Display percentages in the CLI output (#88) (pinellolab#473)

* D3-Enhancements (#78)

* Sam/try plots (#71)

* Fix batch mode pandas warning. (#70)

* refactor to call method on DataFrame, rather than Series.
Removes warning.

* Fix pandas future warning in CRISPRessoWGS

---------



* Functional

* Cole/fix status file name (#69)

* Update config file logging messages

This removes printing the exception (which is essentially a duplicate),
and adds a condition if no config file was provided. Also changes `json`
to `config` so that it is more clear.

* Fix divide by zero when no amplicons are present in Batch mode

* Don't append file_prefix to status file name

* Place status files in output directories

* Update tests branch for file_prefix addition

* Load D3 and plotly figures with pro with multiple amplicons

* Update batch

* Fix bug in CRISPRessoCompare with pointing to report datas with file_prefix

Before this fix, when using a file_prefix the second run that was compared
would not be displayed as a data in the first figure of the report.

* Import CRISPRessoPro instead of importing the version

When installed via conda, the version is not available

* Remove `get_amplicon_output` unused function from CRISPRessoCompare

Also remove unused argparse import

* Implement `get_matching_allele_files` in CRISPRessoCompare and accompanying unit tests

* Allow for matching of multiple guides in the same amplicon

* Fix pandas FutureWarning

* Change test branch back to master

---------



* Try catch all futures

* Fix test fail plots

* Point test to try-plots

* Fix d3 not showing and plotly mixing with matplotlib

* Use logger for warnings and debug statements

* Point tests back at master

---------




* Sam/fix plots (#72)

* Fix batch mode pandas warning. (#70)

* refactor to call method on DataFrame, rather than Series.
Removes warning.

* Fix pandas future warning in CRISPRessoWGS

---------



* Functional

* Cole/fix status file name (#69)

* Update config file logging messages

This removes printing the exception (which is essentially a duplicate),
and adds a condition if no config file was provided. Also changes `json`
to `config` so that it is more clear.

* Fix divide by zero when no amplicons are present in Batch mode

* Don't append file_prefix to status file name

* Place status files in output directories

* Update tests branch for file_prefix addition

* Load D3 and plotly figures with pro with multiple amplicons

* Update batch

* Fix bug in CRISPRessoCompare with pointing to report datas with file_prefix

Before this fix, when using a file_prefix the second run that was compared
would not be displayed as a data in the first figure of the report.

* Import CRISPRessoPro instead of importing the version

When installed via conda, the version is not available

* Remove `get_amplicon_output` unused function from CRISPRessoCompare

Also remove unused argparse import

* Implement `get_matching_allele_files` in CRISPRessoCompare and accompanying unit tests

* Allow for matching of multiple guides in the same amplicon

* Fix pandas FutureWarning

* Change test branch back to master

---------



* Try catch all futures

* Fix test fail plots

* Fix d3 not showing and plotly mixing with matplotlib

---------




* Remove token from integration tests file

* Provide sgRNA_sequences to plot_nucleotide_quilt plots

* Passing sgRNA_sequences to plot

* Refactor check for determining when to use CRISPREssoPro or matplotlib for Batch plots

* Add max-height to Batch report samples

* Change testing branch

* Fix wrong check for large Batch plots

* Fix typo and move flexiguide to debug (#77)

* Change flexiguide output to debug level

* Fix typo in fastp merged output file name

* Adding id tags for d3 script enhancements

* pointing to test branch

* Add amplicon_name parameter to allele heatmap and line plots

* Add function to extract quantification window regions from include_idxs

* Scale the quantification window according to the coordinates of the sgRNA plot

* added c2pro check, added space in args.json

* Correct the quantification window indexes for multiple guides

* Fix name of nucleotide conversion plot when guides are not the same

* Fix jinja variables that aren't found

* Fix multiple guide errors where the wrong sgRNA sequence was associated in d3 plot

* Remove unneeded variable and extra whitespace

* Switch test branch to master

---------





* Display percentages in the CLI output

---------

Co-authored-by: Trevor Martin <60452953+trevormartinj7@users.noreply.github.com>
Co-authored-by: Samuel Nichols <Snic9004@gmail.com>
Co-authored-by: mbowcut2 <55161542+mbowcut2@users.noreply.github.com>

CRISPResso2/CRISPRessoShared.py

@@ -114,8 +114,8 @@ def emit(self, record):
 class LogStreamHandler(logging.StreamHandler):
     def __init__(self, stream=None):
         super().__init__(stream)
-        self.setFormatter(logging.Formatter(
-            '%(levelname)-5s @ %(asctime)s:\n\t %(message)s \n',
+        self.setFormatter(StatusFormatter(
+            '%(levelname)-5s @ %(asctime)s (%(percent_complete)s%% done):\n\t %(message)s \n',
             datefmt='%a, %d %b %Y %H:%M:%S',
         ))
         self.setLevel(logging.INFO)