAATAATAATAATAATt
Caa/AATAATAATAATAATCaa
N239KIIIII
Q240NNNNNQ
Q
NNNNNQ
15


Pf3D7_01_v3
263684
-
NON_SYNONYMOUS_CODING
STOP_GAINED
Tat/Gat
tTa/tGa
Y102D
L223*
L
*
0


Pf3D7_01_v3
266640
-
CODON_CHANGE_PLUS_CODON_DELETION
CODON_DELETION
ggagat/gat
gGAGAt/gAt
GD844D
GD844D
GD
D
-3


Pf3D7_01_v3
288303
+
None
INTRON
None
None
None
None
None
None
-2


Pf3D7_01_v3
329507
-
INTERGENIC
INTRON

None

None
None
None
-2


Pf3D7_01_v3
335111
None
FRAME_SHIFT
INTERGENIC
-
None
-83
None
None
None
-14


Pf3D7_01_v3
335390
None
FRAME_SHIFT
INTERGENIC
-
None
-176
None
None
None
-2


Pf3D7_01_v3
345060
-
INTRAGENIC
INTRON

None

None
None
None
2


Pf3D7_01_v3
345066
-
INTRAGENIC
INTRON

None

None
None
None
0


Pf3D7_01_v3
345730
-
NON_SYNONYMOUS_CODING
SYNONYMOUS_CODING
Tca/Cca
agT/agC
S130P
S268S
S
S
0


Pf3D7_01_v3
353959
-
CODON_CHANGE_PLUS_CODON_DELETION
CODON_DELETION
gataatatgaacatggaa/gaa
gaTAATATGAACATGGAA/gaA
DNMNME746E
DNMNME746E
DNMNME
E
-15


Pf3D7_01_v3
354004
-
CODON_CHANGE_PLUS_CODON_INSERTION
CODON_INSERTION
gaa/gTAGTTATAATATGGAaa
gaA/gaTAGTTATAATATGGAA
E736VVIIWK
E736DSYNME
E
DSYNME
15


Pf3D7_01_v3
355334
-
None
CODON_INSERTION
None
aAt/aGTGGTAGTAGTAATAAt
None
N293SGSSNN
N
SGSSNN
15


Pf3D7_01_v3
362255
-
FRAME_SHIFT
INTRAGENIC
-
None
-106
None
None
None
-16


Pf3D7_01_v3
362551
-
FRAME_SHIFT
INTRAGENIC
-
None
-12
None
None
None
-2


Pf3D7_01_v3
378006
-
CODON_CHANGE_PLUS_CODON_DELETION
CODON_DELETION
aataataaa/aaa
aTAATAAAc/aAc
NNK105K
IIN167N
IIN
N
-6


Pf3D7_01_v3
387715
+
INTRAGENIC
TODO

None

None
None
None
0


Pf3D7_01_v3
387722
+
INTRAGENIC
TODO

None

None
None
None
0


Pf3D7_01_v3
387790
+
INTRAGENIC
TODO

None

None
None
None
12


Pf3D7_01_v3
393224
-
FRAME_SHIFT
INTRAGENIC
-
None
-87
None
None
None
-7


Pf3D7_01_v3
425557
-
STOP_GAINED
CODON_INSERTION
aac/aGATAGATGTGGATAATATTAATAACAAac
aaC/aaGATAGATGTGGATAATATTAATAACAAC
N673R*MWIILITN
N673KIDVDNINNN
N
KIDVDNINNN
27


Pf3D7_01_v3
425752
-
CODON_CHANGE_PLUS_CODON_DELETION
CODON_DELETION
aagaataagatggatgtggataatattaat/aat
aaGAATAAGATGGATGTGGATAATATTAAT/aaT
KNKMDVDNIN599N
KNKMDVDNIN599N
KNKMDVDNIN
N
-27


Pf3D7_01_v3
429234
None
FRAME_SHIFT
INTERGENIC
-/TATA
None
-65Y?
None
None
None
4


Pf3D7_01_v3
429530
None
FRAME_SHIFT
INTERGENIC
-
None
-164
None
None
None
-10


Pf3D7_01_v3
434091
-
CODON_CHANGE_PLUS_CODON_INSERTION
CODON_INSERTION
gat/gaCATAATGATCATAATGATt
Gat/CATAATGATCATAATGATGat
D317DIMIIMI
D318HNDHNDD
D
HNDHNDD
18


Pf3D7_01_v3
443938
-
INTERGENIC
TODO

None

None
None
None
-4


Pf3D7_01_v3
487967
-
NON_SYNONYMOUS_CODING
STOP_GAINED
gaA/gaT
Aga/Tga
E649D
R746*
R
*
0


