Update docs for v.1.1.0

- Docs updated for new output files
- Long output filenames simplified

captus/align.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 """
-Copyright 2020-2024 Edgardo M. Ortiz ([email protected])
+Copyright 2020-2025 Edgardo M. Ortiz ([email protected])
 https://github.com/edgardomortiz/Captus
 
 This file is part of Captus. Captus is free software: you can redistribute it and/or modify
@@ -36,7 +36,7 @@ def align(full_command, args):
 
     captus_start = time.time()
     out_dir, out_dir_msg = make_output_dir(args.out)
-    log.logger = log.Log(Path(args.out, "captus-assembly_align.log"), stdout_verbosity_level=1)
+    log.logger = log.Log(Path(args.out, "captus-align.log"), stdout_verbosity_level=1)
 
     mar = 26  # Margin for aligning parameters and values
 
@@ -1538,7 +1538,7 @@ def write_paralog_stats(out_dir, tsv_comment, shared_paralog_stats):
     if not shared_paralog_stats:
         return red("No paralogs were found...")
     else:
-        stats_tsv_file = Path(out_dir, "captus-assembly_align.paralogs.tsv")
+        stats_tsv_file = Path(out_dir, "captus-align_paralogs.tsv")
         with open(stats_tsv_file, "wt") as tsv_out:
             tsv_out.write(tsv_comment)
             tsv_out.write("\t".join(["marker_type",
@@ -1783,7 +1783,7 @@ def write_aln_stats(out_dir, tsv_comment, shared_aln_stats):
     if not shared_aln_stats:
         return None
     else:
-        stats_tsv_file = Path(out_dir, "captus-assembly_align.alignments.tsv")
+        stats_tsv_file = Path(out_dir, "captus-align_alignments.tsv")
         with open(stats_tsv_file, "wt") as tsv_out:
             tsv_out.write(tsv_comment)
             tsv_out.write("\t".join(["path",
@@ -1817,7 +1817,7 @@ def write_sam_stats(out_dir, tsv_comment, shared_sam_stats):
     if not shared_sam_stats:
         return None
     else:
-        stats_tsv_file = Path(out_dir, "captus-assembly_align.samples.tsv")
+        stats_tsv_file = Path(out_dir, "captus-align_samples.tsv")
         with open(stats_tsv_file, "wt") as tsv_out:
             tsv_out.write(tsv_comment)
             tsv_out.write("\t".join(["sample",

captus/assemble.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 """
-Copyright 2020-2024 Edgardo M. Ortiz ([email protected])
+Copyright 2020-2025 Edgardo M. Ortiz ([email protected])
 https://github.com/edgardomortiz/Captus
 
 This file is part of Captus. Captus is free software: you can redistribute it and/or modify
@@ -33,7 +33,7 @@ def assemble(full_command, args):
 
     captus_start = time.time()
     out_dir, out_dir_msg = make_output_dir(args.out)
-    log.logger = log.Log(Path(args.out, "captus-assembly_assemble.log"), stdout_verbosity_level=1)
+    log.logger = log.Log(Path(args.out, "captus-assemble.log"), stdout_verbosity_level=1)
 
     mar = 21  # Margin for aligning parameters and values
 
@@ -1021,7 +1021,7 @@ def calc_asm_stats(
 
 
         msg = (
-            f"'{sample_name}' {stage.upper()}: {num_contigs:,} contigs, total {tot_length:,} bp,"
+            f"'{sample_name}': {stage.upper()} {num_contigs:,} contigs, total {tot_length:,} bp,"
             f" min {min_length:,} bp, max {max_length:,} bp, avg {avg_length:,} bp, N50 {n50:,} bp"
         )
         return msg
@@ -1096,9 +1096,9 @@ def collect_asm_stats(out_dir, tsv_comment):
     depth_tsv_files = sorted(list(Path(out_dir).resolve().rglob("depth_stats.tsv")))
     length_tsv_files = sorted(list(Path(out_dir).resolve().rglob("length_stats.tsv")))
 
