README.md
In arendsee/rhmmer: Utilities Parsing 'HMMER' Results
rhmmer
HMMER is a powerful package for profile HMM analysis. If
you want to interface with the web server through R, for example to search for
domains in a small number of proteins, consider using the
Bio3D package.rhmmer is
specifically designed for working with the standalone HMMER tool.
Installation
rhmmer is available on CRAN
install.packages('rhmmer')
Alternatively, you may install the github development version
library(devtools)
install_github('arendsee/rhmmer')
Examples
rhmmer currently exports exactly two functions: read_domtblout and
read_tblout. These read the hmmscan outputs specified by the --domtblout
and --tblout arguments, respectively.
The domtblout files have the format:
# --- full sequence --- -------------- this domain ------------- hmm coord ali coord env coord
# target name accession tlen query name accession qlen E-value score bias # of c-Evalue i-Evalue score bias from to from to from to acc description of target
#------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- ---------------------
Rer1 PF03248.12 171 AT2G18240.1 - 221 2.3e-61 206.4 10.4 1 2 4.3e-65 7.1e-61 204.8 11.2 4 168 24 181 21 183 0.96 Rer1 family
Rer1 PF03248.12 171 AT2G18240.1 - 221 2.3e-61 206.4 10.4 2 2 0.43 7.2e+03 -3.6 0.0 55 67 187 199 184 217 0.69 Rer1 family
DUF4220 PF13968.5 352 AT5G45530.1 - 798 4.6e-78 263.0 0.0 1 1 1.5e-81 1.3e-77 261.5 0.0 1 344 51 396 51 427 0.78 Domain of unknown function (DUF4220)
DUF594 PF04578.12 55 AT5G45530.1 - 798 4.7e-24 83.6 1.5 1 1 1.3e-27 1.1e-23 82.4 1.5 3 55 726 778 724 778 0.96 Protein of unknown function, DUF594
DEAD PF00270.28 176 AT1G27880.2 - 890 6.7e-20 71.5 0.1 1 1 3.4e-23 1.9e-19 70.0 0.1 2 171 272 433 271 438 0.83 DEAD/DEAH box helicase
...
#
# Program: hmmscan
# Version: 3.1b2 (February 2015)
# Pipeline mode: SCAN
# Query file: five.faa
# Target file: /home/z/db/Pfam-A.hmm
# Option settings: hmmscan --tblout x.tblout --domtblout x.domtblout --pfamtblout x.pfamtblout --noali /home/z/db/Pfam-A.hmm five.faa
# Current dir: /home/z/src/git/rhmmer/tests/testthat/sample-data
# Date: Fri Dec 15 02:09:00 2017
# [ok]
This is tricky to parse. It is mostly space delimited, but spaces appear freely
in the description of target column. The column names, as given, cannot be
directly used since they 1) contain illegal characters and 2) are not unique
unless information from two rows is considered (e.g. ali_from versus
env_from). The metadata at the end of the file I do not currently extract,
though I will likely add handling for this in the future.
library(rhmmer)
domtblout <- system.file('extdata', 'example.domtblout.txt', package='rhmmer')
read_domtblout(domtblout)
## # A tibble: 70 x 23
## domain_name domain_accession domain_len query_name query_accession qlen
## <chr> <chr> <int> <chr> <chr> <int>
## 1 Rer1 PF03248.12 171 AT2G18240… - 221
## 2 Rer1 PF03248.12 171 AT2G18240… - 221
## 3 DUF4220 PF13968.5 352 AT5G45530… - 798
## 4 DUF594 PF04578.12 55 AT5G45530… - 798
## 5 DEAD PF00270.28 176 AT1G27880… - 890
## 6 Helicase_C PF00271.30 111 AT1G27880… - 890
## 7 Helicase_C PF00271.30 111 AT1G27880… - 890
## 8 ResIII PF04851.14 171 AT1G27880… - 890
## 9 ResIII PF04851.14 171 AT1G27880… - 890
## 10 TIR PF01582.19 176 AT1G56520… - 897
## 11 NB-ARC PF00931.21 288 AT1G56520… - 897
## 12 LRR_3 PF07725.11 20 AT1G56520… - 897
## 13 LRR_3 PF07725.11 20 AT1G56520… - 897
## 14 LRR_8 PF13855.5 61 AT1G56520… - 897
## 15 LRR_8 PF13855.5 61 AT1G56520… - 897
## 16 LRR_8 PF13855.5 61 AT1G56520… - 897
## 17 LRR_8 PF13855.5 61 AT1G56520… - 897
## 18 LRR_8 PF13855.5 61 AT1G56520… - 897
## 19 LRR_8 PF13855.5 61 AT1G56520… - 897
## 20 LRR_4 PF12799.6 43 AT1G56520… - 897
## 21 LRR_4 PF12799.6 43 AT1G56520… - 897
## 22 LRR_4 PF12799.6 43 AT1G56520… - 897
## 23 LRR_4 PF12799.6 43 AT1G56520… - 897
## 24 LRR_4 PF12799.6 43 AT1G56520… - 897
## 25 TIR_2 PF13676.5 102 AT1G56520… - 897
## 