wd="/Volumes/web/scaphapoda/Grace/Transcriptomes/mercenaria"
dircode="me"
cd {wd}
/Volumes/web/scaphapoda/Grace/Transcriptomes/mercenaria
!blastx \
-query query.fa \
-db /Volumes/Data/blast_db/uniprot_sprot \
-max_target_seqs 1 \
-max_hsps 1 \
-outfmt 6 \
-num_threads 8 \
-out blast_sprot.tab
Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 121 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 387 replaced by X Selenocysteine (U) at position 387 replaced by X Selenocysteine (U) at position 388 replaced by X Selenocysteine (U) at position 387 replaced by X Selenocysteine (U) at position 140 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 7 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 196 replaced by X Selenocysteine (U) at position 648 replaced by X Selenocysteine (U) at position 642 replaced by X Selenocysteine (U) at position 651 replaced by X Selenocysteine (U) at position 52 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 75 replaced by X Selenocysteine (U) at position 49 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 52 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 46 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 43 replaced by X Selenocysteine (U) at position 40 replaced by X Selenocysteine (U) at position 40 replaced by X Selenocysteine (U) at position 40 replaced by X Selenocysteine (U) at position 40 replaced by X Selenocysteine (U) at position 40 replaced by X Selenocysteine (U) at position 40 replaced by X Selenocysteine (U) at position 40 replaced by X Selenocysteine (U) at position 40 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 64 replaced by X Selenocysteine (U) at position 15 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 525 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 666 replaced by X Selenocysteine (U) at position 494 replaced by X Selenocysteine (U) at position 648 replaced by X Selenocysteine (U) at position 612 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 510 replaced by X Selenocysteine (U) at position 523 replaced by X Selenocysteine (U) at position 523 replaced by X Selenocysteine (U) at position 525 replaced by X Selenocysteine (U) at position 642 replaced by X Selenocysteine (U) at position 651 replaced by X Selenocysteine (U) at position 120 replaced by X Selenocysteine (U) at position 127 replaced by X Selenocysteine (U) at position 462 replaced by X Selenocysteine (U) at position 64 replaced by X Selenocysteine (U) at position 196 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 196 replaced by X Selenocysteine (U) at position 84 replaced by X Selenocysteine (U) at position 59 replaced by X Selenocysteine (U) at position 297 replaced by X Selenocysteine (U) at position 307 replaced by X Selenocysteine (U) at position 338 replaced by X Selenocysteine (U) at position 350 replaced by X Selenocysteine (U) at position 363 replaced by X Selenocysteine (U) at position 365 replaced by X Selenocysteine (U) at position 372 replaced by X Selenocysteine (U) at position 388 replaced by X Selenocysteine (U) at position 390 replaced by X Selenocysteine (U) at position 397 replaced by X Selenocysteine (U) at position 399 replaced by X Selenocysteine (U) at position 133 replaced by X Selenocysteine (U) at position 266 replaced by X Selenocysteine (U) at position 133 replaced by X Selenocysteine (U) at position 266 replaced by X Selenocysteine (U) at position 133 replaced by X Selenocysteine (U) at position 266 replaced by X Selenocysteine (U) at position 388 replaced by X Selenocysteine (U) at position 17 replaced by X Selenocysteine (U) at position 128 replaced by X Selenocysteine (U) at