add all output

HISTORY.md

@@ -1,5 +1,12 @@
 # History
 
+# 0.4.0 (2023-10-25)
+
+* Implemented a modification to the logic for all cases where the top blastx hit alignment does not begin with a start codon. In this case, dnaapler will find the CDS according the pyrodigal that has the most overlap with the top hit alignment. Thanks @simone-pignotti for this suggestion [here](https://github.com/gbouras13/dnaapler/issues/44).
+* Changes `dnaapler all` output FASTA to `_reoriented.fasta` instead of `_all_reoriented.fasta` for consistency with all other commands (except `dnaapler bulk`).
+* Adds `-a` or `--autocomplete` option with `dnaapler all`.
+* Adds `dnaapler largest` and `-a largest` as an option to orient your sequence beginning with the largest 
+
 # 0.3.2 (2023-09-20)
 
 * Changes `Orffinder` to `Genefinder`  to support `pyrodigal` v3.

README.md

@@ -63,14 +63,17 @@ The full documentation for `dnaapler` can be found [here](https://dnaapler.readt
 
 ## Commands
 
+* `dnaapler all`: Reorients multiple contigs to begin with any of dnaA, terL, repA. 
+  - Practically, this should be the most useful command for most users.
+
 * `dnaapler chromosome`: Reorients your sequence to begin with the dnaA chromosomal replication initiator gene
 * `dnaapler plasmid`: Reorients your sequence to begin with the repA plasmid replication initiation gene
 * `dnaapler phage`: Reorients your sequence to begin with the terL large terminase subunit gene
 * `dnaapler custom`: Reorients your sequence to begin with a custom amino acid FASTA format gene that you specify
 * `dnaapler mystery`: Reorients your sequence to begin with a random CDS
+* `dnaapler mystery`: Reorients your sequence to begin with a random CDS
 * `dnaapler nearest`: Reorients your sequence to begin with the first CDS (nearest to the start). Designed for fixing sequences where a CDS spans the breakpoint.
 * `dnaapler bulk`: Reorients multiple contigs to begin with the desired start gene - either dnaA, terL, repA or a custom gene.
-* `dnaapler all`: Reorients multiple contigs to begin with any of dnaA, terL, repA.
 
 
 ## Installation
@@ -118,17 +121,17 @@ Commands:
   chromosome  Reorients your genome to begin with the dnaA chromosomal...
   citation    Print the citation(s) for this tool
   custom      Reorients your genome with a custom database
+  largest     Reorients your genome the begin with the largest CDS as...
   mystery     Reorients your genome with a random CDS
   nearest     Reorients your genome the begin with the first CDS as...
   phage       Reorients your genome to begin with the terL large...
   plasmid     Reorients your genome to begin with the repA replication...
   ```
 
   ```
-  Usage: dnaapler chromosome [OPTIONS]
+Usage: dnaapler all [OPTIONS]
 
-  Reorients your genome to begin with the dnaA chromosomal replication
-  initiation gene
+  Reorients multiple contigs to begin with any of dnaA, repA or terL
 
 Options:
   -h, --help               Show this message and exit.
@@ -139,9 +142,11 @@ Options:
   -p, --prefix TEXT        Prefix for output files  [default: dnaapler]
   -f, --force              Force overwrites the output directory
   -e, --evalue TEXT        e value for blastx  [default: 1e-10]
+  --ignore PATH            Text file listing contigs (one per row) that are to
+                           be ignored
   -a, --autocomplete TEXT  Choose an option to autocomplete reorientation if
                            BLAST based approach fails. Must be one of: none,
-                           mystery or nearest [default: none]
+                           mystery, largest, or nearest [default: none]
   --seed_value INTEGER     Random seed to ensure reproducibility.  [default:
                            13]
   ```

src/dnaapler/utils/all.py

@@ -24,7 +24,7 @@ def all_process_blast_output_and_reorient(
     autocomplete: str,
     seed_value: int,
 ) -> None:
-    """Processes the blast output,reorients and saves all contigs into os.path.join(output, f"{prefix}_all_reoriented.fasta")
+    """Processes the blast output,reorients and saves all contigs into os.path.join(output, f"{prefix}_reoriented.fasta")
 
     :param input: input file
     :param blast_file: blast output file
@@ -81,7 +81,7 @@ def all_process_blast_output_and_reorient(
     idents = []
     identitys = []
 
-    reoriented_output_file = os.path.join(output, f"{prefix}_all_reoriented.fasta")
+    reoriented_output_file = os.path.join(output, f"{prefix}_reoriented.fasta")
 
     # Read the FASTA file and extract the IDs
     for record in SeqIO.parse(input, "fasta"):