26 TIR_2 PF13676.5 102 AT1G56520… - 897
## 27 AAA_16 PF13191.5 170 AT1G56520… - 897
## 28 AAA_18 PF13238.5 130 AT1G56520… - 897
## 29 AAA_22 PF13401.5 137 AT1G56520… - 897
## 30 ATPase_2 PF01637.17 233 AT1G56520… - 897
## 31 PhoH PF02562.15 205 AT1G56520… - 897
## 32 PhoH PF02562.15 205 AT1G56520… - 897
## 33 NACHT PF05729.11 166 AT1G56520… - 897
## 34 AAA_23 PF13476.5 200 AT1G56520… - 897
## 35 AAA_23 PF13476.5 200 AT1G56520… - 897
## 36 ABC_tran PF00005.26 137 AT1G56520… - 897
## 37 NTPase_1 PF03266.14 168 AT1G56520… - 897
## 38 AAA_29 PF13555.5 61 AT1G56520… - 897
## 39 AAA_29 PF13555.5 61 AT1G56520… - 897
## 40 LRR_1 PF00560.32 23 AT1G56520… - 897
## 41 LRR_1 PF00560.32 23 AT1G56520… - 897
## 42 LRR_1 PF00560.32 23 AT1G56520… - 897
## 43 LRR_1 PF00560.32 23 AT1G56520… - 897
## 44 LRR_1 PF00560.32 23 AT1G56520… - 897
## 45 LRR_1 PF00560.32 23 AT1G56520… - 897
## 46 LRR_1 PF00560.32 23 AT1G56520… - 897
## 47 LRR_1 PF00560.32 23 AT1G56520… - 897
## 48 DAO PF01266.23 352 AT3G10370… - 629
## 49 DAO PF01266.23 352 AT3G10370… - 629
## 50 DAO_C PF16901.4 126 AT3G10370… - 629
## 51 FAD_bindin… PF00890.23 417 AT3G10370… - 629
## 52 FAD_bindin… PF00890.23 417 AT3G10370… - 629
## 53 FAD_oxidor… PF12831.6 433 AT3G10370… - 629
## 54 FAD_oxidor… PF12831.6 433 AT3G10370… - 629
## 55 Pyr_redox_2 PF07992.13 292 AT3G10370… - 629
## 56 FAD_bindin… PF01494.18 356 AT3G10370… - 629
## 57 FAD_bindin… PF01494.18 356 AT3G10370… - 629
## 58 GIDA PF01134.21 392 AT3G10370… - 629
## 59 GIDA PF01134.21 392 AT3G10370… - 629
## 60 Pyr_redox PF00070.26 81 AT3G10370… - 629
## 61 HI0933_like PF03486.13 409 AT3G10370… - 629
## 62 AAA_30 PF13604.5 192 AT3G10370… - 629
## 63 AAA_30 PF13604.5 192 AT3G10370… - 629
## 64 Pyr_redox_3 PF13738.5 305 AT3G10370… - 629
## 65 DUF4179 PF13786.5 88 AT3G10370… - 629
## 66 DUF4179 PF13786.5 88 AT3G10370… - 629
## 67 3HCDH_N PF02737.17 180 AT3G10370… - 629
## 68 3HCDH_N PF02737.17 180 AT3G10370… - 629
## 69 NAD_bindin… PF13450.5 68 AT3G10370… - 629
## 70 NAD_bindin… PF13450.5 68 AT3G10370… - 629
## sequence_evalue sequence_score sequence_bias domain_N domain_of
## <dbl> <dbl> <dbl> <int> <int>
## 1 2.30e-61 206. 10.4 1 2
## 2 2.30e-61 206. 10.4 2 2
## 3 4.60e-78 263 0 1 1
## 4 4.70e-24 83.6 1.5 1 1
## 5 6.70e-20 71.5 0.1 1 1
## 6 3.20e-18 66 0 1 2
## 7 3.20e-18 66 0 2 2
## 8 1.20e- 3 18.8 0.1 1 2
## 9 1.20e- 3 18.8 0.1 2 2
## 10 7.30e-46 156. 0 1 1
## 11 1.90e-17 63.1 0 1 1
## 12 1.00e- 7 31.4 1.1 1 2
## 13 1.00e- 7 31.4 1.1 2 2
## 14 2.30e- 7 30.4 7 1 6
## 15 2.30e- 7 30.4 7 2 6
## 16 2.30e- 7 30.4 7 3 6
## 17 2.30e- 7 30.4 7 4 6
## 18 2.30e- 7 30.4 7 5 6
## 19 2.30e- 7 30.4 7 6 6
## 20 2.70e- 7 30.6 17.6 1 5
## 21 2.70e- 7 30.6 17.6 2 5
## 22 2.70e- 7 30.6 17.6 3 5
## 23 2.70e- 7 30.6 17.6 4 5
## 24 2.70e- 7 30.6 17.6 5 5
## 25 2.60e- 5 24.4 0.1 1 2
## 26 2.60e- 5 24.4 0.1 2 2
## 27 2.00e- 4 21.7 0.3 1 1
## 28 1.00e- 3 19.5 0 1 1
## 29 4.80e- 3 17.1 1 1 1
## 30 1.50e- 2 15.1 0 1 1
## 31 2.80e- 2 13.8 1.1 1 2
## 32 2.80e- 2 13.8 1.1 2 2
## 33 2.90e- 2 14.2 0 1 1
## 34 3.90e- 2 14.4 0 1 2
## 35 3.90e- 2 14.4 0 2 2
## 36 4.40e- 2 14.2 0 1 1
## 37 6.20e- 2 13.1 0 1 1
## 38 7.90e- 2 12.6 0.1 1 2
## 39 7.90e- 2 12.6 0.1 2 2
## 40 1.50e- 1 12.6 14.8 1 8
## 41 1.50e- 1 12.6 14.8 2 8
## 42 1.50e- 1 12.6 14.8 3 8
## 43 1.50e- 1 12.6 14.8 4 8
## 44 1.50e- 1 12.6 14.8 5 8
## 45 1.50e- 1 12.6 14.8 6 8
## 46 1.50e- 1 12.6 14.8 7 8
## 47 1.50e- 1 12.6 14.8 8 8
## 48 3.20e-53 181. 0.1 1 2
## 49 3.20e-53 181. 0.1 2 2
## 50 9.00e-39 132. 0.3 1 1
## 51 6.30e- 7 28.7 1.9 1 2
## 52 6.30e- 7 28.7 1.9 2 2
## 53 1.00e- 4 21.7 1.1 1 2
## 54 1.00e- 4 21.7 1.1 2 2
## 55 1.40e- 2 14.6 0 1 1
## 56 1.50e- 2 14.5 0.2 1 2
## 57 1.50e- 2 14.5 0.2 2 2
## 58 3.60e- 2 13 0.2 1 2
## 59 3.60e- 2 13 0.2 2 2
## 60 6.30e- 2 13.8 0.7 1 1
## 61 7.50e- 2 11.6 0.2 1 1
## 62 7.70e- 2 12.6 0.6 1 2
## 63 7.70e- 2 12.6 0.6 2 2
## 64 1.00e- 1 11.7 0 1 1
## 65 1.80e- 1 12.2 0.9 1 2
## 66 1.80e- 1 12.2 0.9 2 2
## 67 3.10e- 1 10.8 2 1 2
## 68 3.10e- 1 10.8 2 2 2
## 69 1.40e+ 0 9.1 5 1 2
## 70 1.40e+ 0 9.1 5 2 2
## domain_cevalue domain_ievalue domain_score domain_bias hmm_from hmm_to
## <dbl> <dbl> <dbl> <dbl> <int> <int>
## 1 4.30e-65 7.10e-61 205. 