better keyboard escape

Author: pgarrett-scripps

README.md

@@ -19,16 +19,17 @@ Extract MS2 format files (compatible with MS-GF+, Comet, etc.):
 ms2-extractor /path/to/sample.d
 
 # shorthand
-ms2-ex /path/to/sample.d
+ms2-ex 
 ms2-ex /path/to/sample.d --output custom_output.ms2 --min-intensity 100 --min-charge 2
 ms2-ex /path/to/directory_with_multiple_d_folders --output /path/to/output_directory
 ```
 
 ### MGF Extraction  
-Extract MGF format files (compatible with Mascot, MaxQuant, etc.):
+Extract MGF format files
 
 ```bash
 mgf-extractor /path/to/sample.d
+
 #shorthand
 mgf-ex
 mgf-ex /path/to/sample.d --casanovo  # Optimized for Casanovo de novo sequencing

src/tdfextractor/cli_args.py

@@ -171,6 +171,12 @@ def add_common_args(parser: argparse.ArgumentParser) -> None:
         help="Number of decimal places for intensity values (default: 0)",
     )
 
+    parser.add_argument(
+        "--keep-empty-spectra",
+        action="store_true",
+        help="Keep spectra with no peaks (default: False)",
+    )
+
     parser.add_argument(
         "-v", "--verbose", action="store_true", help="Enable verbose logging"
     )
@@ -259,59 +265,60 @@ def log_common_args(logger, args: argparse.Namespace, extractor_type: str) -> No
     logger.info(f"  Precursor Peak Width: {args.precursor_peak_width} Da")
     logger.info(f"  Batch Size: {args.batch_size}")
     logger.info(
-        f"  Top N Peaks: {args.top_n_peaks if args.top_n_peaks else 'All'}"
+        f"  Top N Peaks: {args.top_n_peaks if args.top_n_peaks is not None else 'All'}"
     )
     logger.info(
-        f"  Min Spectra Intensity: {args.min_spectra_intensity if args.min_spectra_intensity else 'None'}"
+        f"  Min Spectra Intensity: {args.min_spectra_intensity if args.min_spectra_intensity is not None else 'None'}"
     )
     logger.info(
-        f"  Max Spectra Intensity: {args.max_spectra_intensity if args.max_spectra_intensity else 'None'}"
+        f"  Max Spectra Intensity: {args.max_spectra_intensity if args.max_spectra_intensity is not None else 'None'}"
     )
     logger.info(
-        f"  Min Spectra m/z: {args.min_spectra_mz if args.min_spectra_mz else 'None'}"
+        f"  Min Spectra m/z: {args.min_spectra_mz if args.min_spectra_mz is not None else 'None'}"
     )
     logger.info(
-        f"  Max Spectra m/z: {args.max_spectra_mz if args.max_spectra_mz else 'None'}"
+        f"  Max Spectra m/z: {args.max_spectra_mz if args.max_spectra_mz is not None else 'None'}"
     )
     logger.info(
-        f"  Min Precursor Intensity: {args.min_precursor_intensity if args.min_precursor_intensity else 'None'}"
+        f"  Min Precursor Intensity: {args.min_precursor_intensity if args.min_precursor_intensity is not None else 'None'}"
     )
     logger.info(
-        f"  Max Precursor Intensity: {args.max_precursor_intensity if args.max_precursor_intensity else 'None'}"
+        f"  Max Precursor Intensity: {args.max_precursor_intensity if args.max_precursor_intensity is not None else 'None'}"
     )
     logger.info(
-        f"  Min Precursor Charge: {args.min_precursor_charge if args.min_precursor_charge else 'None'}"
+        f"  Min Precursor Charge: {args.min_precursor_charge if args.min_precursor_charge is not None else 'None'}"
     )
     logger.info(
-        f"  Max Precursor Charge: {args.max_precursor_charge if args.max_precursor_charge else 'None'}"
+        f"  Max Precursor Charge: {args.max_precursor_charge if args.max_precursor_charge is not None else 'None'}"
     )
     logger.info(
-        f"  Min Precursor m/z: {args.min_precursor_mz if args.min_precursor_mz else 'None'}"
+        f"  Min Precursor m/z: {args.min_precursor_mz if args.min_precursor_mz is not None else 'None'}"
     )
     logger.info(
-        f"  Max Precursor m/z: {args.max_precursor_mz if args.max_precursor_mz else 'None'}"
+        f"  Max Precursor m/z: {args.max_precursor_mz if args.max_precursor_mz is not None else 'None'}"
     )
     logger.info(
-        f"  Min Precursor RT: {args.min_precursor_rt if args.min_precursor_rt else 'None'} seconds"
+        f"  Min Precursor RT: {args.min_precursor_rt if args.min_precursor_rt is not None else 'None'} seconds"
     )
     logger.info(
-        f"  Max Precursor RT: {args.max_precursor_rt if args.max_precursor_rt else 'None'} seconds"
+        f"  Max Precursor RT: {args.max_precursor_rt if args.max_precursor_rt is not None else 'None'} seconds"
     )
     logger.info(
-        f"  Min Precursor CCS: {args.min_precursor_ccs if args.min_precursor_ccs else 'None'}"
+        f"  Min Precursor CCS: {args.min_precursor_ccs if args.min_precursor_ccs is not None else 'None'}"
     )
     logger.info(
-        f"  Max Precursor CCS: {args.max_precursor_ccs if args.max_precursor_ccs else 'None'}"
+        f"  Max Precursor CCS: {args.max_precursor_ccs if args.max_precursor_ccs is not None else 'None'}"
     )
     logger.info(
-        f"  Min Precursor Neutral Mass: {args.min_precursor_neutral_mass if args.min_precursor_neutral_mass else 'None'}"
+        f"  Min Precursor Neutral Mass: {args.min_precursor_neutral_mass if args.min_precursor_neutral_mass is not None else 'None'}"
     )
     logger.info(
-        f"  Max Precursor Neutral Mass: {args.max_precursor_neutral_mass if args.max_precursor_neutral_mass else 'None'}"
+        f"  Max Precursor Neutral Mass: {args.max_precursor_neutral_mass if args.max_precursor_neutral_mass is not None else 'None'}"
     )
     logger.info(f"  Overwrite Existing Output: {args.overwrite}")
     logger.info(f"  m/z Precision: {args.mz_precision} decimal places")
     logger.info(f"  Intensity Precision: {args.intensity_precision} decimal places")
+    logger.info(f"  Keep Empty Spectra: {args.keep_empty_spectra}")
     logger.info(f"  Verbose Logging: {args.verbose}")
 
