Merge branch 'main' of github.com:Adamtaranto/TIRmite

Author: Adamtaranto

README.md

@@ -94,7 +94,7 @@ Test installation.
 ```bash
 # Print version number and exit.
 % tirmite --version
-tirmite 1.3.0
+tirmite 1.4.0
 
 # Get usage information
 % tirmite --help

docs/tutorials/tirmite-pair.md

@@ -618,6 +618,31 @@ tirmite pair \
   --outdir MY_TIR_OUTPUT
 ```
 
+### Disabling sequence extraction
+
+Extracting sequences from a large genome FASTA or BLAST database can be time-consuming. Use `--no-hits` and/or `--no-elements` to skip FASTA output when the sequences are not required.
+
+| Flag | Effect |
+|------|--------|
+| `--no-hits` | Skip writing individual terminus hit sequences to FASTA |
+| `--no-elements` | Skip extraction and writing of full-length paired element sequences to FASTA |
+
+These flags are independent and can be combined. GFF3 output, summary reports, and flank/insertion-site extraction are unaffected.
+
+```bash
+tirmite pair \
+  --genome $GENOME \
+  --nhmmer-file $NHMMERFILE \
+  --hmm-file $HMMFILE \
+  --orientation F,R \
+  --mincov 0.4 \
+  --maxdist 20000 \
+  --no-hits \
+  --no-elements \
+  --gff \
+  --outdir MY_TIR_OUTPUT
+```
+
 ## Key Options Reference
 
 | Option | Description |
@@ -647,4 +672,6 @@ tirmite pair \
 | `--tsd-in-model` | The TSD is encoded at the inner end of the terminus HMM model |
 | `--gff-report` | Reporting mode: `all`, `paired`, or `unpaired` |
 | `--gff` | Write GFF3 annotation file |
+| `--no-hits` | Skip writing individual hit sequences to FASTA |
+| `--no-elements` | Skip extraction and writing of paired element sequences to FASTA |
 | `--logfile` | Write log to file |

src/tirmite/cli/hmm_pair.py

@@ -845,6 +845,30 @@ def _configure_pair_parser(parser: argparse.ArgumentParser) -> None:
         help='Only report individual hits, skip pairing.',
     )
 
+    parser.add_argument(
+        '--no-hits',
+        action='store_true',
+        default=False,
+        dest='no_hits',
+        help=(
+            'Skip writing individual hit sequences to FASTA. '
+            'Useful when extracting sequences from a large genome or BLAST database '
+            'would be time-consuming and hit sequences are not required.'
+        ),
+    )
+
+    parser.add_argument(
+        '--no-elements',
+        action='store_true',
+        default=False,
+        dest='no_elements',
+        help=(
+            'Skip extraction and writing of paired element sequences to FASTA. '
+            'Useful when extracting full-length elements from a large genome or '
+            'BLAST database would be time-consuming and element sequences are not required.'
+        ),
+    )
+
     parser.add_argument(
         '--gff',
         action='store_true',
@@ -1803,7 +1827,7 @@ def main(args: Optional[argparse.Namespace] = None) -> int:
         # Write individual hits
         # In pairing_map mode individual hits are written per pair (below),
         # so only write to the base outDir when no pairing map is used.
-        if not pairing_map:
+        if not pairing_map and not args.no_hits:
             logging.info('Writing individual hits to FASTA...')
             tirmite.writeTIRs(
                 outDir=outDir,
@@ -1908,17 +1932,18 @@ def main(args: Optional[argparse.Namespace] = None) -> int:
                 # Write individual hits for the models in this pair
                 pair_hit_models = {left_feature, right_feature}
                 pair_hitTable_tirs = hitTable[hitTable['model'].isin(pair_hit_models)]
-                logging.info(f'Writing individual hits for pair {pair_label}...')
-                tirmite.writeTIRs(
-                    outDir=pair_outDir,
-                    hitTable=pair_hitTable_tirs,
-                    maxeval=args.maxeval,
-                    genome=genome,
-                    prefix=args.prefix,
-                    padlen=args.padlen,
-                    genome_descriptions=genome_descriptions,
-                    blastdb=args.blastdb if args.blastdb else None,
-                )
+                if not args.no_hits:
+                    logging.info(f'Writing individual hits for pair {pair_label}...')
+                    tirmite.writeTIRs(
+                        outDir=pair_outDir,
+                        hitTable=pair_hitTable_tirs,
+                        maxeval=args.maxeval,
+                        genome=genome,
+                        prefix=args.prefix,
+                        padlen=args.padlen,
+                        genome_descriptions=genome_descriptions,
+                        blastdb=args.blastdb if args.blastdb else None,
+                    )
 
                 # Write paired TIRs
                 if args.gff_report in ['all', 'paired']:
@@ -1934,16 +1959,19 @@ def main(args: Optional[argparse.Namespace] = None) -> int:
                     )
 
                 # Extract and write elements for this pair
-                pair_pairedEles = tirmite.fetchElements(
-                    paired=pair_paired,
-                    hitIndex=pair_hitIndex,
-                    genome=genome,
-                    genome_descriptions=genome_descriptions,
-                    blastdb=args.blastdb if args.blastdb else None,
-                )
-                tirmite.writeElements(
-                    pair_outDir, eleDict=pair_pairedEles, prefix=args.prefix
-                )
+                if not args.no_elements:
+                    pair_pairedEles = tirmite.fetchElements(
+                        paired=pair_paired,
+                        hitIndex=pair_hitIndex,
+                        genome=genome,
+                        genome_descriptions=genome_descriptions,
+                        blastdb=args.blastdb if args.blastdb else None,
+                    )
+                    tirmite.writeElements(
+                        pair_outDir, eleDict=pair_pairedEles, prefix=args.prefix
+                    )
+                else:
+                    pair_pairedEles = {}
 
                 # Extract and write flanks for this pair
                 if args.flanks or args.flanks_paired:
@@ -2125,17 +2153,20 @@ def main(args: Optional[argparse.Namespace] = None) -> int:
                 )
 
             # Extract and write elements
-            logging.info('Extracting paired elements...')
-            pairedEles = tirmite.fetchElements(
-                paired=paired,
-                hitIndex=hitIndex,
-                genome=genome,
-                genome_descriptions=genome_descriptions,
-                blastdb=args.blastdb if args.blastdb else None,
-            )
+            if not args.no_elements:
+                logging.info('Extracting paired elements...')
+                pairedEles = tirmite.fetchElements(
+                    paired=paired,
+                    hitIndex=hitIndex,
+                    genome=genome,
+                    genome_descriptions=genome_descriptions,
+                    blastdb=args.blastdb if args.blastdb else None,
+                )
 
-            logging.info('Writing paired elements to FASTA...')
-            tirmite.writeElements(outDir, eleDict=pairedEles, prefix=args.prefix)
+                logging.info('Writing paired elements to FASTA...')
+                tirmite.writeElements(outDir, eleDict=pairedEles, prefix=args.prefix)
+            else:
+                pairedEles = {}
 
             # Write summary report for single-pairing mode
             if config is not None: