diff --git a/change_log.txt b/change_log.txt index 1aecd6e..966fc25 100644 --- a/change_log.txt +++ b/change_log.txt @@ -1,5 +1,13 @@ Major changes to ClipKIT are summarized here. +2.2.1 +Removed "Processing" block from CLI output. Reordered CLI output to +put user arguments first followed by outputs. Added original length of +the alignment to output statistics. + +2.2.0 +Incorporated C3 trimming, which can be evoked using the c3 trimming mode. + 2.1.2 Incorporate codon-based trimming. When one position in a codon gets trimmed based on the mode being used, the whole codon will get trimmed from the alignment. diff --git a/clipkit/clipkit.py b/clipkit/clipkit.py index a97360d..f3d79ec 100644 --- a/clipkit/clipkit.py +++ b/clipkit/clipkit.py @@ -31,7 +31,6 @@ from .write import ( write_user_args, write_output_stats, - write_processing_aln, write_output_files_message, ) @@ -145,7 +144,6 @@ def execute( # for reporting runtime duration to user start_time = time.time() - write_processing_aln() trim_run, stats = run( input_file, input_file_format, @@ -160,7 +158,6 @@ def execute( use_log, quiet, ) - write_output_files_message(output_file, complement, use_log) # display to user what args are being used in stdout write_user_args( @@ -177,6 +174,8 @@ def execute( use_log, ) + write_output_files_message(output_file, complement, use_log) + if use_log: warn_if_all_sites_were_trimmed(trim_run.msa) warn_if_entry_contains_only_gaps(trim_run.msa) diff --git a/clipkit/write.py b/clipkit/write.py index 5c37f8b..d6dbf48 100644 --- a/clipkit/write.py +++ b/clipkit/write.py @@ -11,19 +11,6 @@ from .modes import TrimmingMode -def write_processing_aln() -> None: - logger.info( - textwrap.dedent( - """\ - - ------------------------ - | Processing Alignment | - ------------------------ - """ # noqa - ) - ) - - def write_user_args( in_file_name: str, in_file_format: "FileFormat", @@ -75,7 +62,6 @@ def write_output_files_message( textwrap.dedent( f"""\ - ------------------------ | Writing output files | ------------------------ @@ -98,9 +84,9 @@ def write_output_stats(stats: "TrimmingStats", start_time: float) -> None: --------------------- | Output Statistics | --------------------- + Original length: {stats.alignment_length} Number of sites kept: {stats.output_length} Number of sites trimmed: {stats.trimmed_length} - Percentage of alignment trimmed: {stats.trimmed_percentage}% Execution time: {round(time.time() - start_time, 3)}s