results¶
The results module contains functions to handle the final reports.
merging results of each sequence
generate a summary
or filter the calin
-
integron_finder.results.
_log
= <Logger integron_finder.results (WARNING)>¶ utilities to manage results
-
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
-
integron_finder.results.
integrons_report
(integrons)[source]¶ - Parameters
integrons (list of
integron_finder.integron.Integron
object.) – list of integrons used to generate a report- Returns
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”
-
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.
-
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’