position 261 replaced by X Selenocysteine (U) at position 642 replaced by X Selenocysteine (U) at position 613 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 648 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 65 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 49 replaced by X Selenocysteine (U) at position 53 replaced by X Selenocysteine (U) at position 49 replaced by X Selenocysteine (U) at position 49 replaced by X Selenocysteine (U) at position 49 replaced by X Selenocysteine (U) at position 54 replaced by X Selenocysteine (U) at position 613 replaced by X Selenocysteine (U) at position 613 replaced by X Selenocysteine (U) at position 59 replaced by X Selenocysteine (U) at position 267 replaced by X Selenocysteine (U) at position 273 replaced by X Selenocysteine (U) at position 279 replaced by X Selenocysteine (U) at position 290 replaced by X Selenocysteine (U) at position 292 replaced by X Selenocysteine (U) at position 294 replaced by X Selenocysteine (U) at position 310 replaced by X Selenocysteine (U) at position 320 replaced by X Selenocysteine (U) at position 322 replaced by X Selenocysteine (U) at position 336 replaced by X Selenocysteine (U) at position 338 replaced by X Selenocysteine (U) at position 346 replaced by X Selenocysteine (U) at position 353 replaced by X Selenocysteine (U) at position 355 replaced by X Selenocysteine (U) at position 362 replaced by X Selenocysteine (U) at position 364 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 121 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 75 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 43 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 129 replaced by X Selenocysteine (U) at position 129 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 387 replaced by X Selenocysteine (U) at position 132 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 49 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 52 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 46 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 43 replaced by X Selenocysteine (U) at position 18 replaced by X Selenocysteine (U) at position 38 replaced by X Selenocysteine (U) at position 13 replaced by X Selenocysteine (U) at position 17 replaced by X Selenocysteine (U) at position 17 replaced by X Selenocysteine (U) at position 15 replaced by X Selenocysteine (U) at position 17 replaced by X Selenocysteine (U) at position 15 replaced by X Selenocysteine (U) at position 15 replaced by X Selenocysteine (U) at position 15 replaced by X Selenocysteine (U) at position 25 replaced by X Selenocysteine (U) at position 16 replaced by X Selenocysteine (U) at position 17 replaced by X Selenocysteine (U) at position 13 replaced by X Selenocysteine (U) at position 16 replaced by X Selenocysteine (U) at position 16 replaced by X Selenocysteine (U) at position 16 replaced by X Selenocysteine (U) at position 16 replaced by X Selenocysteine (U) at position 21 replaced by X Selenocysteine (U) at position 24 replaced by X Selenocysteine (U) at position 60 replaced by X Selenocysteine (U) at position 63 replaced by X Selenocysteine (U) at position 63 replaced by X Selenocysteine (U) at position 666 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 15 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 612 replaced by X Selenocysteine (U) at position 122 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 523 replaced by X Selenocysteine (U) at position 525 replaced by X Selenocysteine (U) at position 642 replaced by X Selenocysteine (U) at position 349 replaced by X Selenocysteine (U) at position 18 replaced by X Selenocysteine (U) at position 38 replaced by X Selenocysteine (U) at position 16 replaced by X Selenocysteine (U) at position 13 replaced by X Selenocysteine (U) at position 17 replaced by X Selenocysteine (U) at position 17 replaced by X Selenocysteine (U) at position 15 replaced by X Selenocysteine (U) at position 17 replaced by X Selenocysteine (U) at position 15 replaced by X Selenocysteine (U) at position 15 replaced by X Selenocysteine (U) at position 15 replaced by X Selenocysteine (U) at position 25 replaced by X Selenocysteine (U) at position 16 replaced by X Selenocysteine (U) at position 17 replaced by X Selenocysteine (U) at position 13 replaced by X Selenocysteine (U) at position 16 replaced by X Selenocysteine (U) at position 16 replaced by X Selenocysteine (U) at position 19 replaced by X Selenocysteine (U) at position 16 replaced by X Selenocysteine (U) at position 7 replaced by X Selenocysteine (U) at position 16 replaced by X Selenocysteine (U) at position 21 replaced by X Selenocysteine (U) at position 189 replaced by X Selenocysteine (U) at position 24 replaced by X Selenocysteine (U) at position 60 replaced by X Selenocysteine (U) at position 63 replaced by X Selenocysteine (U) at position 63 replaced by X Selenocysteine (U) at position 196 replaced by X Selenocysteine (U) at position 189 replaced by X Selenocysteine (U) at position 350 replaced by X
!wc -l blast_sprot.tab
7174 blast_sprot.tab
!tr '|' "\t" <blast_sprot.tab> blast_sprot_sql.tab
!head blast_sprot_sql.tab
Mmercenaria_Contig_1 sp P06538 DPOL_ADE12 26.09 46 34 0 141 4 100 145 6.2 28.5 Mmercenaria_Contig_2 sp Q6DRI1 EI3EA_DANRE 75.00 68 17 0 5 208 114 181 2e-29 112 Mmercenaria_Contig_3 sp O94823 AT10B_HUMAN 61.11 18 7 0 162 215 99 116 2.2 29.6 Mmercenaria_Contig_5 sp P0A5H8 EFPP_MYCTU 63.16 19 7 0 117 61 20 38 0.64 31.2 Mmercenaria_Contig_6 sp Q9WU60 ATRN_MOUSE 28.85 52 33 1 168 13 808 855 0.12 33.9 Mmercenaria_Contig_8 sp P18547 VNCS_PAVPN 50.00 22 11 0 111 176 362 383 0.85 30.8 Mmercenaria_Contig_9 sp A8WGF4 IF122_XENTR 67.16 67 22 0 1 201 894 960 6e-24 99.4 Mmercenaria_Contig_10 sp Q4QK86 MUKB_HAEI8 29.79 47 33 0 16 156 262 308 1.6 30.0 Mmercenaria_Contig_11 sp Q0AQ76 THIG_MARMM 34.09 44 27 1 210 79 84 125 3.4 28.9 Mmercenaria_Contig_12 sp P15106 GLNA_STRCO 39.29 28 17 0 40 123 124 151 0.84 30.8
!python /Applications/sqlshare-pythonclient-master/tools/singleupload.py \
-d {dircode}_uniprot \
blast_sprot_sql.tab
processing chunk line 0 to 7174 (0.00331497192383 s elapsed) pushing blast_sprot_sql.tab... parsing 458F0DA2... finished me_uniprot
!python /Applications/sqlshare-pythonclient-master/tools/fetchdata.py \
-s "SELECT Column1, term, GOSlim_bin, aspect, ProteinName FROM [graceac9@washington.edu].[me_uniprot]me left join [samwhite@washington.edu].[UniprotProtNamesReviewed_yes20130610]sp on me.Column3=sp.SPID left join [sr320@washington.edu].[SPID and GO Numbers]go on me.Column3=go.SPID left join [sr320@washington.edu].[GO_to_GOslim]slim on go.GOID=slim.GO_id where aspect like 'P'" \
-f tsv \
-o {dircode}_descriptions.txt
!head {dircode}_descriptions.txt
!egrep --color "male|female|genitalia|gonad|ovarian|reproduction|estrogen|testosterone|gametogenesis|germination|ovulation|penile|prostate|vulval" {dircode}_descriptions.txt / {dircode}_reprot.txt
egrep: /: Is a directory
!head {dircode}_reprot.txt
!wc -l {dircode}_reprot.txt
288 me_reprot.txt
pylab inline
Populating the interactive namespace from numpy and matplotlib
from pandas import *
jslim = read_table("me_reprot.txt", # name of the data file
#sep=",", # what character separates each column?
na_values=["", " "]) # what values should be considered "blank" values?