Pf3D7_01_v3
487970
-
CODON_CHANGE_PLUS_CODON_DELETION
CODON_DELETION
gatgaagaa/gaa
TGAAGAAga/Aga
DEE646E
*RR743R
*RR
R
-6


Pf3D7_01_v3
487988
-
CODON_CHANGE_PLUS_CODON_INSERTION
CODON_INSERTION
gat/gAGATGATGAat
Tga/AGATGATGATga
D642EMMN
*739R***
*
R***
9


Pf3D7_01_v3
488006
-
CODON_CHANGE_PLUS_CODON_DELETION
CODON_DELETION
gatgctgaa/gaa
TGCTGAAga/Aga
DAE634E
C*R731R
C*R
R
-6


Pf3D7_01_v3
488135
-
CODON_CHANGE_PLUS_CODON_DELETION
CODON_DELETION
gaagaagaagaagaagag/gag
AGAAGAAGAAGAAGAGga/Gga
EEEEEE588E
RRRRRG685G
RRRRRG
G
-15


Pf3D7_01_v3
488776
-
CODON_CHANGE_PLUS_CODON_INSERTION
CODON_INSERTION
cac/caGAAGAAGGAGAACACc
cAa/cGAAGAAGGAGAACACAa
H379QKKENT
Q476RRRRTQ
Q
RRRRTQ
15


Pf3D7_01_v3
488912
-
CODON_CHANGE_PLUS_CODON_DELETION
CODON_DELETION
aagaaaaaa/aaa
GAAAAAAca/Aca
KKK332K
EKT429T
EKT
T
-6


Pf3D7_01_v3
489431
-
CODON_CHANGE_PLUS_CODON_INSERTION
CODON_INSERTION
gat/gAAAAAAACATAAAAAAGAat
Taa/AAAAAAACATAAAAAAGATaa
D161EKNIKKN
*258KKT*KR*
*
KKT*KR*
18



...

In [13]:

    

tbl.selectnotin('veff_effect', {'INTERGENIC', 'INTRON'}).display(40)


    

    








CHROM
POS
strand
snpeff_effect
veff_effect
snpeff_codon_change
veff_codon_change
snpeff_aa_change
veff_aa_change
veff_ref_aa
veff_alt_aa
vlen




Pf3D7_01_v3
95518
+
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
aGa/aTa
aGa/aTa
R156I
R156I
R
I
0


Pf3D7_01_v3
95621
+
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
caT/caA
caT/caA
H190Q
H190Q
H
Q
0


Pf3D7_01_v3
95632
+
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
tGt/tAt
tGt/tAt
C194Y
C194Y
C
Y
0


Pf3D7_01_v3
95641
+
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
tGt/tAt
tGt/tAt
C197Y
C197Y
C
Y
0


Pf3D7_01_v3
95680
+
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
aAt/aGt
aAt/aGt
N210S
N210S
N
S
0


Pf3D7_01_v3
95685
+
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
Gat/Tat
Gat/Tat
D212Y
D212Y
D
Y
0


Pf3D7_01_v3
95686
+
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
gAt/gCt
gAt/gCt
D212A
D212A
D
A
0


Pf3D7_01_v3
95710
+
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
tGt/tCt
tGt/tCt
C220S
C220S
C
S
0


Pf3D7_01_v3
95715
+
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
Agt/Ggt
Agt/Ggt
S222G
S222G
S
G
0


Pf3D7_01_v3
95716
+
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
aGt/aTt
aGt/aTt
S222I
S222I
S
I
0


Pf3D7_01_v3
95742
+
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
Gct/Act
Gct/Act
A231T
A231T
A
T
0


Pf3D7_01_v3
95754
+
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
Gct/Tct
Gct/Tct
A235S
A235S
A
S
0


Pf3D7_01_v3
98868
+
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
gAt/gGt
gAt/gGt
D17G
D17G
D
G
0


Pf3D7_01_v3
101269
+
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
Gta/Tta
Gta/Tta
V749L
V749L
V
L
0


Pf3D7_01_v3
101790
+
CODON_DELETION
CODON_DELETION
aat/-
gaAAAT/gaA
N923-
EN922E
EN
E
-3


Pf3D7_01_v3
107756
-
STOP_LOST
STOP_LOST
tAa/tCa
tAa/tCa
*198S
*198S
*
S
0


Pf3D7_01_v3
107823
-
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
Atg/Gtg
Atg/Gtg
M176V
M176V
M
V
0


Pf3D7_01_v3
114473
-
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
Aaa/Caa
Aaa/Caa
K443Q
K443Q
K
Q
0


Pf3D7_01_v3
120736
-
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
aaA/aaT
Att/Ttt
K116N
I206F
I
F
0