-    assembly_stats_tsv = Path(out_dir, "captus-assembly_assemble.assembly_stats.tsv")
-    depth_stats_tsv = Path(out_dir, "captus-assembly_assemble.depth_stats.tsv")
-    length_stats_tsv = Path(out_dir, "captus-assembly_assemble.length_stats.tsv")
+    assembly_stats_tsv = Path(out_dir, "captus-assemble_assembly_stats.tsv")
+    depth_stats_tsv = Path(out_dir, "captus-assemble_depth_stats.tsv")
+    length_stats_tsv = Path(out_dir, "captus-assemble_length_stats.tsv")
 
     if not assembly_tsv_files or not depth_tsv_files or not length_tsv_files:
         return None, None, None

captus/bait.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 """
-Copyright 2020-2024 Edgardo M. Ortiz ([email protected])
+Copyright 2020-2025 Edgardo M. Ortiz ([email protected])
 https://github.com/edgardomortiz/Captus
 
 This file is part of Captus. Captus is free software: you can redistribute it and/or modify
@@ -36,7 +36,7 @@ def bait(full_command, args):
 
     captus_start = time.time()
     out_dir, out_dir_msg = make_output_dir(args.out)
-    log.logger = log.Log(Path(out_dir, "captus-design_bait.log"), stdout_verbosity_level=1)
+    log.logger = log.Log(Path(out_dir, "captus-bait.log"), stdout_verbosity_level=1)
 
     mar = 28  # Margin for aligning parameters and values
 

captus/bioformats.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 """
-Copyright 2020-2024 Edgardo M. Ortiz ([email protected])
+Copyright 2020-2025 Edgardo M. Ortiz ([email protected])
 https://github.com/edgardomortiz/Captus
 
 This file is part of Captus. Captus is free software: you can redistribute it and/or modify

captus/captus_assembly.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 """
-Copyright 2020-2024 Edgardo M. Ortiz ([email protected])
+Copyright 2020-2025 Edgardo M. Ortiz ([email protected])
 https://github.com/edgardomortiz/Captus
 
 This is the control program for the assembly pipeline of Captus.

captus/captus_design.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 """
-Copyright 2020-2024 Edgardo M. Ortiz ([email protected])
+Copyright 2020-2025 Edgardo M. Ortiz ([email protected])
 https://github.com/edgardomortiz/Captus
 
 This is the control program for the bait design pipeline of Captus.

captus/clean.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 """
-Copyright 2020-2024 Edgardo M. Ortiz ([email protected])
+Copyright 2020-2025 Edgardo M. Ortiz ([email protected])
 https://github.com/edgardomortiz/Captus
 
 This file is part of Captus. Captus is free software: you can redistribute it and/or modify
@@ -32,7 +32,7 @@ def clean(full_command, args):
 
     captus_start = time.time()
     out_dir, out_dir_msg = make_output_dir(args.out)
-    log.logger = log.Log(Path(out_dir, "captus-assembly_clean.log"), stdout_verbosity_level=1)
+    log.logger = log.Log(Path(out_dir, "captus-clean.log"), stdout_verbosity_level=1)
 
     mar = 21  # Margin for aligning parameters and values
 

captus/cluster.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 """
-Copyright 2020-2024 Edgardo M. Ortiz ([email protected])
+Copyright 2020-2025 Edgardo M. Ortiz ([email protected])
 https://github.com/edgardomortiz/Captus
 
 This file is part of Captus. Captus is free software: you can redistribute it and/or modify
@@ -35,7 +35,7 @@ def cluster(full_command, args):
 
     captus_start = time.time()
     out_dir, out_dir_msg = make_output_dir(args.out)
-    log.logger = log.Log(Path(out_dir, "captus-design_cluster.log"), stdout_verbosity_level=1)
+    log.logger = log.Log(Path(out_dir, "captus-cluster.log"), stdout_verbosity_level=1)
 
     mar = 23  # Margin for aligning parameters and values
 
@@ -1274,7 +1274,7 @@ def min_copies(aln_trimmed: dict, aln_width: int):
 
 
 def write_aln_stats(out_dir: Path, shared_aln_stats: list):
-    stats_tsv_file = Path(out_dir, "captus-design_cluster.alignments.tsv")
+    stats_tsv_file = Path(out_dir, "captus-cluster_alignments.tsv")
     if not shared_aln_stats:
         if stats_tsv_file.exists() and not file_is_empty(stats_tsv_file):
             return stats_tsv_file

captus/extract.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 """
-Copyright 2020-2024 Edgardo M. Ortiz ([email protected])
+Copyright 2020-2025 Edgardo M. Ortiz ([email protected])
 https://github.com/edgardomortiz/Captus
 