11.2 4 168
## 2 4.30e- 1 7.20e+ 3 -3.6 0 55 67
## 3 1.50e-81 1.30e-77 262. 0 1 344
## 4 1.30e-27 1.10e-23 82.4 1.5 3 55
## 5 3.40e-23 1.90e-19 70 0.1 2 171
## 6 3.10e- 1 1.70e+ 3 -0.7 0 21 72
## 7 5.40e-21 3.00e-17 62.9 0 15 110
## 8 1.70e+ 0 9.40e+ 3 -3.7 0.1 102 123
## 9 1.50e- 6 8.40e- 3 16 0 4 169
## 10 1.30e-48 1.20e-45 155. 0 2 164
## 11 3.60e-20 3.50e-17 62.3 0 4 262
## 12 1.00e-10 1.00e- 7 31.4 1.1 1 20
## 13 1.30e+ 0 1.30e+ 3 -0.6 0.5 1 14
## 14 1.10e+ 0 1.10e+ 3 -0.6 0 15 31
## 15 1.30e- 3 1.30e+ 0 8.8 0.3 2 58
## 16 6.40e- 3 6.20e+ 0 6.6 0.2 2 59
## 17 1.10e- 1 1.10e+ 2 2.6 0.1 2 57
## 18 4.90e- 6 4.80e- 3 16.5 0 2 60
## 19 2.00e- 3 2.00e+ 0 8.2 0.1 27 59
## 20 8.40e+ 0 8.30e+ 3 -2.6 0 19 33
## 21 6.60e- 3 6.50e+ 0 7.2 0.1 2 33
## 22 1.00e- 2 1.00e+ 1 6.6 0.3 12 38
## 23 1.70e- 3 1.60e+ 0 9.1 0 1 39
## 24 4.80e- 6 4.70e- 3 17.2 0.2 3 42
## 25 9.50e- 8 9.30e- 5 22.6 0 1 85
## 26 6.10e+ 0 6.00e+ 3 -2.5 0.1 16 55
## 27 7.80e- 7 7.70e- 4 19.8 0.3 3 63
## 28 2.40e- 6 2.40e- 3 18.3 0 1 69
## 29 2.40e- 5 2.40e- 2 14.8 1 7 113
## 30 4.70e- 5 4.60e- 2 13.5 0 8 82
## 31 3.60e- 3 3.50e+ 0 6.9 0.2 18 39
## 32 1.10e- 2 1.10e+ 1 5.3 0 87 161
## 33 5.80e- 5 5.70e- 2 13.2 0 3 95
## 34 3.50e- 4 3.40e- 1 11.3 0 20 50
## 35 1.40e+ 0 1.40e+ 3 -0.5 0 118 143
## 36 9.60e- 5 9.50e- 2 13.1 0 12 36
## 37 1.60e- 4 1.60e- 1 11.8 0 2 87
## 38 1.30e- 3 1.30e+ 0 8.7 0.1 18 42
## 39 3.60e- 1 3.50e+ 2 0.9 0 3 25
## 40 8.60e+ 0 8.50e+ 3 -1.9 0 1 13
## 41 1.90e+ 0 1.90e+ 3 0.1 0.1 1 12
## 42 7.10e- 1 7.00e+ 2 1.4 0 1 21
## 43 1.90e- 1 1.90e+ 2 3.1 0 1 13
## 44 6.40e+ 0 6.20e+ 3 -1.5 0 3 13
## 45 2.40e- 2 2.40e+ 1 5.9 0 2 12
## 46 1.70e- 1 1.60e+ 2 3.3 0.3 1 16
## 47 4.40e+ 0 4.30e+ 3 -1 0 8 21
## 48 7.20e-56 8.60e-53 180. 0 1 351
## 49 1.40e+ 0 1.70e+ 3 -1.8 0.1 68 106
## 50 1.30e-41 1.60e-38 131. 0.3 1 125
## 51 1.90e- 6 2.30e- 3 17 1.2 1 41
## 52 2.40e- 4 2.90e- 1 10.1 0 154 213
## 53 3.60e- 7 4.30e- 4 19.7 0.3 1 40
## 54 3.40e- 1 4.10e+ 2 -0.1 0 100 143
## 55 2.60e- 5 3.10e- 2 13.4 0 2 36
## 56 3.30e- 4 3.90e- 1 9.8 0.5 3 51
## 57 6.90e- 2 8.30e+ 1 2.2 0 117 179
## 58 1.90e- 4 2.30e- 1 10.4 0.1 1 29
## 59 2.70e- 1 3.30e+ 2 0 0 110 159
## 60 2.30e- 4 2.80e- 1 11.7 0.7 2 32
## 61 1.20e- 4 1.50e- 1 10.6 0.2 2 32
## 62 3.10e+ 0 3.70e+ 3 -2.7 0.1 5 39
## 63 1.40e- 4 1.70e- 1 11.5 0 32 81
## 64 1.50e- 4 1.80e- 1 10.9 0 166 220
## 65 5.90e- 4 7.10e- 1 10.3 0 5 37
## 66 1.50e+ 0 1.80e+ 3 -0.6 0.1 10 57
## 67 3.00e- 4 3.60e- 1 10.6 0.2 2 32
## 68 1.90e+ 0 2.20e+ 3 -1.8 0.1 30 65
## 69 2.70e- 4 3.20e- 1 11.2 0.6 1 42
## 70 4.60e+ 0 5.50e+ 3 -2.4 0 31 40
## # ... with 6 more variables: ali_from <int>, ali_to <int>, env_from <int>,
## # env_to <int>, acc <dbl>, description <chr>
The tblout output is fairly similar and presents the same parsing difficulties:
# --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
# target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target
#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- ---------------------
Rer1 PF03248.12 AT2G18240.1 - 2.3e-61 206.4 10.4 7.1e-61 204.8 11.2 1.3 2 0 0 2 2 2 1 Rer1 family
DUF4220 PF13968.5 AT5G45530.1 - 4.6e-78 263.0 0.0 1.3e-77 261.5 0.0 1.7 1 1 0 1 1 1 1 Domain of unknown function (DUF4220)
DUF594 PF04578.12 AT5G45530.1 - 4.7e-24 83.6 1.5 1.1e-23 82.4 1.5 1.7 1 0 0 1 1 1 1 Protein of unknown function, DUF594
DEAD PF00270.28 AT1G27880.2 - 6.7e-20 71.5 0.1 1.9e-19 70.0 0.1 1.8 1 0 0 1 1 1 1 DEAD/DEAH box helicase
Helicase_C PF00271.30 AT1G27880.2 - 3.2e-18 66.0 0.0 3e-17 62.9 0.0 2.5 2 0 0 2 2 2 1 Helicase conserved C-terminal domain
ResIII PF04851.14 AT1G27880.2 - 0.0012 18.8 0.1 0.0084 16.0 0.0 2.4 2 1 0 2 2 2 1 Type III restriction enzyme, res subunit
...