Pf3D7_01_v3
127256
-
CODON_DELETION
CODON_DELETION
aat/-
AATTgt/Tgt
N295-
NC295C
NC
C
-3


Pf3D7_01_v3
127692
-
CODON_CHANGE_PLUS_CODON_INSERTION
CODON_INSERTION
aac/aTAATAAac
aaC/aaTAATAAC
N150IIN
N150NNN
N
NNN
6


Pf3D7_01_v3
127725
-
SYNONYMOUS_CODING
SYNONYMOUS_CODING
aaC/aaT
aaC/aaT
N139
N139N
N
N
0


Pf3D7_01_v3
130339
-
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
Gca/Aca
Gca/Aca
A168T
A168T
A
T
0


Pf3D7_01_v3
135874
-
CODON_CHANGE_PLUS_CODON_DELETION
CODON_DELETION
aaggaaaaggaaaat/aat
aaGGAAAAGGAAAAT/aaT
KEKEN1124N
KEKEN1124N
KEKEN
N
-12


Pf3D7_01_v3
136422
-
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
Caa/Aaa
Caa/Aaa
Q946K
Q946K
Q
K
0


Pf3D7_01_v3
137201
-
CODON_CHANGE_PLUS_CODON_DELETION
CODON_DELETION
aatata/ata
aATATa/aTa
NI685I
NI685I
NI
I
-3


Pf3D7_01_v3
137258
-
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
aCg/aTg
aCg/aTg
T667M
T667M
T
M
0


Pf3D7_01_v3
138966
-
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
Caa/Gaa
Caa/Gaa
Q98E
Q98E
Q
E
0


Pf3D7_01_v3
139191
-
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
Gca/Aca
Gca/Aca
A23T
A23T
A
T
0


Pf3D7_01_v3
145560
-
SYNONYMOUS_CODING
SYNONYMOUS_CODING
tcT/tcA
tcT/tcA
S279
S279S
S
S
0


Pf3D7_01_v3
146124
-
CODON_CHANGE_PLUS_CODON_DELETION
CODON_DELETION
aataaa/aaa
aaTAAA/aaA
NK90K
NK90K
NK
K
-3


Pf3D7_01_v3
147952
-
CODON_INSERTION
CODON_INSERTION
-/GTAAAA
aAt/aGTAAAAAt
-1609VK
N1609SKN
N
SKN
6


Pf3D7_01_v3
148490
-
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
Tca/Gca
Tca/Gca
S1430A
S1430A
S
A
0


Pf3D7_01_v3
148768
-
CODON_CHANGE_PLUS_CODON_DELETION
CODON_DELETION
ggtgataatttccaccgtgat/gat
gGTGATAATTTCCACCGTGAt/gAt
GDNFHRD1331D
GDNFHRD1331D
GDNFHRD
D
-18


Pf3D7_01_v3
148917
-
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
aaT/aaA
aaT/aaA
N1287K
N1287K
N
K
0


Pf3D7_01_v3
155281
+
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
tAt/tTt
tAt/tTt
Y369F
Y369F
Y
F
0


Pf3D7_01_v3
155819
+
CODON_INSERTION
CODON_INSERTION
-/AATAATAAT
ctA/ctAAATAATAAT
-549NNN
L548LNNN
L
LNNN
9


Pf3D7_01_v3
155877
+
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
Gac/Aac
Gac/Aac
D568N
D568N
D
N
0


Pf3D7_01_v3
155977
+
NON_SYNONYMOUS_CODING
NON_SYNONYMOUS_CODING
gGc/gAc
gGc/gAc
G601D
G601D
G
D
0


Pf3D7_01_v3
155978
+
SYNONYMOUS_CODING
SYNONYMOUS_CODING
ggC/ggT
ggC/ggT
G601
G601G
G
G
0



...

In [14]:

    

from collections import Counter


    

In [15]:

    

tbl_indels = (tbl
    .selectnotin('veff_effect', {'INTERGENIC', 'INTRON', 'INTRAGENIC', 'TODO', 'FRAME_SHIFT'})
    .selectne('vlen', 0)
    .cutout('snpeff_effect', 'snpeff_codon_change', 'snpeff_aa_change')
    .rename({'veff_effect': 'effect', 
             'veff_codon_change': 'codon_change',
             'veff_ref_aa': 'ref_aa',
             'veff_alt_aa': 'alt_aa',
             'veff_aa_change': 'aa_change', })
    .cutout('codon_change')
    .addfield('aa_added', lambda row: Counter(row.alt_aa) - Counter(row.ref_aa))
    .addfield('aa_subtracted', lambda row: Counter(row.ref_aa) - Counter(row.alt_aa))
)
tbl_indels.display(100)


    

    








