rstoolbox.io.read_hmmsearch

rstoolbox.io.read_hmmsearch(filename)

Read output from hmmsearch or hmmscan.

Processess the output of Hidden Markov Models search over a set of sequences with hmmsearch.

Will return a DataFrame with the following columns:

Column Name Data Content
query Query identifier.
description In hmmseach only. Sequence identifier.
domain In hmmscan only. Domain identifier.
definition In hmmscan only. Definition of the domain name.
full-e-value E-value for full sequence match.
full-score Score for full sequence match.
full-bias Bias for full sequence.
dom-e-value E-values for best scored domain.
dom-score Score for best scored domain.
dom-bias Bias for best scored domain.
dom-exp Expected number of domains.
dom-N Actual number of domains.
sequence Part of the sequence aligned on its own.

It will include more columns related with the alignment data itself.

Parameters:

filename (str) – Name of the hmmsearch output file.

Returns:

DataFrame

Raises:
IOError:if filename does not exist.

Example

In [1]: from rstoolbox.io import read_hmmsearch
   ...: import pandas as pd
   ...: pd.set_option('display.width', 1000)
   ...: pd.set_option('display.max_columns', 500)
   ...: df = read_hmmsearch("../rstoolbox/tests/data/search.hmm.gz")
   ...: df.head()
   ...: 
Out[1]: 
    acc  alifrom  alito  bias  c-Evalue                        description  dom-N  dom-bias  dom-e-value  dom-exp  dom-score  envfrom  envto  full-bias  full-e-value  full-score  hmmfrom  hmmto  i-Evalue                       query  score sequence
0  0.83  15.0     74.0   0.0   0.000001  nubinitio_auto_55313_1mw7A_0256:A  1.0    0.0       0.000002     1.1      26.7       5.0      75.0   0.0        0.000002      26.7        12.0     69.0   0.000002  cath|4_1_0|1mw7A03/131-205  26.7          
1  0.86  4.0      67.0   0.1   0.000002  nubinitio_auto_68083_1mw7A_0296:A  1.0    0.1       0.000003     1.0      26.1       2.0      73.0   0.1        0.000003      26.2        4.0      62.0   0.000003  cath|4_1_0|1mw7A03/131-205  26.1          
2  0.89  11.0     71.0   0.1   0.000002  nubinitio_auto_70010_1mw7A_0347:A  1.0    0.1       0.000004     1.0      25.9       6.0      73.0   0.1        0.000004      26.1        10.0     66.0   0.000004  cath|4_1_0|1mw7A03/131-205  25.9          
3  0.89  18.0     66.0   0.1   0.000002  nubinitio_auto_68083_1mw7A_0395:A  1.0    0.1       0.000005     1.1      25.7       4.0      72.0   0.1        0.000004      25.9        13.0     61.0   0.000005  cath|4_1_0|1mw7A03/131-205  25.7          
4  0.92  2.0      72.0   0.6   0.000002  nubinitio_auto_65350_1mw7A_0393:A  1.0    0.6       0.000005     1.0      25.7       2.0      75.0   0.6        0.000004      25.9        2.0      67.0   0.000005  cath|4_1_0|1mw7A03/131-205  25.7