#
# Program: hmmscan
# Version: 3.1b2 (February 2015)
# Pipeline mode: SCAN
# Query file: five.faa
# Target file: /home/z/db/Pfam-A.hmm
# Option settings: hmmscan --tblout x.tblout --domtblout x.domtblout --pfamtblout x.pfamtblout --noali /home/z/db/Pfam-A.hmm five.faa
# Current dir: /home/z/src/git/rhmmer/tests/testthat/sample-data
# Date: Fri Dec 15 02:09:00 2017
# [ok]
tblout <- system.file('extdata', 'example.tblout.txt', package='rhmmer')
read_tblout(tblout)
## # A tibble: 37 x 19
## domain_name domain_accession query_name query_accession sequence_evalue
## <chr> <chr> <chr> <chr> <dbl>
## 1 Rer1 PF03248.12 AT2G18240… - 2.30e-61
## 2 DUF4220 PF13968.5 AT5G45530… - 4.60e-78
## 3 DUF594 PF04578.12 AT5G45530… - 4.70e-24
## 4 DEAD PF00270.28 AT1G27880… - 6.70e-20
## 5 Helicase_C PF00271.30 AT1G27880… - 3.20e-18
## 6 ResIII PF04851.14 AT1G27880… - 1.20e- 3
## 7 TIR PF01582.19 AT1G56520… - 7.30e-46
## 8 NB-ARC PF00931.21 AT1G56520… - 1.90e-17
## 9 LRR_3 PF07725.11 AT1G56520… - 1.00e- 7
## 10 LRR_8 PF13855.5 AT1G56520… - 2.30e- 7
## 11 LRR_4 PF12799.6 AT1G56520… - 2.70e- 7
## 12 TIR_2 PF13676.5 AT1G56520… - 2.60e- 5
## 13 AAA_16 PF13191.5 AT1G56520… - 2.00e- 4
## 14 AAA_18 PF13238.5 AT1G56520… - 1.00e- 3
## 15 AAA_22 PF13401.5 AT1G56520… - 4.80e- 3
## 16 ATPase_2 PF01637.17 AT1G56520… - 1.50e- 2
## 17 PhoH PF02562.15 AT1G56520… - 2.80e- 2
## 18 NACHT PF05729.11 AT1G56520… - 2.90e- 2
## 19 AAA_23 PF13476.5 AT1G56520… - 3.90e- 2
## 20 ABC_tran PF00005.26 AT1G56520… - 4.40e- 2
## 21 NTPase_1 PF03266.14 AT1G56520… - 6.20e- 2
## 22 AAA_29 PF13555.5 AT1G56520… - 7.90e- 2
## 23 LRR_1 PF00560.32 AT1G56520… - 1.50e- 1
## 24 DAO PF01266.23 AT3G10370… - 3.20e-53
## 25 DAO_C PF16901.4 AT3G10370… - 9.00e-39
## 26 FAD_bindin… PF00890.23 AT3G10370… - 6.30e- 7
## 27 FAD_oxidor… PF12831.6 AT3G10370… - 1.00e- 4
## 28 Pyr_redox_2 PF07992.13 AT3G10370… - 1.40e- 2
## 29 FAD_bindin… PF01494.18 AT3G10370… - 1.50e- 2
## 30 GIDA PF01134.21 AT3G10370… - 3.60e- 2
## 31 Pyr_redox PF00070.26 AT3G10370… - 6.30e- 2
## 32 HI0933_like PF03486.13 AT3G10370… - 7.50e- 2
## 33 AAA_30 PF13604.5 AT3G10370… - 7.70e- 2
## 34 Pyr_redox_3 PF13738.5 AT3G10370… - 1.00e- 1
## 35 DUF4179 PF13786.5 AT3G10370… - 1.80e- 1
## 36 3HCDH_N PF02737.17 AT3G10370… - 3.10e- 1
## 37 NAD_bindin… PF13450.5 AT3G10370… - 1.40e+ 0
## sequence_score sequence_bias best_domain_eva… best_domain_sco…
## <dbl> <dbl> <dbl> <dbl>
## 1 206. 10.4 7.10e-61 205.
## 2 263 0 1.30e-77 262.
## 3 83.6 1.5 1.10e-23 82.4
## 4 71.5 0.1 1.90e-19 70
## 5 66 0 3.00e-17 62.9
## 6 18.8 0.1 8.40e- 3 16
## 7 156. 0 1.20e-45 155.
## 8 63.1 0 3.50e-17 62.3
## 9 31.4 1.1 1.00e- 7 31.4
## 10 30.4 7 4.80e- 3 16.5
## 11 30.6 17.6 4.70e- 3 17.2
## 12 24.4 0.1 9.30e- 5 22.6
## 13 21.7 0.3 7.70e- 4 19.8
## 14 19.5 0 2.40e- 3 18.3
## 15 17.1 1 2.40e- 2 14.8
## 16 15.1 0 4.60e- 2 13.5
## 17 13.8 1.1 3.50e+ 0 6.9
## 18 14.2 0 5.70e- 2 13.2
## 19 14.4 0 3.40e- 1 11.3
## 20 14.2 0 9.50e- 2 13.1
## 21 13.1 0 1.60e- 1 11.8
## 22 12.6 0.1 1.30e+ 0 8.7
## 23 12.6 14.8 2.40e+ 1 5.9
## 24 181. 0.1 8.60e-53 180.
## 25 132. 0.3 1.60e-38 131.
## 26 28.7 1.9 2.30e- 3 17
## 27 21.7 1.1 4.30e- 4 19.7
## 28 14.6 0 3.10e- 2 13.4
## 29 14.5 0.2 3.90e- 1 9.8
## 30 13 0.2 2.30e- 1 10.4
## 31 13.8 0.7 2.80e- 1 11.7
## 32 11.6 0.2 1.50e- 1 10.6
## 33 12.6 0.6 1.70e- 1 11.5
## 34 11.7 0 1.80e- 1 10.9
## 35 12.2 0.9 7.10e- 1 10.3
## 36 10.8 2 3.60e- 1 10.6
## 37 9.1 5 3.20e- 1 11.2
## best_domain_bis domain_number_e… domain_number_r… domain_number_c…
## <dbl> <dbl> <int> <int>
## 1 11.2 1.3 2 0
## 2 0 1.7 1 1
## 3 1.5 1.7 1 0
## 4 0.1 1.8 1 0
## 5 0 2.5 2 0
## 6 0 2.4 2 1
## 7 0 1.4 1 0
## 8 0 1.4 1 0
## 9 1.1 2.7 2 0
## 10 0 5.5 3 2
## 11 0.2 6.1 6 1
## 12 0 1.9 2 0
## 13 0.3 2 1 1
## 14 0 1.7 1 0
## 15 1 2.1 1 1
## 16 0 1.8 1 1
## 17 0.2 2.3 1 1
## 18 0 1.5 1 0
## 19 0 2.3 2 0
## 20 0 1.5 1 0
## 21 0 1.7 1 1
## 22 0.1 2.3 2 0
## 23 0 7.8 8 1
## 24 0 1.6 2 0
## 25 0.3 1.4 1 0
## 26 1.2 2.3 2 0
## 27 0.3 2.2 2 0
## 28 0 1.5 1 0
## 29 0.5 2.1 2 0
## 30 0.1 2 2 0
## 31 0.7 2.1 1 0
## 32 0.2 1.5 1 0
## 33 0 1.9 2 0
## 34 0 1.3 1 0
## 35 0 2.2 2 0
## 36 0.2 2 2 0
## 37 0.6 2.3 3 0
## # ... with 6 more variables: domain_number_ov <int>,
## # domain_number_env <int>, domain_number_dom <int>,
## # domain_number_rep <int>, domain_number_inc <chr>, description <chr>
What rhmmer does and doesn't
What rhmmer currently does
- parse HMMER output (tblout and domtblout) into tidy data frames
What rhmmer may do in the future
-
provide visualization or analysis of HMMER results
-
provide simple wrappers for calling some of the HMMER functions
-
parse metadata from the comments in HMMER output files
-
read pfamtblout and the raw output (with alignments)
-
read the HMM models
-
download databases for you (e.g. PFAM)
-
access precompiled PFAM results
What rhmmer will never do
-
interface with the HMMER web server (use Bio3D)
-
duplicate the whole HMMER api (just use the CLI tool)
TODO
[ ] Rewrite the parser in C++
[ ] Parse out the file metadata
arendsee/rhmmer documentation built on Dec. 3, 2022, 2:40 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
rhmmer
HMMER is a powerful package for profile HMM analysis. If
you want to interface with the web server through R, for example to search for
domains in a small number of proteins, consider using the
Bio3D package.rhmmer is
specifically designed for working with the standalone HMMER tool.