 This file is part of Captus. Captus is free software: you can redistribute it and/or modify
@@ -43,7 +43,7 @@ def extract(full_command, args):
 
     captus_start = time.time()
     out_dir, out_dir_msg = make_output_dir(args.out)
-    log.logger = log.Log(Path(args.out, "captus-assembly_extract.log"), stdout_verbosity_level=1)
+    log.logger = log.Log(Path(args.out, "captus-extract.log"), stdout_verbosity_level=1)
     mar = 25  # Margin for aligning parameters and values
 
     ################################################################################################
@@ -1997,7 +1997,7 @@ def blat_misc_dna(
         else:
             if not keep_all:
                 Path(blat_dna_out_file).unlink()
-            write_gff3(dna_hits, marker_type, disable_stitching, dna_gff_file)
+            write_gff3(dna_hits, marker_type, disable_stitching, tsv_comment, dna_gff_file)
             recovery_stats = write_fastas_and_report(dna_hits, sample_name, dna_target,
                                                      blat_dna_out_dir, marker_type,
                                                      max_loci_files, tsv_comment, overwrite)
@@ -2470,7 +2470,7 @@ def collect_ext_stats(out_dir, tsv_comment):
     if not samples_stats:
         return None
     else:
-        stats_file_out = Path(out_dir, "captus-assembly_extract.stats.tsv")
+        stats_file_out = Path(out_dir, "captus-extract_stats.tsv")
         header = "\t".join(settings.EXT_STATS_HEADER) + "\n"
         with open(stats_file_out, "wt") as tsv_out:
             tsv_out.write(tsv_comment)

captus/log.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 """
-Copyright 2020-2024 Edgardo M. Ortiz ([email protected])
+Copyright 2020-2025 Edgardo M. Ortiz ([email protected])
 https://github.com/edgardomortiz/Captus
 
 This module contains Unicycler's class for writing output to both stdout and a log file.

captus/misc.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 """
-Copyright 2020-2024 Edgardo M. Ortiz ([email protected])
+Copyright 2020-2025 Edgardo M. Ortiz ([email protected])
 https://github.com/edgardomortiz/Captus
 
 This file is part of Captus. Captus is free software: you can redistribute it and/or modify

captus/report.py

@@ -1516,7 +1516,7 @@ def build_qc_report(out_dir, qc_extras_dir):
             <pre><code>Version: {version}{command}</code></pre>
         </body>
     """
-    qc_html_report = Path(out_dir, "captus-assembly_clean.report.html")
+    qc_html_report = Path(out_dir, "captus-clean_report.html")
     with open(qc_html_report, "w") as f:
         f.write(html_header)
         for fig in figs:
@@ -2312,7 +2312,7 @@ def build_assembly_report(out_dir, asm_stats_tsv, len_stats_tsv, dep_stats_tsv):
             <pre><code>Version: {version}{command}</code></pre>
         </body>
     """
-    asm_html_report = Path(out_dir, "captus-assembly_assemble.report.html")
+    asm_html_report = Path(out_dir, "captus-assemble_report.html")
     with open(asm_html_report, "w") as f:
         f.write(html_header)
         for fig in figs:
@@ -2864,7 +2864,7 @@ def build_extraction_report(out_dir, ext_stats_tsv):
             <pre><code>Version: {version}{command}</code></pre>
         </body>
     """
-    ext_html_report = Path(out_dir, "captus-assembly_extract.report.html")
+    ext_html_report = Path(out_dir, "captus-extract_report.html")
     with open(ext_html_report, "w") as f:
         f.write(html_header)
         for fig in figs:
@@ -3750,7 +3750,7 @@ def build_alignment_report(out_dir, aln_stats_tsv, sam_stats_tsv):
         </body>
     """
     # Save plot in html
-    aln_html_report = Path(out_dir, "captus-assembly_align.report.html")
+    aln_html_report = Path(out_dir, "captus-align_report.html")
     with open(aln_html_report, "w") as f:
         f.write(html_header)
         for i, fig in enumerate(figs):
@@ -4066,10 +4066,10 @@ def build_design_report(out_dir, des_stats_tsv, step):
     )
     if step == "cluster":
         report_title = "Captus-design: Cluster (Alignment Report)"
-        des_html_report = Path(out_dir, "captus-design_cluster.report.html")
+        des_html_report = Path(out_dir, "captus-cluster_report.html")
     elif step == "select":
         report_title = "Captus-design: Select (Alignment Report)"
-        des_html_report = Path(out_dir, "captus-design_select.report.html")
+        des_html_report = Path(out_dir, "captus-select_report.html")
     with open(des_stats_tsv, "r") as f:
         version = f.readline().lstrip("#")
         command = f.readline().lstrip("#")

captus/select.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 """
-Copyright 2020-2024 Edgardo M. Ortiz ([email protected])
+Copyright 2020-2025 Edgardo M. Ortiz ([email protected])
 https://github.com/edgardomortiz/Captus
 