jslim.head
<bound method DataFrame.head of Mmercenaria_Contig_4590 \
0 Mmercenaria_Contig_6594
1 Mmercenaria_Contig_6594
2 Mmercenaria_Contig_4590
3 Mmercenaria_Contig_994
4 Mmercenaria_Contig_3849
5 Mmercenaria_Contig_6357
6 Mmercenaria_Contig_4457
7 Mmercenaria_Contig_6907
8 Mmercenaria_Contig_3802
9 Mmercenaria_Contig_3802
10 Mmercenaria_Contig_3021
11 Mmercenaria_Contig_2419
12 Mmercenaria_Contig_7280
13 Mmercenaria_Contig_1013
14 Mmercenaria_Contig_7184
15 Mmercenaria_Contig_7184
16 Mmercenaria_Contig_4005
17 Mmercenaria_Contig_2798
18 Mmercenaria_Contig_1822
19 Mmercenaria_Contig_8084
20 Mmercenaria_Contig_4799
21 Mmercenaria_Contig_4643
22 Mmercenaria_Contig_4643
23 Mmercenaria_Contig_6035
24 Mmercenaria_Contig_1613
25 Mmercenaria_Contig_5587
26 Mmercenaria_Contig_8025
27 Mmercenaria_Contig_4114
28 Mmercenaria_Contig_5917
29 Mmercenaria_Contig_5917
30 Mmercenaria_Contig_5917
31 Mmercenaria_Contig_7150
32 Mmercenaria_Contig_4544
33 Mmercenaria_Contig_6933
34 Mmercenaria_Contig_732
35 Mmercenaria_Contig_732
36 Mmercenaria_Contig_4544
37 Mmercenaria_Contig_6933
38 Mmercenaria_Contig_7602
39 Mmercenaria_Contig_7602
40 Mmercenaria_Contig_7602
41 Mmercenaria_Contig_1696
42 Mmercenaria_Contig_1696
43 Mmercenaria_Contig_1696
44 Mmercenaria_Contig_1696
45 Mmercenaria_Contig_3537
46 Mmercenaria_Contig_6233
47 Mmercenaria_Contig_6233
48 Mmercenaria_Contig_3227
49 Mmercenaria_Contig_1530
50 Mmercenaria_Contig_5828
51 Mmercenaria_Contig_5828
52 Mmercenaria_Contig_1535
53 Mmercenaria_Contig_1535
54 Mmercenaria_Contig_782
55 Mmercenaria_Contig_782
56 Mmercenaria_Contig_6010
57 Mmercenaria_Contig_2766
58 Mmercenaria_Contig_3625
59 Mmercenaria_Contig_6364
...
female pronucleus formation \
0 female pronucleus formation
1 male pronucleus formation
2 male pronucleus formation
3 negative regulation of seed germination
4 viral reproduction
5 reproduction
6 sporulation resulting in formation of a cellul...
7 viral reproduction
8 reproduction
9 hermaphrodite genitalia development
10 reproduction
11 response to testosterone stimulus
12 viral reproduction
13 female pregnancy
14 hermaphrodite genitalia development
15 reproduction
16 male gonad development
17 male gonad development
18 external genitalia morphogenesis
19 pollen germination
20 response to estrogen stimulus
21 ovulation from ovarian follicle
22 sexual reproduction
23 viral reproduction
24 viral reproduction
25 response to estrogen stimulus
26 male sex determination
27 ovulation
28 ovarian follicle cell development
29 female gonad development
30 ovarian follicle cell stalk formation
31 male courtship behavior
32 germarium-derived female germ-line cyst formation
33 germarium-derived female germ-line cyst formation
34 ovarian follicle cell development
35 germarium-derived female germ-line cyst formation
36 ovarian follicle cell development
37 ovarian follicle cell development
38 negative regulation of transcription, DNA-depe...
39 multicellular organismal development
40 terminal region determination
41 response to estrogen stimulus
42 response to gonadotropin stimulus
43 estrogen biosynthetic process
44 male gonad development
45 response to estrogen stimulus
46 response to estrogen stimulus
47 ovulation
48 reproduction
49 reproduction
50 female pregnancy
51 embryonic process involved in female pregnancy
52 spindle assembly involved in female meiosis I
53 spindle assembly involved in female meiosis I
54 transport
55 protein transport
56 viral reproduction
57 viral reproduction
58 prostate gland growth
59 reproduction
...
cell organization and biogenesis P \
0 cell organization and biogenesis P
1 cell organization and biogenesis P
2 cell organization and biogenesis P
3 developmental processes P
4 other biological processes P
5 other biological processes P
6 other biological processes P
7 other biological processes P
8 other biological processes P
9 developmental processes P
10 other biological processes P
11 other biological processes P
12 other biological processes P
13 other biological processes P
14 developmental processes P
15 other biological processes P
16 developmental processes P
17 developmental processes P
18 developmental processes P
19 other biological processes P
20 other biological processes P
21 developmental processes P
22 other biological processes P
23 other biological processes P
24 other biological processes P
25 other biological processes P
26 developmental processes P
27 other biological processes P
28 other biological processes P
29 developmental processes P
30 cell organization and biogenesis P
31 other biological processes P
32 cell cycle and proliferation P
33 cell cycle and proliferation P
34 other biological processes P
35 cell cycle and proliferation P
36 other biological processes P
37 other biological processes P
38 RNA metabolism P
39 developmental processes P
40 developmental processes P
41 other biological processes P
42 other biological processes P
43 other metabolic processes P
44 developmental processes P
45 other biological processes P
46 other biological processes P
47 other biological processes P
48 other biological processes P
49 other biological processes P
50 other biological processes P
51 developmental processes P
52 cell cycle and proliferation P
53 cell organization and biogenesis P
54 transport P
55 transport P
56 other biological processes P
57 other biological processes P
58 developmental processes P
59 other biological processes P
... ..