Installation
rhmmer is available on CRAN
install.packages('rhmmer')
Alternatively, you may install the github development version
library(devtools)
install_github('arendsee/rhmmer')
Examples
rhmmer currently exports exactly two functions: read_domtblout and
read_tblout. These read the hmmscan outputs specified by the --domtblout
and --tblout arguments, respectively.
The domtblout files have the format:
# --- full sequence --- -------------- this domain ------------- hmm coord ali coord env coord
# target name accession tlen query name accession qlen E-value score bias # of c-Evalue i-Evalue score bias from to from to from to acc description of target
#------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- ---------------------
Rer1 PF03248.12 171 AT2G18240.1 - 221 2.3e-61 206.4 10.4 1 2 4.3e-65 7.1e-61 204.8 11.2 4 168 24 181 21 183 0.96 Rer1 family
Rer1 PF03248.12 171 AT2G18240.1 - 221 2.3e-61 206.4 10.4 2 2 0.43 7.2e+03 -3.6 0.0 55 67 187 199 184 217 0.69 Rer1 family
DUF4220 PF13968.5 352 AT5G45530.1 - 798 4.6e-78 263.0 0.0 1 1 1.5e-81 1.3e-77 261.5 0.0 1 344 51 396 51 427 0.78 Domain of unknown function (DUF4220)
DUF594 PF04578.12 55 AT5G45530.1 - 798 4.7e-24 83.6 1.5 1 1 1.3e-27 1.1e-23 82.4 1.5 3 55 726 778 724 778 0.96 Protein of unknown function, DUF594
DEAD PF00270.28 176 AT1G27880.2 - 890 6.7e-20 71.5 0.1 1 1 3.4e-23 1.9e-19 70.0 0.1 2 171 272 433 271 438 0.83 DEAD/DEAH box helicase
...
#
# Program: hmmscan
# Version: 3.1b2 (February 2015)
# Pipeline mode: SCAN
# Query file: five.faa
# Target file: /home/z/db/Pfam-A.hmm
# Option settings: hmmscan --tblout x.tblout --domtblout x.domtblout --pfamtblout x.pfamtblout --noali /home/z/db/Pfam-A.hmm five.faa
# Current dir: /home/z/src/git/rhmmer/tests/testthat/sample-data
# Date: Fri Dec 15 02:09:00 2017
# [ok]
This is tricky to parse. It is mostly space delimited, but spaces appear freely
in the description of target column. The column names, as given, cannot be
directly used since they 1) contain illegal characters and 2) are not unique
unless information from two rows is considered (e.g. ali_from versus
env_from). The metadata at the end of the file I do not currently extract,
though I will likely add handling for this in the future.
library(rhmmer)
domtblout <- system.file('extdata', 'example.domtblout.txt', package='rhmmer')
read_domtblout(domtblout)
## # A tibble: 70 x 23
## domain_name domain_accession domain_len query_name query_accession qlen
## <chr> <chr> <int> <chr> <chr> <int>
## 1 Rer1 PF03248.12 171 AT2G18240… - 221
## 2 Rer1 PF03248.12 171 AT2G18240… - 221
## 3 DUF4220 PF13968.5 352 AT5G45530… - 798
## 4 DUF594 PF04578.12 55 AT5G45530… - 798
## 5 DEAD PF00270.28 176 AT1G27880… - 890
## 6 Helicase_C PF00271.30 111 AT1G27880… - 890
## 7 Helicase_C PF00271.30 111 AT1G27880… - 890
## 8 ResIII PF04851.14 171 AT1G27880… - 890
## 9 ResIII PF04851.14 171 AT1G27880… - 890
## 10 TIR PF01582.19 176 AT1G56520… - 897
## 11 NB-ARC PF00931.21 288 AT1G56520… - 897
## 12 LRR_3 PF07725.11 20 AT1G56520… - 897
## 13 LRR_3 PF07725.11 20 AT1G56520… - 897
## 14 LRR_8 PF13855.5 61 AT1G56520… - 897
## 15 LRR_8 PF13855.5 61 AT1G56520… - 897
## 16 LRR_8 PF13855.5 61 AT1G56520… - 897
## 17 LRR_8 PF13855.5 61 AT1G56520… - 897
## 18 LRR_8 PF13855.5 61 AT1G56520… - 897
## 19 LRR_8 PF13855.5 61 AT1G56520… - 897
## 20 LRR_4 PF12799.6 43 AT1G56520… - 897
## 21 LRR_4 PF12799.6 43 AT1G56520… - 897
## 22 LRR_4 PF12799.6 43 AT1G56520… - 897
## 23 LRR_4 PF12799.6 43 AT1G56520… - 897
## 24 LRR_4 PF12799.6 43 AT1G56520… - 897
## 25 TIR_2 PF13676.5 102 AT1G56520… - 897
## 26 TIR_2 PF13676.5 102 AT1G56520… - 897
## 27 AAA_16 PF13191.5 170 AT1G56520… - 897
## 28 AAA_18 PF13238.5 130 AT1G56520… - 897
## 29 AAA_22 PF13401.5 137 AT1G56520… - 897
## 30 ATPase_2 PF01637.17 233 AT1G56520… - 897
## 31 PhoH PF02562.15 