     # Log preset-specific settings

src/tdfextractor/mgf_exctractor.py

@@ -4,6 +4,8 @@
 
 import logging
 import os
+import signal
+import sys
 import time
 import threading
 import queue
@@ -12,12 +14,11 @@
 
 from tqdm import tqdm
 
-from .utils import get_ms2_dda_content
+from .utils import get_ms2_dda_content, get_tdf_df
 from .cli_args import create_mgf_parser, apply_preset_settings, log_common_args
 
 logger = logging.getLogger(__name__)
 
-
 def write_mgf_file(
     analysis_dir: str,
     output_file: Optional[str] = None,
@@ -43,6 +44,7 @@ def write_mgf_file(
     max_precursor_neutral_mass: Optional[float] = None,
     mz_precision: int = 5,
     intensity_precision: int = 0,
+    keep_empty_spectra: bool = False,
 ):
 
     start_time = time.time()
@@ -53,10 +55,27 @@ def write_mgf_file(
     logger.info("Generating Ms2 Spectra (producer-consumer mode)")
     spectra_queue = queue.Queue(maxsize=100)
 
+    merged_df = get_tdf_df(
+        analysis_dir,
+        min_precursor_intensity,
+        max_precursor_intensity,
+        min_precursor_charge,
+        max_precursor_charge,
+        min_precursor_mz,
+        max_precursor_mz,
+        min_precursor_rt,
+        max_precursor_rt,
+        min_precursor_ccs,
+        max_precursor_ccs,
+        min_precursor_neutral_mass,
+        max_precursor_neutral_mass,
+    )
+
     def producer():
         try:
             ms2_spectra = get_ms2_dda_content(
                 analysis_dir=analysis_dir,
+                merged_df=merged_df,
                 remove_precursor=remove_precursor,
                 precursor_peak_width=precursor_peak_width,
                 batch_size=batch_size,
@@ -65,18 +84,6 @@ def producer():
                 max_spectra_intensity=max_spectra_intensity,
                 min_spectra_mz=min_spectra_mz,
                 max_spectra_mz=max_spectra_mz,
-                min_precursor_intensity=min_precursor_intensity,
-                max_precursor_intensity=max_precursor_intensity,
-                min_precursor_charge=min_precursor_charge,
-                max_precursor_charge=max_precursor_charge,
-                min_precursor_mz=min_precursor_mz,
-                max_precursor_mz=max_precursor_mz,
-                min_precursor_rt=min_precursor_rt,
-                max_precursor_rt=max_precursor_rt,
-                min_precursor_ccs=min_precursor_ccs,
-                max_precursor_ccs=max_precursor_ccs,
-                min_precursor_neutral_mass=min_precursor_neutral_mass,
-                max_precursor_neutral_mass=max_precursor_neutral_mass,
             )
             for spectrum in ms2_spectra:
                 spectra_queue.put(spectrum)
@@ -86,7 +93,9 @@ def producer():
     def consumer():
         logger.info("Writing Contents To File")
         with open(output_file, "w", encoding="UTF-8") as file:
-            with tqdm(desc="Writing MGF File", unit="spectra") as pbar:
+            with tqdm(
+                desc="Writing MGF File", unit="spectra", total=len(merged_df)
+            ) as pbar:
                 # https://www.matrixscience.com/help/data_file_help.html
                 header_lines = []
                 header_lines.append(f"INSTRUMENT=TimsTOF")
@@ -96,23 +105,35 @@ def consumer():
