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 |
||
|---|---|---|---|
| Returns: | |||
| Raises: |
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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