 This file is part of Captus. Captus is free software: you can redistribute it and/or modify
@@ -28,7 +28,7 @@ def select(full_command, args):
 
     captus_start = time.time()
     out_dir, out_dir_msg = make_output_dir(args.out)
-    log.logger = log.Log(Path(out_dir, "captus-design_select.log"), stdout_verbosity_level=1)
+    log.logger = log.Log(Path(out_dir, "captus-select.log"), stdout_verbosity_level=1)
 
     mar = 33  # Margin for aligning parameters and values
 
@@ -145,7 +145,7 @@ def select(full_command, args):
 
 def load_aln_stats_tsv(clusters_dir: Path):
     start = time.time()
-    aln_stats_tsv_path = Path(clusters_dir, "captus-design_cluster.alignments.tsv")
+    aln_stats_tsv_path = Path(clusters_dir, "captus-cluster_alignments.tsv")
     if aln_stats_tsv_path.exists():
         aln_stats = {}
         with open(aln_stats_tsv_path, "rt") as stats:
@@ -457,7 +457,7 @@ def copy_loci(aln_stats: dict, out_dir: Path, overwrite: bool, show_more: bool):
 
 
 def write_aln_stats(out_dir: Path, aln_stats_filtered: dict):
-    stats_tsv_file = Path(out_dir, "captus-design_select.alignments.tsv")
+    stats_tsv_file = Path(out_dir, "captus-select_alignments.tsv")
     if not aln_stats_filtered:
         if stats_tsv_file.exists() and not file_is_empty(stats_tsv_file):
             return stats_tsv_file

captus/settings.py

@@ -1,9 +1,9 @@
 #!/usr/bin/env python3
 """
-Copyright 2020-2024 Edgardo M. Ortiz ([email protected])
+Copyright 2020-2025 Edgardo M. Ortiz ([email protected])
 https://github.com/edgardomortiz/Captus
 
-This module contains hard-coded settings for Captus-assembly
+This module contains hard-coded settings for Captus
 
 This file is part of Captus. Captus is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by the Free Software Foundation,
@@ -336,7 +336,7 @@
 TRANSLATED_REF_SUFFIX = ".captus.faa"
 
 # JSON with paths to references filename
-JSON_REFS = "captus-assembly_extract.refs.json"
+JSON_REFS = "captus-extract_refs.json"
 
 # Valid combinations of marker directories and format directories
 VALID_MARKER_FORMAT_COMBO =  [(m, f) for m in ["NUC","PTD","MIT"] for f in ["AA","NT","GE","GF"]]
@@ -598,7 +598,7 @@
 
 # File name for sequence-to-sample equivalence table used by ASTRAL-Pro to analyze trees that
 # include paralogs
-ASTRAL_PRO_EQ = "captus-assembly_align.astral-pro.tsv"
+ASTRAL_PRO_EQ = "captus-align_astral-pro.tsv"
 
 # Import data for clustering file names
 DES_SUFFIXES = {

captus/version.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 """
-Copyright 2020-2024 Edgardo M. Ortiz ([email protected])
+Copyright 2020-2025 Edgardo M. Ortiz ([email protected])
 https://github.com/edgardomortiz/Captus
 
 Captus' version is stored here in a separate file so it can exist in only one place.

captus_assembly-runner.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 """
-Copyright 2020-2024 Edgardo M. Ortiz ([email protected])
+Copyright 2020-2025 Edgardo M. Ortiz ([email protected])
 https://github.com/edgardomortiz/Captus
 
 This file is a convenience wrapper for running Captus assemble directly from the source tree. By

captus_design-runner.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 """
-Copyright 2020-2024 Edgardo M. Ortiz ([email protected])
+Copyright 2020-2025 Edgardo M. Ortiz ([email protected])
 https://github.com/edgardomortiz/Captus
 
 This file is a convenience wrapper for running Captus design directly from the source tree. By