Postacrosomal sheath WW domain-binding protein (WW domain-binding protein 2-like)
0 Postacrosomal sheath WW domain-binding protein...
1 Postacrosomal sheath WW domain-binding protein...
2 Postacrosomal sheath WW domain-binding protein...
3 ARM REPEAT PROTEIN INTERACTING WITH ABF2 (ARIA)
4 26S proteasome non-ATPase regulatory subunit 1...
5 60S ribosomal protein L7
6 Probable spore germination protein GerPC
7 Zinc finger protein 197 (Zinc finger protein w...
8 Poly(A) RNA polymerase gld-2 (EC 2.7.7.19) (De...
9 Poly(A) RNA polymerase gld-2 (EC 2.7.7.19) (De...
10 Membrane-associated tyrosine- and threonine-sp...
11 Caspase-6 (CASP-6) (EC 3.4.22.59) (Apoptotic p...
12 Genome polyprotein [Cleaved into: Core protein...
13 Interferon tau (IFN-tau) (Antiluteolysin) (Tro...
14 Eukaryotic translation initiation factor 3 sub...
15 Eukaryotic translation initiation factor 3 sub...
16 Cold shock domain-containing protein E1 (N-ras...
17 Cold shock domain-containing protein E1 (N-ras...
18 Low-density lipoprotein receptor-related prote...
19 Signal peptide peptidase (AtSPP) (EC 3.4.23.-)...
20 Sodium-dependent phosphate transport protein 2...
21 Alpha-fetoprotein (Alpha-1-fetoprotein) (Alpha...
22 Alpha-fetoprotein (Alpha-1-fetoprotein) (Alpha...
23 Envelope glycoprotein gp160 (Env polyprotein) ...
24 Gag-Pol polyprotein (Pr160Gag-Pol) [Cleaved in...
25 Fructose-bisphosphate aldolase A (EC 4.1.2.13)...
26 Insulin-like growth factor 1 receptor (EC 2.7....
27 Esterase-6 (Est-6) (EC 3.1.1.1) (Carboxylic-es...
28 Homeobox protein cut
29 Homeobox protein cut
30 Homeobox protein cut
31 40S ribosomal protein S12, mitochondrial (MRP-...
32 Spectrin alpha chain
33 Spectrin alpha chain
34 Spectrin alpha chain
35 Spectrin alpha chain
36 Spectrin alpha chain
37 Spectrin alpha chain
38 Homeotic protein female sterile (Fragile-chori...
39 Homeotic protein female sterile (Fragile-chori...
40 Homeotic protein female sterile (Fragile-chori...
41 Cholesterol side-chain cleavage enzyme, mitoch...
42 Cholesterol side-chain cleavage enzyme, mitoch...
43 Cholesterol side-chain cleavage enzyme, mitoch...
44 Cholesterol side-chain cleavage enzyme, mitoch...
45 Arylsulfatase B (ASB) (EC 3.1.6.12) (N-acetylg...
46 Interleukin-4 receptor subunit alpha (IL-4 rec...
47 Interleukin-4 receptor subunit alpha (IL-4 rec...
48 Collagen alpha-1(IV) chain
49 Collagen alpha-1(IV) chain
50 Transcription factor jun-B
51 Transcription factor jun-B
52 Kinesin-like protein Nod
53 Kinesin-like protein Nod
54 Vesicle-fusing ATPase (EC 3.6.4.6) (N-ethylmal...
55 Vesicle-fusing ATPase (EC 3.6.4.6) (N-ethylmal...
56 Gag-Pol polyprotein (Pr170Gag-Pol) [Cleaved in...
57 Gag-Pol polyprotein (Pr170Gag-Pol) [Cleaved in...
58 Saposin-C (Co-beta-glucosidase) (Glucosylceram...
59 Heat shock 70 kDa protein D
...
