updated CLI output. E.g., removed 'processing' block.

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.

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)

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