results¶
The results module contains functions to handle the final reports.
- merging results of each sequence
- generate a summary
- or filter the calin
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integron_finder.results.
_log
= <Logger integron_finder.results (WARNING)>¶ utilities to manage results
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integron_finder.results.
filter_calin
(result, threshold=2)[source]¶ filter integron report, remove ‘CALIN’ integron where number of attC sites is lower than threshold.
Parameters: - result (
pandas.dataFrame
object) – the output ofintegrons_report()
- threshold (int) – the integron CALIN with less attc site than threshold are removed
Returns: filtered integron report
Return type: pandas.dataFrame
object- result (
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integron_finder.results.
integrons_report
(integrons)[source]¶ Parameters: integrons (list of integron_finder.integron.Integron
object.) – list of integrons used to generate a reportReturns: a report off all integrons from a replicon Return type: pandas.DataFrame
object. this datafame have following columns:”ID_integron”, “ID_replicon”, “element”, “pos_beg”, “pos_end”, “strand”, “evalue”, “type_elt”, “annotation”, “model”, “type”, “default”, “distance_2attC”, “considered_topology”
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integron_finder.results.
merge_results
(*results_file)[source]¶ Parameters: results_file (str) – The path of the files to merge. The files can be parsed by pandas as DataFrame and have the same columns. It is used to merge the integrons files (.integrons) or summary files (.summary) from different replicons. Returns: all results aggregated in one pandas.DataFrame
object. if there is no results to merge, return an empty DataFrame.Return type: a pandas.DataFrame
object.
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integron_finder.results.
summary
(result)[source]¶ Create a summary of an integron report. Count the number of ‘CALIN’, ‘In0’ or ‘complete’ for each replicon.
Parameters: result – the integron to summarize Returns: a pandas.DataFrame
object. with columns ‘ID_replicon’, ‘ID_integron’, ‘complete’, ‘In0’, ‘CALIN’