CHROM
POS
strand
effect
aa_change
ref_aa
alt_aa
vlen
aa_added
aa_subtracted




Pf3D7_01_v3
101790
+
CODON_DELETION
EN922E
EN
E
-3
Counter()
Counter({'N': 1})


Pf3D7_01_v3
127256
-
CODON_DELETION
NC295C
NC
C
-3
Counter()
Counter({'N': 1})


Pf3D7_01_v3
127692
-
CODON_INSERTION
N150NNN
N
NNN
6
Counter({'N': 2})
Counter()


Pf3D7_01_v3
135874
-
CODON_DELETION
KEKEN1124N
KEKEN
N
-12
Counter()
Counter({'K': 2, 'E': 2})


Pf3D7_01_v3
137201
-
CODON_DELETION
NI685I
NI
I
-3
Counter()
Counter({'N': 1})


Pf3D7_01_v3
146124
-
CODON_DELETION
NK90K
NK
K
-3
Counter()
Counter({'N': 1})


Pf3D7_01_v3
147952
-
CODON_INSERTION
N1609SKN
N
SKN
6
Counter({'S': 1, 'K': 1})
Counter()


Pf3D7_01_v3
148768
-
CODON_DELETION
GDNFHRD1331D
GDNFHRD
D
-18
Counter()
Counter({'D': 1, 'G': 1, 'F': 1, 'H': 1, 'N': 1, 'R': 1})


Pf3D7_01_v3
155819
+
CODON_INSERTION
L548LNNN
L
LNNN
9
Counter({'N': 3})
Counter()


Pf3D7_01_v3
161439
+
CODON_INSERTION
D103DN
D
DN
3
Counter({'N': 1})
Counter()


Pf3D7_01_v3
162124
+
CODON_INSERTION
H332HDQVKNKHDQVKNKDDKIKNKD
H
HDQVKNKHDQVKNKDDKIKNKD
63
Counter({'K': 7, 'D': 5, 'N': 3, 'Q': 2, 'V': 2, 'I': 1, 'H': 1})
Counter()


Pf3D7_01_v3
162967
+
CODON_INSERTION
H613HNN
H
HNN
6
Counter({'N': 2})
Counter()


Pf3D7_01_v3
164206
+
CODON_INSERTION
V1026VNKNINI
V
VNKNINI
18
Counter({'N': 3, 'I': 2, 'K': 1})
Counter()


Pf3D7_01_v3
173982
+
CODON_INSERTION
Y373YN
Y
YN
3
Counter({'N': 1})
Counter()


Pf3D7_01_v3
190317
+
CODON_DELETION
HNN17H
HNN
H
-6
Counter()
Counter({'N': 2})


Pf3D7_01_v3
190862
+
CODON_DELETION
NNN198N
NNN
N
-6
Counter()
Counter({'N': 2})


Pf3D7_01_v3
190944
+
CODON_INSERTION
D226DSINNSINN
D
DSINNSINN
24
Counter({'N': 4, 'I': 2, 'S': 2})
Counter()


Pf3D7_01_v3
191685
+
CODON_DELETION
YN473Y
YN
Y
-3
Counter()
Counter({'N': 1})


Pf3D7_01_v3
192608
+
CODON_DELETION
KG780K
KG
K
-3
Counter()
Counter({'G': 1})


Pf3D7_01_v3
192623
+
CODON_INSERTION
K785KDDDD
K
KDDDD
12
Counter({'D': 4})
Counter()


Pf3D7_01_v3
194843
+
CODON_DELETION
DKYE1525D
DKYE
D
-9
Counter()
Counter({'Y': 1, 'K': 1, 'E': 1})


Pf3D7_01_v3
195383
+
CODON_INSERTION
K1705KN
K
KN
3
Counter({'N': 1})
Counter()


Pf3D7_01_v3
206406
+
CODON_INSERTION
E79EKDD
E
EKDD
9
Counter({'D': 2, 'K': 1})
Counter()


Pf3D7_01_v3
207421
+
CODON_INSERTION
N418NDNYDNNNYDNYDNNNYDNY
N
NDNYDNNNYDNYDNNNYDNY
57
Counter({'N': 9, 'Y': 5, 'D': 5})
Counter()


Pf3D7_01_v3
216756
+
CODON_INSERTION
Y327YNNNNN
Y
YNNNNN
15
Counter({'N': 5})
Counter()


Pf3D7_01_v3
239206
+
CODON_INSERTION
Y181YNNN
Y
YNNN
9
Counter({'N': 3})
Counter()


Pf3D7_01_v3
239511
+
CODON_INSERTION
K282KTNDVK
K
KTNDVK
15
Counter({'K': 1, 'N': 1, 'T': 1, 'D': 1, 'V': 1})
Counter()