205 AT1G56520… - 897
## 32 PhoH PF02562.15 205 AT1G56520… - 897
## 33 NACHT PF05729.11 166 AT1G56520… - 897
## 34 AAA_23 PF13476.5 200 AT1G56520… - 897
## 35 AAA_23 PF13476.5 200 AT1G56520… - 897
## 36 ABC_tran PF00005.26 137 AT1G56520… - 897
## 37 NTPase_1 PF03266.14 168 AT1G56520… - 897
## 38 AAA_29 PF13555.5 61 AT1G56520… - 897
## 39 AAA_29 PF13555.5 61 AT1G56520… - 897
## 40 LRR_1 PF00560.32 23 AT1G56520… - 897
## 41 LRR_1 PF00560.32 23 AT1G56520… - 897
## 42 LRR_1 PF00560.32 23 AT1G56520… - 897
## 43 LRR_1 PF00560.32 23 AT1G56520… - 897
## 44 LRR_1 PF00560.32 23 AT1G56520… - 897
## 45 LRR_1 PF00560.32 23 AT1G56520… - 897
## 46 LRR_1 PF00560.32 23 AT1G56520… - 897
## 47 LRR_1 PF00560.32 23 AT1G56520… - 897
## 48 DAO PF01266.23 352 AT3G10370… - 629
## 49 DAO PF01266.23 352 AT3G10370… - 629
## 50 DAO_C PF16901.4 126 AT3G10370… - 629
## 51 FAD_bindin… PF00890.23 417 AT3G10370… - 629
## 52 FAD_bindin… PF00890.23 417 AT3G10370… - 629
## 53 FAD_oxidor… PF12831.6 433 AT3G10370… - 629
## 54 FAD_oxidor… PF12831.6 433 AT3G10370… - 629
## 55 Pyr_redox_2 PF07992.13 292 AT3G10370… - 629
## 56 FAD_bindin… PF01494.18 356 AT3G10370… - 629
## 57 FAD_bindin… PF01494.18 356 AT3G10370… - 629
## 58 GIDA PF01134.21 392 AT3G10370… - 629
## 59 GIDA PF01134.21 392 AT3G10370… - 629
## 60 Pyr_redox PF00070.26 81 AT3G10370… - 629
## 61 HI0933_like PF03486.13 409 AT3G10370… - 629
## 62 AAA_30 PF13604.5 192 AT3G10370… - 629
## 63 AAA_30 PF13604.5 192 AT3G10370… - 629
## 64 Pyr_redox_3 PF13738.5 305 AT3G10370… - 629
## 65 DUF4179 PF13786.5 88 AT3G10370… - 629
## 66 DUF4179 PF13786.5 88 AT3G10370… - 629
## 67 3HCDH_N PF02737.17 180 AT3G10370… - 629
## 68 3HCDH_N PF02737.17 180 AT3G10370… - 629
## 69 NAD_bindin… PF13450.5 68 AT3G10370… - 629
## 70 NAD_bindin… PF13450.5 68 AT3G10370… - 629
## sequence_evalue sequence_score sequence_bias domain_N domain_of
## <dbl> <dbl> <dbl> <int> <int>
## 1 2.30e-61 206. 10.4 1 2
## 2 2.30e-61 206. 10.4 2 2
## 3 4.60e-78 263 0 1 1
## 4 4.70e-24 83.6 1.5 1 1
## 5 6.70e-20 71.5 0.1 1 1
## 6 3.20e-18 66 0 1 2
## 7 3.20e-18 66 0 2 2
## 8 1.20e- 3 18.8 0.1 1 2
## 9 1.20e- 3 18.8 0.1 2 2
## 10 7.30e-46 156. 0 1 1
## 11 1.90e-17 63.1 0 1 1
## 12 1.00e- 7 31.4 1.1 1 2
## 13 1.00e- 7 31.4 1.1 2 2
## 14 2.30e- 7 30.4 7 1 6
## 15 2.30e- 7 30.4 7 2 6
## 16 2.30e- 7 30.4 7 3 6
## 17 2.30e- 7 30.4 7 4 6
## 18 2.30e- 7 30.4 7 5 6
## 19 2.30e- 7 30.4 7 6 6
## 20 2.70e- 7 30.6 17.6 1 5
## 21 2.70e- 7 30.6 17.6 2 5
## 22 2.70e- 7 30.6 17.6 3 5
## 23 2.70e- 7 30.6 17.6 4 5
## 24 2.70e- 7 30.6 17.6 5 5
## 25 2.60e- 5 24.4 0.1 1 2
## 26 2.60e- 5 24.4 0.1 2 2
## 27 2.00e- 4 21.7 0.3 1 1
## 28 1.00e- 3 19.5 0 1 1
## 29 4.80e- 3 17.1 1 1 1
## 30 1.50e- 2 15.1 0 1 1
## 31 2.80e- 2 13.8 1.1 1 2
## 32 2.80e- 2 13.8 1.1 2 2
## 33 2.90e- 2 14.2 0 1 1
## 34 3.90e- 2 14.4 0 1 2
## 35 3.90e- 2 14.4 0 2 2
## 36 4.40e- 2 14.2 0 1 1
## 37 6.20e- 2 13.1 0 1 1
## 38 7.90e- 2 12.6 0.1 1 2
## 39 7.90e- 2 12.6 0.1 2 2
## 40 1.50e- 1 12.6 14.8 1 8
## 41 1.50e- 1 12.6 14.8 2 8
## 42 1.50e- 1 12.6 14.8 3 8
## 43 1.50e- 1 12.6 14.8 4 8
## 44 1.50e- 1 12.6 14.8 5 8
## 45 1.50e- 1 12.6 14.8 6 8
## 46 1.50e- 1 12.6 14.8 7 8
## 47 1.50e- 1 12.6 14.8 8 8
## 48 3.20e-53 181. 0.1 1 2
## 49 3.20e-53 181. 0.1 2 2
## 50 9.00e-39 132. 0.3 1 1
## 51 6.30e- 7 28.7 1.9 1 2
## 52 6.30e- 7 28.7 1.9 2 2
## 53 1.00e- 4 21.7 1.1 1 2
## 54 1.00e- 4 21.7 1.1 2 2
## 55 1.40e- 2 14.6 0 1 1
## 56 1.50e- 2 14.5 0.2 1 2
## 57 1.50e- 2 14.5 0.2 2 2
## 58 3.60e- 2 13 0.2 1 2
## 59 3.60e- 2 13 0.2 2 2
## 60 6.30e- 2 13.8 0.7 1 1
## 61 7.50e- 2 11.6 0.2 1 1
## 62 7.70e- 2 12.6 0.6 1 2
## 63 7.70e- 2 12.6 0.6 2 2
## 64 1.00e- 1 11.7 0 1 1
## 65 1.80e- 1 12.2 0.9 1 2
## 66 1.80e- 1 12.2 0.9 2 2
## 67 3.10e- 1 10.8 2 1 2
## 68 3.10e- 1 10.8 2 2 2
## 69 1.40e+ 0 9.1 5 1 2
## 70 1.40e+ 0 9.1 5 2 2
## domain_cevalue domain_ievalue domain_score domain_bias hmm_from hmm_to
## <dbl> <dbl> <dbl> <dbl> <int> <int>
## 1 4.30e-65 7.10e-61 205. 