[287 rows x 5 columns]>
#how do I group them by egrep term?
jslim.groupby('columns').Column1.count().plot(kind='bar')
--------------------------------------------------------------------------- KeyError Traceback (most recent call last) <ipython-input-35-65a1a2f62646> in <module>() ----> 1 jslim.groupby('columns').Column1.count().plot(kind='bar') /usr/local/bioinformatics/anaconda/lib/python2.7/site-packages/pandas/core/generic.pyc in groupby(self, by, axis, level, as_index, sort, group_keys, squeeze) 2670 axis = self._get_axis_number(axis) 2671 return groupby(self, by, axis=axis, level=level, as_index=as_index, -> 2672 sort=sort, group_keys=group_keys, squeeze=squeeze) 2673 2674 def asfreq(self, freq, method=None, how=None, normalize=False): /usr/local/bioinformatics/anaconda/lib/python2.7/site-packages/pandas/core/groupby.pyc in groupby(obj, by, **kwds) 787 raise TypeError('invalid type: %s' % type(obj)) 788 --> 789 return klass(obj, by, **kwds) 790 791 /usr/local/bioinformatics/anaconda/lib/python2.7/site-packages/pandas/core/groupby.pyc in __init__(self, obj, keys, axis, level, grouper, exclusions, selection, as_index, sort, group_keys, squeeze) 236 if grouper is None: 237 grouper, exclusions = _get_grouper(obj, keys, axis=axis, --> 238 level=level, sort=sort) 239 240 self.grouper = grouper /usr/local/bioinformatics/anaconda/lib/python2.7/site-packages/pandas/core/groupby.pyc in _get_grouper(obj, key, axis, level, sort) 1610 exclusions.append(gpr) 1611 name = gpr -> 1612 gpr = obj[gpr] 1613 1614 if isinstance(gpr, Categorical) and len(gpr) != len(obj): /usr/local/bioinformatics/anaconda/lib/python2.7/site-packages/pandas/core/frame.pyc in __getitem__(self, key) 1656 return self._getitem_multilevel(key) 1657 else: -> 1658 return self._getitem_column(key) 1659 1660 def _getitem_column(self, key): /usr/local/bioinformatics/anaconda/lib/python2.7/site-packages/pandas/core/frame.pyc in _getitem_column(self, key) 1663 # get column 1664 if self.columns.is_unique: -> 1665 return self._get_item_cache(key) 1666 1667 # duplicate columns & possible reduce dimensionaility /usr/local/bioinformatics/anaconda/lib/python2.7/site-packages/pandas/core/generic.pyc in _get_item_cache(self, item) 1003 res = cache.get(item) 1004 if res is None: -> 1005 values = self._data.get(item) 1006 res = self._box_item_values(item, values) 1007 cache[item] = res /usr/local/bioinformatics/anaconda/lib/python2.7/site-packages/pandas/core/internals.pyc in get(self, item) 2871 return self.get_for_nan_indexer(indexer) 2872 -> 2873 _, block = self._find_block(item) 2874 return block.get(item) 2875 else: /usr/local/bioinformatics/anaconda/lib/python2.7/site-packages/pandas/core/internals.pyc in _find_block(self, item) 3183 3184 def _find_block(self, item): -> 3185 self._check_have(item) 3186 for i, block in enumerate(self.blocks): 3187 if item in block: /usr/local/bioinformatics/anaconda/lib/python2.7/site-packages/pandas/core/internals.pyc in _check_have(self, item) 3190 def _check_have(self, item): 3191 if item not in self.items: -> 3192 raise KeyError('no item named %s' % com.pprint_thing(item)) 3193 3194 def reindex_axis(self, new_axis, indexer=None, method=None, axis=0, KeyError: u'no item named columns'