Pf3D7_01_v3
242535
+
CODON_DELETION
HNIQ1290H
HNIQ
H
-9
Counter()
Counter({'I': 1, 'Q': 1, 'N': 1})


Pf3D7_01_v3
244758
+
CODON_INSERTION
D2031DNNNNNNNN
D
DNNNNNNNN
24
Counter({'N': 8})
Counter()


Pf3D7_01_v3
246384
+
CODON_DELETION
NN2573N
NN
N
-3
Counter()
Counter({'N': 1})


Pf3D7_01_v3
247606
+
CODON_INSERTION
Y2981YNN
Y
YNN
6
Counter({'N': 2})
Counter()


Pf3D7_01_v3
247675
+
CODON_DELETION
YTNH3004Y
YTNH
Y
-9
Counter()
Counter({'H': 1, 'T': 1, 'N': 1})


Pf3D7_01_v3
257826
-
CODON_INSERTION
Q240NNNNNQ
Q
NNNNNQ
15
Counter({'N': 5})
Counter()


Pf3D7_01_v3
266640
-
CODON_DELETION
GD844D
GD
D
-3
Counter()
Counter({'G': 1})


Pf3D7_01_v3
282010
+
CODON_DELETION
YDN286Y
YDN
Y
-6
Counter()
Counter({'D': 1, 'N': 1})


Pf3D7_01_v3
282425
+
CODON_DELETION
GDGDDDDDDVGDDNVD424G
GDGDDDDDDVGDDNVD
G
-45
Counter()
Counter({'D': 10, 'V': 2, 'G': 2, 'N': 1})


Pf3D7_01_v3
282546
+
CODON_DELETION
DDN464D
DDN
D
-6
Counter()
Counter({'D': 1, 'N': 1})


Pf3D7_01_v3
282549
+
CODON_DELETION
DN465D
DN
D
-3
Counter()
Counter({'N': 1})


Pf3D7_01_v3
282555
+
CODON_DELETION
DD467D
DD
D
-3
Counter()
Counter({'D': 1})


Pf3D7_01_v3
282597
+
CODON_DELETION
NDDDD481N
NDDDD
N
-12
Counter()
Counter({'D': 4})


Pf3D7_01_v3
282609
+
CODON_INSERTION
D485DN
D
DN
3
Counter({'N': 1})
Counter()


Pf3D7_01_v3
283273
+
CODON_INSERTION
N707NDDDDDDD
N
NDDDDDDD
21
Counter({'D': 7})
Counter()


Pf3D7_01_v3
283356
+
CODON_INSERTION
G734GDDDEND
G
GDDDEND
18
Counter({'D': 4, 'E': 1, 'N': 1})
Counter()


Pf3D7_01_v3
283406
+
CODON_INSERTION
I751ID
I
ID
3
Counter({'D': 1})
Counter()


Pf3D7_01_v3
315518
+
CODON_DELETION
YN301Y
YN
Y
-3
Counter()
Counter({'N': 1})


Pf3D7_01_v3
316004
+
CODON_DELETION
ENVK463E
ENVK
E
-9
Counter()
Counter({'K': 1, 'N': 1, 'V': 1})


Pf3D7_01_v3
318006
+
CODON_DELETION
NIMF1130N
NIMF
N
-9
Counter()
Counter({'I': 1, 'M': 1, 'F': 1})


Pf3D7_01_v3
320629
+
CODON_DELETION
NNN154N
NNN
N
-6
Counter()
Counter({'N': 2})


Pf3D7_01_v3
322875
+
CODON_INSERTION
N169NNIYH
N
NNIYH
12
Counter({'I': 1, 'Y': 1, 'N': 1, 'H': 1})
Counter()


Pf3D7_01_v3
323333
+
CODON_DELETION
NE321N
NE
N
-3
Counter()
Counter({'E': 1})


Pf3D7_01_v3
324213
+
CODON_INSERTION
D615DN
D
DN
3
Counter({'N': 1})
Counter()


Pf3D7_01_v3
338214
+
CODON_DELETION
DDEDDDDDE349D
DDEDDDDDE
D
-24
Counter()
Counter({'D': 6, 'E': 2})


Pf3D7_01_v3
338340
+
CODON_INSERTION
E391EDDEDYDDDD
E
EDDEDYDDDD
27
Counter({'D': 7, 'Y': 1, 'E': 1})
Counter()


Pf3D7_01_v3
338598
+
CODON_INSERTION
I477IN
I
IN
3
Counter({'N': 1})
Counter()


Pf3D7_01_v3
339060
+
CODON_INSERTION
N631NN
N
NN
3
Counter({'N': 1})
Counter()