11.2 4 168
## 2 4.30e- 1 7.20e+ 3 -3.6 0 55 67
## 3 1.50e-81 1.30e-77 262. 0 1 344
## 4 1.30e-27 1.10e-23 82.4 1.5 3 55
## 5 3.40e-23 1.90e-19 70 0.1 2 171
## 6 3.10e- 1 1.70e+ 3 -0.7 0 21 72
## 7 5.40e-21 3.00e-17 62.9 0 15 110
## 8 1.70e+ 0 9.40e+ 3 -3.7 0.1 102 123
## 9 1.50e- 6 8.40e- 3 16 0 4 169
## 10 1.30e-48 1.20e-45 155. 0 2 164
## 11 3.60e-20 3.50e-17 62.3 0 4 262
## 12 1.00e-10 1.00e- 7 31.4 1.1 1 20
## 13 1.30e+ 0 1.30e+ 3 -0.6 0.5 1 14
## 14 1.10e+ 0 1.10e+ 3 -0.6 0 15 31
## 15 1.30e- 3 1.30e+ 0 8.8 0.3 2 58
## 16 6.40e- 3 6.20e+ 0 6.6 0.2 2 59
## 17 1.10e- 1 1.10e+ 2 2.6 0.1 2 57
## 18 4.90e- 6 4.80e- 3 16.5 0 2 60
## 19 2.00e- 3 2.00e+ 0 8.2 0.1 27 59
## 20 8.40e+ 0 8.30e+ 3 -2.6 0 19 33
## 21 6.60e- 3 6.50e+ 0 7.2 0.1 2 33
## 22 1.00e- 2 1.00e+ 1 6.6 0.3 12 38
## 23 1.70e- 3 1.60e+ 0 9.1 0 1 39
## 24 4.80e- 6 4.70e- 3 17.2 0.2 3 42
## 25 9.50e- 8 9.30e- 5 22.6 0 1 85
## 26 6.10e+ 0 6.00e+ 3 -2.5 0.1 16 55
## 27 7.80e- 7 7.70e- 4 19.8 0.3 3 63
## 28 2.40e- 6 2.40e- 3 18.3 0 1 69
## 29 2.40e- 5 2.40e- 2 14.8 1 7 113
## 30 4.70e- 5 4.60e- 2 13.5 0 8 82
## 31 3.60e- 3 3.50e+ 0 6.9 0.2 18 39
## 32 1.10e- 2 1.10e+ 1 5.3 0 87 161
## 33 5.80e- 5 5.70e- 2 13.2 0 3 95
## 34 3.50e- 4 3.40e- 1 11.3 0 20 50
## 35 1.40e+ 0 1.40e+ 3 -0.5 0 118 143
## 36 9.60e- 5 9.50e- 2 13.1 0 12 36
## 37 1.60e- 4 1.60e- 1 11.8 0 2 87
## 38 1.30e- 3 1.30e+ 0 8.7 0.1 18 42
## 39 3.60e- 1 3.50e+ 2 0.9 0 3 25
## 40 8.60e+ 0 8.50e+ 3 -1.9 0 1 13
## 41 1.90e+ 0 1.90e+ 3 0.1 0.1 1 12
## 42 7.10e- 1 7.00e+ 2 1.4 0 1 21
## 43 1.90e- 1 1.90e+ 2 3.1 0 1 13
## 44 6.40e+ 0 6.20e+ 3 -1.5 0 3 13
## 45 2.40e- 2 2.40e+ 1 5.9 0 2 12
## 46 1.70e- 1 1.60e+ 2 3.3 0.3 1 16
## 47 4.40e+ 0 4.30e+ 3 -1 0 8 21
## 48 7.20e-56 8.60e-53 180. 0 1 351
## 49 1.40e+ 0 1.70e+ 3 -1.8 0.1 68 106
## 50 1.30e-41 1.60e-38 131. 0.3 1 125
## 51 1.90e- 6 2.30e- 3 17 1.2 1 41
## 52 2.40e- 4 2.90e- 1 10.1 0 154 213
## 53 3.60e- 7 4.30e- 4 19.7 0.3 1 40
## 54 3.40e- 1 4.10e+ 2 -0.1 0 100 143
## 55 2.60e- 5 3.10e- 2 13.4 0 2 36
## 56 3.30e- 4 3.90e- 1 9.8 0.5 3 51
## 57 6.90e- 2 8.30e+ 1 2.2 0 117 179
## 58 1.90e- 4 2.30e- 1 10.4 0.1 1 29
## 59 2.70e- 1 3.30e+ 2 0 0 110 159
## 60 2.30e- 4 2.80e- 1 11.7 0.7 2 32
## 61 1.20e- 4 1.50e- 1 10.6 0.2 2 32
## 62 3.10e+ 0 3.70e+ 3 -2.7 0.1 5 39
## 63 1.40e- 4 1.70e- 1 11.5 0 32 81
## 64 1.50e- 4 1.80e- 1 10.9 0 166 220
## 65 5.90e- 4 7.10e- 1 10.3 0 5 37
## 66 1.50e+ 0 1.80e+ 3 -0.6 0.1 10 57
## 67 3.00e- 4 3.60e- 1 10.6 0.2 2 32
## 68 1.90e+ 0 2.20e+ 3 -1.8 0.1 30 65
## 69 2.70e- 4 3.20e- 1 11.2 0.6 1 42
## 70 4.60e+ 0 5.50e+ 3 -2.4 0 31 40
## # ... with 6 more variables: ali_from <int>, ali_to <int>, env_from <int>,
## # env_to <int>, acc <dbl>, description <chr>
The tblout output is fairly similar and presents the same parsing difficulties:
# --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
# target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target
#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- ---------------------
Rer1 PF03248.12 AT2G18240.1 - 2.3e-61 206.4 10.4 7.1e-61 204.8 11.2 1.3 2 0 0 2 2 2 1 Rer1 family
DUF4220 PF13968.5 AT5G45530.1 - 4.6e-78 263.0 0.0 1.3e-77 261.5 0.0 1.7 1 1 0 1 1 1 1 Domain of unknown function (DUF4220)
DUF594 PF04578.12 AT5G45530.1 - 4.7e-24 83.6 1.5 1.1e-23 82.4 1.5 1.7 1 0 0 1 1 1 1 Protein of unknown function, DUF594
DEAD PF00270.28 AT1G27880.2 - 6.7e-20 71.5 0.1 1.9e-19 70.0 0.1 1.8 1 0 0 1 1 1 1 DEAD/DEAH box helicase
Helicase_C PF00271.30 AT1G27880.2 - 3.2e-18 66.0 0.0 3e-17 62.9 0.0 2.5 2 0 0 2 2 2 1 Helicase conserved C-terminal domain
ResIII PF04851.14 AT1G27880.2 - 0.0012 18.8 0.1 0.0084 16.0 0.0 2.4 2 1 0 2 2 2 1 Type III restriction enzyme, res subunit
...
