| Previous changeset 1:3c7f20b24047 (2024-02-26) Next changeset 3:b3d41b1fcb18 (2024-09-26) |
|
Commit message:
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/misc commit 6d6720ef358935ad4bb7c5f26efb55647567eb14 |
|
modified:
use_theoretical_mz_annotations.xml |
|
added:
use_theoretical_mz_annotations.py |
| b |
| diff -r 3c7f20b24047 -r e0cac9994a72 use_theoretical_mz_annotations.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/use_theoretical_mz_annotations.py Mon Feb 26 10:40:17 2024 +0000 |
| [ |
| @@ -0,0 +1,88 @@ +import argparse +from typing import Iterator, Tuple + + +def get_peak_values(peak: str) -> Tuple[float, float, str]: + """ Get the m/z and intensity value from the line containing the peak information. """ + splitted_line = peak.split(maxsplit=2) + mz = float(splitted_line[0].strip()) + intensity = float(splitted_line[1].strip()) + comment = '' + if (len(splitted_line) == 3): + comment = splitted_line[2].strip() + return mz, intensity, comment + + +def get_peak_tuples(rline: str) -> Iterator[str]: + """ Splits line at ';' and performs additional string cleaning. """ + tokens = filter(None, rline.split(";")) + peak_pairs = map(lambda x: x.lstrip().rstrip(), tokens) + return peak_pairs + + +def overwrite_peaks(file: str, output: str, only_contains_annotation: bool = False) -> None: + """This function overwrites peaks in the input file with annotated peaks. + + Args: + file (str): The path to the input file. + output (str): The path to the output file. + only_contains_annotation (bool, optional): If True, only peaks with annotations are processed. Defaults to False. + + Returns: + None: The function writes the output to a file and does not return anything. + """ + annotated_msp = [] + annotated_msp_list = [] + peaks = [] + + with open(file, 'r') as file: + while True: + line = file.readline() + if not line.strip(): + if len(peaks) > 0: + annotated_msp_list.append(annotated_msp) + annotated_msp = [] + if line == '': + break + if line.startswith('Num Peaks:'): + num_peaks = int(line.split(':')[1].strip()) + peaks = [] + for i in range(num_peaks): + line = file.readline() + peak_pairs = get_peak_tuples(line) + + for peak in peak_pairs: + mz, intensity, comment = get_peak_values(peak) + if comment != '': + tokens = comment.split() + mz = float(tokens[2].strip().rstrip(',')) + peak_text = '%s\t%s\t%s\n' % (str(mz), str(intensity), str(comment)) + peaks.append(peak_text) + + if only_contains_annotation is False and comment == '': + peak_text = '%s\t%s\n' % (str(mz), str(intensity)) + peaks.append(peak_text) + + annotated_msp.append("Num Peaks: %d\n" % len(peaks)) + for item in peaks: + annotated_msp.append(item) + else: + annotated_msp.append(line) + + with open(output, 'w') as file: + for spectra in annotated_msp_list: + file.writelines(spectra) + + +def parse_arguments() -> argparse.Namespace: + parser = argparse.ArgumentParser() + parser.add_argument('-i', '--input_filename', type=str, required=True, help='Input file name') + parser.add_argument('-o', '--output_filename', type=str, required=True, help='Output file name') + parser.add_argument('-a', '--annotated', action='store_true', help='Process only peaks with annotations') + args = parser.parse_args() + return args + + +if __name__ == "__main__": + args = parse_arguments() + overwrite_peaks(args.input_filename, args.output_filename, args.annotated) |
| b |
| diff -r 3c7f20b24047 -r e0cac9994a72 use_theoretical_mz_annotations.xml --- a/use_theoretical_mz_annotations.xml Mon Feb 26 10:24:28 2024 +0000 +++ b/use_theoretical_mz_annotations.xml Mon Feb 26 10:40:17 2024 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="use_theoretical_mz_annotations" name="use theoretical m/z values" version="@TOOL_VERSION@+galaxy0" profile="21.09"> +<tool id="use_theoretical_mz_annotations" name="use theoretical m/z values" version="@TOOL_VERSION@+galaxy1" profile="21.09"> <description>Overwrite experimentally measured mz values for peaks with theoretical values from peak comments.</description> <macros> <import>macros.xml</import> @@ -6,7 +6,7 @@ <expand macro="creator"/> <command detect_errors="exit_code"><![CDATA[ - python3 '$__tool_directory__/use_theoretical_mz_annotations.py' + python3 '${__tool_directory__}/use_theoretical_mz_annotations.py' -i '${input}' -o '${output_data}' #if $only_theoretical_annotated |