Fix #90 add support for contig ends with dnaapler all

HISTORY.md

@@ -3,7 +3,7 @@
 # 1.0.1 (2024-11-22)
 
 * Thanks to the inimitable @[rrwick](https://github.com/rrwick), v1.0.1 is a patch fixing a string-parsing bug.
-* If your contig headers were integers, `dnaapler` did not rotate the found `BLAST/MMseqs2` hits. This was pre-existing (not introduced by v1.0.0).
+* If your contig headers were integers, `dnaapler` did not rotate the found `BLAST/MMseqs2` hits. This was a pre-existing issue (not introduced by v1.0.0).
 
 # 1.0.0 (2024-11-21)
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dnaapler"
-version = "1.0.1" # change VERSION too
+version = "1.1.0" # change VERSION too
 description = "Reorients assembled microbial sequences"
 authors = ["George Bouras <[email protected]>"]
 license = "MIT"

src/dnaapler/__init__.py

@@ -21,6 +21,7 @@
 )
 from dnaapler.utils.constants import DNAAPLER_DB
 from dnaapler.utils.external_tools import ExternalTool
+from dnaapler.utils.processing import rotate_input
 from dnaapler.utils.util import (
     begin_dnaapler,
     check_duplicate_headers,
@@ -841,7 +842,7 @@ def bulk(
     default="all",
     type=click.STRING,
     callback=validate_choice_db,
-    help="Lets you choose a subset of databases rather than all 3. Must be one of: 'all', 'dnaa', 'repa', terl', 'dnaa,repa', 'dnaa,terl' or 'repa,terl' ",
+    help="Lets you choose a subset of databases rather than all 4. Must be one of: 'all', 'dnaa', 'repa', terl', 'cog1474', 'dnaa,repa', 'dnaa,terl', 'repa,terl',  'dnaA,cog1474', 'cog1474,terl', 'cog1474,repa', 'dnaa,cog1474,repa', 'dnaa,cog1474,terl' or 'cog1474,repa,terl'",
     show_default=True,
 )
 @click.option(
@@ -968,9 +969,14 @@ def all(
     else:
         custom_db = None
 
+    # rotate all replicons by half the length of the contig
+    # the rotated input for MMSeqs2 will have the original contigs + the rotated ones with suffix "rotated_"
+    rotated_input = os.path.join(output, "rotated_input.fasta")
+    rotate_input(input, rotated_input)
+
     # runs bulk MMseqs2
     run_bulk_MMseqs2(
-        ctx, input, output, prefix, gene, evalue, threads, custom_db=custom_db
+        ctx, rotated_input, output, prefix, gene, evalue, threads, custom_db=custom_db
     )
 
     # rerorients MMseqs2
@@ -998,6 +1004,7 @@ def all(
         autocomplete,
         seed_value,
         custom_db=custom_db,
+        gene=gene,
     )
 
     # end dnaapler

src/dnaapler/utils/VERSION

@@ -1 +1 @@
-1.0.1
+1.1.0