#
# Program: hmmscan
# Version: 3.1b2 (February 2015)
# Pipeline mode: SCAN
# Query file: five.faa
# Target file: /home/z/db/Pfam-A.hmm
# Option settings: hmmscan --tblout x.tblout --domtblout x.domtblout --pfamtblout x.pfamtblout --noali /home/z/db/Pfam-A.hmm five.faa
# Current dir: /home/z/src/git/rhmmer/tests/testthat/sample-data
# Date: Fri Dec 15 02:09:00 2017
# [ok]
tblout <- system.file('extdata', 'example.tblout.txt', package='rhmmer')
read_tblout(tblout)
## # A tibble: 37 x 19
## domain_name domain_accession query_name query_accession sequence_evalue
## <chr> <chr> <chr> <chr> <dbl>
## 1 Rer1 PF03248.12 AT2G18240… - 2.30e-61
## 2 DUF4220 PF13968.5 AT5G45530… - 4.60e-78
## 3 DUF594 PF04578.12 AT5G45530… - 4.70e-24
## 4 DEAD PF00270.28 AT1G27880… - 6.70e-20
## 5 Helicase_C PF00271.30 AT1G27880… - 3.20e-18
## 6 ResIII PF04851.14 AT1G27880… - 1.20e- 3
## 7 TIR PF01582.19 AT1G56520… - 7.30e-46
## 8 NB-ARC PF00931.21 AT1G56520… - 1.90e-17
## 9 LRR_3 PF07725.11 AT1G56520… - 1.00e- 7
## 10 LRR_8 PF13855.5 AT1G56520… - 2.30e- 7
## 11 LRR_4 PF12799.6 AT1G56520… - 2.70e- 7
## 12 TIR_2 PF13676.5 AT1G56520… - 2.60e- 5
## 13 AAA_16 PF13191.5 AT1G56520… - 2.00e- 4
## 14 AAA_18 PF13238.5 AT1G56520… - 1.00e- 3
## 15 AAA_22 PF13401.5 AT1G56520… - 4.80e- 3
## 16 ATPase_2 PF01637.17 AT1G56520… - 1.50e- 2
## 17 PhoH PF02562.15 AT1G56520… - 2.80e- 2
## 18 NACHT PF05729.11 AT1G56520… - 2.90e- 2
## 19 AAA_23 PF13476.5 AT1G56520… - 3.90e- 2
## 20 ABC_tran PF00005.26 AT1G56520… - 4.40e- 2
## 21 NTPase_1 PF03266.14 AT1G56520… - 6.20e- 2
## 22 AAA_29 PF13555.5 AT1G56520… - 7.90e- 2
## 23 LRR_1 PF00560.32 AT1G56520… - 1.50e- 1
## 24 DAO PF01266.23 AT3G10370… - 3.20e-53
## 25 DAO_C PF16901.4 AT3G10370… - 9.00e-39
## 26 FAD_bindin… PF00890.23 AT3G10370… - 6.30e- 7
## 27 FAD_oxidor… PF12831.6 AT3G10370… - 1.00e- 4
## 28 Pyr_redox_2 PF07992.13 AT3G10370… - 1.40e- 2
## 29 FAD_bindin… PF01494.18 AT3G10370… - 1.50e- 2
## 30 GIDA PF01134.21 AT3G10370… - 3.60e- 2
## 31 Pyr_redox PF00070.26 AT3G10370… - 6.30e- 2
## 32 HI0933_like PF03486.13 AT3G10370… - 7.50e- 2
## 33 AAA_30 PF13604.5 AT3G10370… - 7.70e- 2
## 34 Pyr_redox_3 PF13738.5 AT3G10370… - 1.00e- 1
## 35 DUF4179 PF13786.5 AT3G10370… - 1.80e- 1
## 36 3HCDH_N PF02737.17 AT3G10370… - 3.10e- 1
## 37 NAD_bindin… PF13450.5 AT3G10370… - 1.40e+ 0
## sequence_score sequence_bias best_domain_eva… best_domain_sco…
## <dbl> <dbl> <dbl> <dbl>
## 1 206. 10.4 7.10e-61 205.
## 2 263 0 1.30e-77 262.
## 3 83.6 1.5 1.10e-23 82.4
## 4 71.5 0.1 1.90e-19 70
## 5 66 0 3.00e-17 62.9
## 6 18.8 0.1 8.40e- 3 16
## 7 156. 0 1.20e-45 155.
## 8 63.1 0 3.50e-17 62.3
## 9 31.4 1.1 1.00e- 7 31.4
## 10 30.4 7 4.80e- 3 16.5
## 11 30.6 17.6 4.70e- 3 17.2
## 12 24.4 0.1 9.30e- 5 22.6
## 13 21.7 0.3 7.70e- 4 19.8
## 14 19.5 0 2.40e- 3 18.3
## 15 17.1 1 2.40e- 2 14.8
## 16 15.1 0 4.60e- 2 13.5
## 17 13.8 1.1 3.50e+ 0 6.9
## 18 14.2 0 5.70e- 2 13.2
## 19 14.4 0 3.40e- 1 11.3
## 20 14.2 0 9.50e- 2 13.1
## 21 13.1 0 1.60e- 1 11.8
## 22 12.6 0.1 1.30e+ 0 8.7
## 23 12.6 14.8 2.40e+ 1 5.9
## 24 181. 0.1 8.60e-53 180.
## 25 132. 0.3 1.60e-38 131.
## 26 28.7 1.9 2.30e- 3 17
## 27 21.7 1.1 4.30e- 4 19.7
## 28 14.6 0 3.10e- 2 13.4
## 29 14.5 0.2 3.90e- 1 9.8
## 30 13 0.2 2.30e- 1 10.4
## 31 13.8 0.7 2.80e- 1 11.7
## 32 11.6 0.2 1.50e- 1 10.6
## 33 12.6 0.6 1.70e- 1 11.5
## 34 11.7 0 1.80e- 1 10.9
## 35 12.2 0.9 7.10e- 1 10.3
## 36 10.8 2 3.60e- 1 10.6
## 37 9.1 5 3.20e- 1 11.2
## best_domain_bis domain_number_e… domain_number_r… domain_number_c…
## <dbl> <dbl> <int> <int>
## 1 11.2 1.3 2 0
## 2 0 1.7 1 1
## 3 1.5 1.7 1 0
## 4 0.1 1.8 1 0
## 5 0 2.5 2 0
## 6 0 2.4 2 1
## 7 0 1.4 1 0
## 8 0 1.4 1 0
## 9 1.1 2.7 2 0
## 10 0 5.5 3 2
## 11 0.2 6.1 6 1
## 12 0 1.9 2 0
## 13 0.3 2 1 1
## 14 0 1.7 1 0
## 15 1 2.1 1 1
## 16 0 1.8 1 1
## 17 0.2 2.3 1 1
## 18 0 1.5 1 0
## 19 0 2.3 2 0
## 20 0 1.5 1 0
## 21 0 1.7 1 1
## 22 0.1 2.3 2 0
## 23 0 7.8 8 1
## 24 0 1.6 2 0
## 25 0.3 1.4 1 0
## 26 1.2 2.3 2 0
## 27 0.3 2.2 2 0
## 28 0 1.5 1 0
## 29 0.5 2.1 2 0
## 30 0.1 2 2 0
## 31 0.7 2.1 1 0
## 32 0.2 1.5 1 0
## 33 0 1.9 2 0
## 34 0 1.3 1 0
## 35 0 2.2 2 0
## 36 0.2 2 2 0
## 37 0.6 2.3 3 0
## # ... with 6 more variables: domain_number_ov <int>,
## # domain_number_env <int>, domain_number_dom <int>,
## # domain_number_rep <int>, domain_number_inc <chr>, description <chr>
What rhmmer does and doesn't
What rhmmer currently does
- parse HMMER output (tblout and domtblout) into tidy data frames
What rhmmer may do in the future
-
provide visualization or analysis of HMMER results
-
provide simple wrappers for calling some of the HMMER functions
-
parse metadata from the comments in HMMER output files
-
read pfamtblout and the raw output (with alignments)
-
read the HMM models
-
download databases for you (e.g. PFAM)
-
access precompiled PFAM results
What rhmmer will never do
-
interface with the HMMER web server (use Bio3D)
-
duplicate the whole HMMER api (just use the CLI tool)
TODO
[ ] Rewrite the parser in C++
[ ] Parse out the file metadata
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