Pf3D7_01_v3
340513
+
CODON_CHANGE_PLUS_CODON_DELETION
IH1116N
IH
N
-3
Counter({'N': 1})
Counter({'I': 1, 'H': 1})


Pf3D7_01_v3
342021
+
CODON_INSERTION
K1618KN
K
KN
3
Counter({'N': 1})
Counter()


Pf3D7_01_v3
342450
+
CODON_DELETION
SN1761S
SN
S
-3
Counter()
Counter({'N': 1})


Pf3D7_01_v3
342833
+
CODON_INSERTION
I1889INN
I
INN
6
Counter({'N': 2})
Counter()


Pf3D7_01_v3
343374
+
CODON_DELETION
NN2069N
NN
N
-3
Counter()
Counter({'N': 1})


Pf3D7_01_v3
343596
+
CODON_INSERTION
E2143ENN
E
ENN
6
Counter({'N': 2})
Counter()


Pf3D7_01_v3
349643
+
CODON_DELETION
NEEPANEEPAN158N
NEEPANEEPAN
N
-30
Counter()
Counter({'E': 4, 'A': 2, 'P': 2, 'N': 2})


Pf3D7_01_v3
353959
-
CODON_DELETION
DNMNME746E
DNMNME
E
-15
Counter()
Counter({'M': 2, 'N': 2, 'D': 1})


Pf3D7_01_v3
354004
-
CODON_INSERTION
E736DSYNME
E
DSYNME
15
Counter({'Y': 1, 'S': 1, 'M': 1, 'D': 1, 'N': 1})
Counter()


Pf3D7_01_v3
354918
-
CODON_DELETION
ND431D
ND
D
-3
Counter()
Counter({'N': 1})


Pf3D7_01_v3
355334
-
CODON_INSERTION
N293SGSSNN
N
SGSSNN
15
Counter({'S': 3, 'G': 1, 'N': 1})
Counter()


Pf3D7_01_v3
378006
-
CODON_DELETION
IIN167N
IIN
N
-6
Counter()
Counter({'I': 2})


Pf3D7_01_v3
381393
+
CODON_INSERTION
D233DN
D
DN
3
Counter({'N': 1})
Counter()


Pf3D7_01_v3
397115
+
CODON_INSERTION
K175KCGDIKDK
K
KCGDIKDK
21
Counter({'K': 2, 'D': 2, 'I': 1, 'C': 1, 'G': 1})
Counter()


Pf3D7_01_v3
397494
+
CODON_DELETION
DNNNNNFDDN302D
DNNNNNFDDN
D
-27
Counter()
Counter({'N': 6, 'D': 2, 'F': 1})


Pf3D7_01_v3
398369
+
CODON_DELETION
SINTNIN593S
SINTNIN
S
-18
Counter()
Counter({'N': 3, 'I': 2, 'T': 1})


Pf3D7_01_v3
407116
+
CODON_DELETION
ENKSQ460E
ENKSQ
E
-12
Counter()
Counter({'Q': 1, 'K': 1, 'S': 1, 'N': 1})


Pf3D7_01_v3
408474
+
CODON_INSERTION
E912EGEDGEE
E
EGEDGEE
18
Counter({'E': 3, 'G': 2, 'D': 1})
Counter()


Pf3D7_01_v3
408489
+
CODON_INSERTION
E917EEGEDGEDDEEDD
E
EEGEDGEDDEEDD
36
Counter({'E': 5, 'D': 5, 'G': 2})
Counter()


Pf3D7_01_v3
424959
-
CODON_DELETION
NG872G
NG
G
-3
Counter()
Counter({'N': 1})


Pf3D7_01_v3
425557
-
CODON_INSERTION
N673KIDVDNINNN
N
KIDVDNINNN
27
Counter({'N': 3, 'I': 2, 'D': 2, 'K': 1, 'V': 1})
Counter()


Pf3D7_01_v3
425752
-
CODON_DELETION
KNKMDVDNIN599N
KNKMDVDNIN
N
-27
Counter()
Counter({'D': 2, 'K': 2, 'N': 2, 'I': 1, 'M': 1, 'V': 1})


Pf3D7_01_v3
426936
-
CODON_DELETION
TNSNSND208D
TNSNSND
D
-18
Counter()
Counter({'N': 3, 'S': 2, 'T': 1})


Pf3D7_01_v3
434091
-
CODON_INSERTION
D318HNDHNDD
D
HNDHNDD
18
Counter({'H': 2, 'D': 2, 'N': 2})
Counter()


Pf3D7_01_v3
434295
-
CODON_DELETION
LKEEKM245M
LKEEKM
M
-15
Counter()
Counter({'K': 2, 'E': 2, 'L': 1})


