diff matchms_split.py @ 0:169c72b2ce79 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/matchms_split.py	Thu Apr 27 12:02:44 2023 +0000
@@ -0,0 +1,114 @@
+import argparse
+import itertools
+import os
+from typing import List
+
+from matchms import Spectrum
+from matchms.exporting import save_as_msp
+from matchms.importing import load_from_msp
+
+
+def read_spectra(filename: str) -> List[Spectrum]:
+    """Read spectra from file.
+
+    Args:
+        filename (str): Path to .msp file from which to load the spectra.
+
+    Returns:
+        List[Spectrum]: Spectra contained in the file.
+    """
+    return list(load_from_msp(filename, True))
+
+
+def get_spectra_names(spectra: list) -> List[str]:
+    """Read the keyword 'compound_name' from a spectra.
+
+    Args:
+        spectra (list): List of individual spectra.
+
+    Returns:
+        List[str]: List with 'compoud_name' of individual spectra.
+    """
+    return [x.get("compound_name") for x in spectra]
+
+
+def make_outdir(outdir: str):
+    """Create destination directory.
+
+    Args:
+        outdir (str): Path to destination directory where split spectra files are generated.
+    """
+    return os.mkdir(outdir)
+
+
+def write_spectra(spectra, outdir):
+    """Generates MSP files of individual spectra.
+
+    Args:
+        spectra (List[Spectrum]): Spectra to write to file
+        outdir   (str): Path to destination directory.
+    """
+    names = get_spectra_names(spectra)
+    for i in range(len(spectra)):
+        outpath = assemble_outpath(names[i], outdir)
+        save_as_msp(spectra[i], outpath)
+
+
+def assemble_outpath(name, outdir):
+    """Filter special chracteres from name.
+
+    Args:
+        name   (str): Name to be filetered.
+        outdir (str): Path to destination directory.
+    """
+    filename = ''.join(filter(str.isalnum, name))
+    outfile = str(filename) + ".msp"
+    outpath = os.path.join(outdir, outfile)
+    return outpath
+
+
+def split_spectra(filename, outdir):
+    """Save individual MSP spectra files in the destination directory.
+
+    Args:
+        filename (str): MSP file that contains the spectra.
+        outdir   (str): Path to destination directory where split spectra files are saved.
+    """
+    make_outdir(outdir)
+    return write_spectra(filename, outdir)
+
+
+def split_round_robin(iterable, num_chunks):
+    chunks = [list() for _ in range(num_chunks)]
+    index = itertools.cycle(range(num_chunks))
+    for value in iterable:
+        chunks[next(index)].append(value)
+    chunks = filter(lambda x: len(x) > 0, chunks)
+    return chunks
+
+
+listarg = argparse.ArgumentParser()
+listarg.add_argument('--filename', type=str)
+listarg.add_argument('--method', type=str)
+listarg.add_argument('--outdir', type=str)
+listarg.add_argument('--parameter', type=int)
+args = listarg.parse_args()
+outdir = args.outdir
+filename = args.filename
+method = args.method
+parameter = args.parameter
+
+
+if __name__ == "__main__":
+    spectra = load_from_msp(filename)
+    make_outdir(outdir)
+
+    if method == "one-per-file":
+        write_spectra(list(spectra), outdir)
+    else:
+        if method == "chunk-size":
+            chunks = iter(lambda: list(itertools.islice(spectra, parameter)), [])
+        elif method == "num-chunks":
+            chunks = split_round_robin(spectra, parameter)
+        for i, x in enumerate(chunks):
+            save_as_msp(x, os.path.join(outdir, f"chunk_{i}.msp"))