                     spectrum = spectra_queue.get()
                     if spectrum is None:
                         break
+
+                    pbar.update(1)
+
+                    if len(spectrum.mz_spectra) == 0 and keep_empty_spectra is False:
+                        continue
+
                     mgf_lines = []
                     mgf_lines.append("BEGIN IONS")
                     mgf_lines.append(
                         f"TITLE={Path(analysis_dir).stem}.{spectrum.low_scan}.{spectrum.high_scan}.{spectrum.charge} "
                         f'File="{Path(analysis_dir).stem}", NativeID="merged={spectrum.precursor_id} frame={spectrum.parent_id} '
                         f'scanStart={spectrum.scan_begin} scanEnd={spectrum.scan_end} scan={spectrum.low_scan}"'
                     )
-                    mgf_lines.append(f"RTINSECONDS={spectrum.rt:.2f}")                    
+                    mgf_lines.append(f"RTINSECONDS={spectrum.rt:.2f}")
                     # Pepmass is actually mz? huh?
-                    mgf_lines.append(f"PEPMASS={spectrum.mz:.6f} {spectrum.prec_intensity:.{intensity_precision}f}")
+                    mgf_lines.append(
+                        f"PEPMASS={spectrum.mz:.6f} {spectrum.prec_intensity:.{intensity_precision}f}"
+                    )
                     mgf_lines.append(f"CHARGE={spectrum.charge}+")
-                    for mz, intensity in zip(spectrum.mz_spectra, spectrum.intensity_spectra):
-                        mgf_lines.append(f"{mz:.{mz_precision}f} {intensity:.{intensity_precision}f}")
+                    for mz, intensity in zip(
+                        spectrum.mz_spectra, spectrum.intensity_spectra
+                    ):
+                        mgf_lines.append(
+                            f"{mz:.{mz_precision}f} {intensity:.{intensity_precision}f}"
+                        )
                     mgf_lines.append("END IONS")
                     file.write("\n".join(mgf_lines) + "\n\n")
-                    pbar.update(1)
 
+    
     producer_thread = threading.Thread(target=producer)
     consumer_thread = threading.Thread(target=consumer)
 
@@ -129,6 +150,7 @@ def main():
     """
     Command-line interface for MGF extraction from TimsTOF data.
     """
+
     parser = create_mgf_parser()
     args = parser.parse_args()
 
@@ -224,7 +246,6 @@ def main():
             continue
 
         try:
-
             write_mgf_file(
                 analysis_dir=str(d_folder),
                 output_file=output,
@@ -248,13 +269,15 @@ def main():
                 max_precursor_ccs=args.max_precursor_ccs,
                 min_precursor_neutral_mass=args.min_precursor_neutral_mass,
                 max_precursor_neutral_mass=args.max_precursor_neutral_mass,
+                keep_empty_spectra=args.keep_empty_spectra,
             )
             logger.info("MGF extraction completed successfully!")
         except Exception as e:
             logger.error(f"Error during MGF extraction: {e}... skipping {d_folder}")
+            continue
         except KeyboardInterrupt:
-            logger.info("Extraction interrupted by user.")
-            return 0
+            logger.info("\nExtraction interrupted by user.")
+            os._exit(0)
 
 
 if __name__ == "__main__":