Pf3D7_01_v3
437159
+
CODON_INSERTION
I251IN
I
IN
3
Counter({'N': 1})
Counter()


Pf3D7_01_v3
437479
+
CODON_DELETION
DNN358D
DNN
D
-6
Counter()
Counter({'N': 2})


Pf3D7_01_v3
446589
+
CODON_INSERTION
S188SN
S
SN
3
Counter({'N': 1})
Counter()


Pf3D7_01_v3
477167
+
CODON_INSERTION
G255GYI
G
GYI
6
Counter({'Y': 1, 'I': 1})
Counter()


Pf3D7_01_v3
487939
-
CODON_DELETION
RI754I
RI
I
-3
Counter()
Counter({'R': 1})


Pf3D7_01_v3
487970
-
CODON_DELETION
*RR743R
*RR
R
-6
Counter()
Counter({'*': 1, 'R': 1})


Pf3D7_01_v3
487988
-
CODON_INSERTION
*739R***
*
R***
9
Counter({'*': 2, 'R': 1})
Counter()


Pf3D7_01_v3
488006
-
CODON_DELETION
C*R731R
C*R
R
-6
Counter()
Counter({'C': 1, '*': 1})


Pf3D7_01_v3
488135
-
CODON_DELETION
RRRRRG685G
RRRRRG
G
-15
Counter()
Counter({'R': 5})


Pf3D7_01_v3
488683
-
CODON_DELETION
RRRTQKRRTQI497I
RRRTQKRRTQI
I
-30
Counter()
Counter({'R': 5, 'Q': 2, 'T': 2, 'K': 1})


Pf3D7_01_v3
488776
-
CODON_INSERTION
Q476RRRRTQ
Q
RRRRTQ
15
Counter({'R': 4, 'T': 1})
Counter()


Pf3D7_01_v3
488912
-
CODON_DELETION
EKT429T
EKT
T
-6
Counter()
Counter({'K': 1, 'E': 1})


Pf3D7_01_v3
489431
-
CODON_INSERTION
*258KKT*KR*
*
KKT*KR*
18
Counter({'K': 3, '*': 1, 'R': 1, 'T': 1})
Counter()


Pf3D7_01_v3
497228
+
CODON_INSERTION
K607KEYDEVEYDEV
K
KEYDEVEYDEV
30
Counter({'E': 4, 'Y': 2, 'D': 2, 'V': 2})
Counter()


Pf3D7_01_v3
498978
+
CODON_INSERTION
E1190EDIDEDTNEYMYE
E
EDIDEDTNEYMYE
36
Counter({'E': 3, 'D': 3, 'Y': 2, 'I': 1, 'M': 1, 'N': 1, 'T': 1})
Counter()


Pf3D7_01_v3
505700
-
CODON_INSERTION
T429IIHVGLIT
T
IIHVGLIT
21
Counter({'I': 3, 'H': 1, 'L': 1, 'G': 1, 'V': 1})
Counter()


Pf3D7_01_v3
508956
-
CODON_INSERTION
D334NEKD
D
NEKD
9
Counter({'K': 1, 'E': 1, 'N': 1})
Counter()


Pf3D7_01_v3
514421
+
CODON_INSERTION
K779KGPTTS
K
KGPTTS
15
Counter({'T': 2, 'P': 1, 'S': 1, 'G': 1})
Counter()


Pf3D7_01_v3
532418
+
CODON_INSERTION
Y1682YDMNEHNMNEF
Y
YDMNEHNMNEF
30
Counter({'N': 3, 'E': 2, 'M': 2, 'D': 1, 'F': 1, 'H': 1})
Counter()


Pf3D7_01_v3
532602
+
CODON_INSERTION
K1743KKN
K
KKN
6
Counter({'K': 1, 'N': 1})
Counter()



...

In [16]:

    

import operator


    

In [17]:

    

all_aa_added = reduce(operator.add, tbl_indels.values('aa_added'))
all_aa_added.most_common(10)


    

    
Out[17]:





[('N', 3021),
 ('D', 804),
 ('K', 556),
 ('E', 535),
 ('I', 441),
 ('S', 346),
 ('T', 200),
 ('H', 198),
 ('Y', 190),
 ('G', 188)]

In [18]:

    

all_aa_subtracted = reduce(operator.add, tbl_indels.values('aa_subtracted'))
all_aa_subtracted.most_common(10)


    

    
Out[18]:





[('N', 3469),
 ('D', 1005),
 ('K', 664),
 ('E', 615),
 ('I', 433),
 ('S', 327),
 ('V', 217),
 ('H', 210),
 ('Y', 198),
 ('M', 185)]

In [19]:

