Documentation updates and rename pretext_to_tpf to pretext_to_asm

README.md

@@ -15,11 +15,17 @@ Added to your `PATH` if the suggested development venv is set up. Run with
 
 Parses and reformats AGP and TPF files, converting into either format.
 
-### [`pretext-to-tpf`](src/tola/assembly/scripts/pretext_to_tpf.py)
+### [`pretext-to-asm`](src/tola/assembly/scripts/pretext_to_asm.py)
 
 Takes the AGP file output by
 [PretextView](https://github.com/wtsi-hpag/PretextView)
-and creates TPF files containing precise coordinates of the curated assembly.
+and the input assembly (usually FASTA), and produces an output assembly in
+FASTA and AGP formats. The input and output file formats are determined from
+the extensions of the files. FASTA input and output uses the `.fai` index
+format, as produced by
+[`faidx`](http://www.htslib.org/doc/samtools-faidx.html), and uses a streaming
+strategy with a 250 KB buffer to keep memory usage low no matter how large
+the chromosome.
 
 ## File Formats
 

pyproject.toml

@@ -21,8 +21,8 @@ devel = [
 
 [project.scripts]
 asm-format = "tola.assembly.scripts.asm_format:cli"
-pretext-to-asm = "tola.assembly.scripts.pretext_to_tpf:cli"
-pretext-to-tpf = "tola.assembly.scripts.pretext_to_tpf:cli"
+pretext-to-asm = "tola.assembly.scripts.pretext_to_asm:cli"
+pretext-to-tpf = "tola.assembly.scripts.pretext_to_asm:cli"
 find-overlaps = "tola.assembly.scripts.find_overlaps:cli"
 
 [tool.setuptools.packages.find]

src/tola/assembly/scripts/pretext_to_tpf.py → src/tola/assembly/scripts/pretext_to_asm.py

@@ -30,7 +30,7 @@ def ul(txt):
 @click.command(
     help=f"""
       Uses fragments in the assembly (AGP) produced by PretextView to find
-      matching fragments in the assembly (TPF) which was fed into Pretext and
+      matching fragments in the assembly which was fed into Pretext and
       output an assembly made from the input assembly fragments.
 
       {ul("Named Chromsomes")}
@@ -78,9 +78,13 @@ def ul(txt):
         path_type=pathlib.Path,
         exists=True,
         readable=True,
+        resolve_path=True,
     ),
     required=True,
-    help="Assembly file from before curation, which is usually a TPF.",
+    help="""Assembly before curation, usually a FASTA file.
+      FASTA files will be indexed, creating a '.fai' and a '.agp' file
+      alongside the assembly if they are missing or are older than the
+      FASTA.""",
 )
 @click.option(
     "--pretext",
@@ -102,8 +106,11 @@ def ul(txt):
         path_type=pathlib.Path,
         dir_okay=False,
     ),
-    help="""Output file, usually a TPF.
-      If not given, prints to STDOUT in 'STR' format.""",
+    help="""Output file, usually a FASTA file.
+      If not given, prints to STDOUT in 'STR' format.
+      The output file type is determined from its extension. If the outuput is
+      FASTA ('.fa'), an AGP format file ('.fa.agp') is also written. Other
+      output files are named after the output file minus its extension.""",
 )
 # @click.option(
 #     "--version",

tests/pretext_to_tpf_test.py → tests/pretext_to_asm_test.py

@@ -6,7 +6,7 @@
 import pytest
 from click.testing import CliRunner
 
-from tola.assembly.scripts.pretext_to_tpf import cli
+from tola.assembly.scripts.pretext_to_asm import cli
 
 
 def list_example_assemblies():