    

all_aa_combined = all_aa_added + all_aa_subtracted
all_aa_combined.most_common(10)


    

    
Out[19]:





[('N', 6490),
 ('D', 1809),
 ('K', 1220),
 ('E', 1150),
 ('I', 874),
 ('S', 673),
 ('H', 408),
 ('V', 394),
 ('Y', 388),
 ('G', 357)]

In [34]:

    

%matplotlib inline
import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns
sns.set_style('white')


    

In [35]:

    

keys = [k for k, v in all_aa_combined.most_common(30)]
y1 = [all_aa_added[k] for k in keys]
y2 = [all_aa_subtracted[k] for k in keys]
x1 = np.arange(len(keys)) + .1
x2 = np.arange(len(keys)) + .5
fig = plt.figure(figsize=(16, 6))
ax = fig.add_subplot(111)
sns.despine(ax=ax, offset=10)
ax.bar(x1, y1, width=.4, color='w', label='insertions')
ax.bar(x2, y2, width=.4, color='k', label='deletions')
ax.set_xticks(np.arange(len(keys)) + .5)
ax.set_xticklabels(keys)
ax.legend()
ax.set_xlim(0, len(keys));


    

    
Out[35]:





21

In [13]:

    

genome._tbl_features.eq('type', 'gene').rowslice(15, 19).display()


    

    








seqid
source
type
start
stop
score
strand
phase
feature_id
parent_id




Pf3D7_01_v3
chado
gene
98819
102282
.
+
.
PF3D7_0102200
None


Pf3D7_01_v3
chado
gene
104704
105209
.
+
.
PF3D7_0102300
None


Pf3D7_01_v3
chado
gene
110750
115799
.
-
.
PF3D7_0102500
None


Pf3D7_01_v3
chado
gene
119041
121249
.
-
.
PF3D7_0102600
None

In [32]:

    

genome._tbl_features.counts('type').displayall()


    

    








type
count
frequency




CDS
374
0.406080347448


polypeptide
148
0.160694896851


gene
141
0.153094462541


mRNA
135
0.14657980456


polypeptide_motif
39
0.042345276873


pseudogenic_exon
36
0.0390879478827


pseudogene
13
0.014115092291


pseudogenic_transcript
13
0.014115092291


repeat_region
12
0.0130293159609


rRNA
5
0.00542888165038


ncRNA
4
0.0043431053203


centromere
1
0.00108577633008

In [34]:

    

genome._tbl_features.eq('type', 'rRNA').displayall()


    

    








seqid
source
type
start
stop
score
strand
phase
feature_id
parent_id




Pf3D7_01_v3
chado
rRNA
473739
475887
.
+
.
PF3D7_0112300.1
PF3D7_0112300


Pf3D7_01_v3
chado
rRNA
475888
476281
.
+
.
PF3D7_0112400.1
PF3D7_0112400


Pf3D7_01_v3
chado
rRNA
476282
476402
.
+
.
PF3D7_0112500.1
PF3D7_0112500


Pf3D7_01_v3
chado
rRNA
476403
477278
.
+
.
PF3D7_0112600.1
PF3D7_0112600


Pf3D7_01_v3
chado
rRNA
477279
481382
.
+
.
PF3D7_0112700.1
PF3D7_0112700

In [35]:

    

genome.get_feature('PF3D7_0112300')


    

    
Out[35]:





('Pf3D7_01_v3',
 'chado',
 'gene',
 473739,
 475887,
 '.',
 '+',
 '.',
 'PF3D7_0112300',
 None)

In [36]:

    

genome.get_children('PF3D7_0112300.1')


    

    
Out[36]:





[('Pf3D7_01_v3',
  'chado',
  'CDS',
  473739,
  475887,
  '.',
  '+',
  '0',
  'PF3D7_0112300.1:exon:1',
  'PF3D7_0112300.1')]

In [39]:

    

genome.get_feature('PF3D7_0108900')


    

    
Out[39]:





('Pf3D7_01_v3',
 'chado',
 'gene',
 361987,
 362586,
 '.',
 '-',
 '.',
 'PF3D7_0108900',
 None)

In [38]:

    

genome.get_children('PF3D7_0108900')


    

    
Out[38]:





[('Pf3D7_01_v3',
  'chado',
  'ncRNA',
  361987,
  362586,
  '.',
  '-',
  '.',
  'PF3D7_0108900.1',
  'PF3D7_0108900')]

In [40]:

    

genome.get_children('PF3D7_0108900.1')


    

    
Out[40]:





[('Pf3D7_01_v3',
  'chado',
  'CDS',
  361987,
  362586,
  '.',
  '-',
  '0',
  'PF3D7_0108900.1:exon:1',
  'PF3D7_0108900.1')]