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Read MGF and task-level inputs #22

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f126060
initial read mgf
benpullman Nov 22, 2021
4d10cf6
fix reading of task files
benpullman Nov 23, 2021
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26 changes: 21 additions & 5 deletions tools/peptide_statistics_hpp/cosine_to_synthetics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -82,6 +82,17 @@ def read_mzxml_spectrum(spectrum):
None
)

def read_mgf_spectrum(spectrum):
peaks = [processing.Peak(float(p[0]),float(p[1])) for p in zip(spectrum['m/z array'],spectrum['intensity array'])]
precursor = float(spectrum['params']['pepmass'][0])
return processing.Spectrum(
peaks,
precursor,
None,
"scan={}".format(spectrum['params']['scans']),
None
)

def get_mzxml_spectrum(mzxml_object, scan):
#thermo only for now
spectrum = mzxml_object.get_by_id(scan)
Expand Down Expand Up @@ -231,6 +242,8 @@ def main():
elif 'f.' in filename:
# checking uploads directory
filepath = filename.replace('f.','/data/ccms-data/uploads/')
if not Path(filepath).exists():
filepath = filename.replace('f.','/data/ccms-data/tasks/')
else:
filepath = filename

Expand Down Expand Up @@ -271,14 +284,19 @@ def main():
get_spectrum_func = None
read_scan = None

if len(psms_to_consider[filename]) >= min_spectra_to_load_file:
read_full_file = len(psms_to_consider[filename]) >= min_spectra_to_load_file or exts[0] == '.mgf'

if read_full_file:
if exts[0] == '.mzML':
file = open(filepath, 'rb')
file_object = mzml.MzML(file)
get_spectrum_func = read_mzml_spectrum
read_scan = lambda s: str(s['id'].split('scan=')[1])
if exts[0] == '.mgf':
pass
file = open(filepath, 'r')
file_object = mgf.MGF(file)
get_spectrum_func = read_mgf_spectrum
read_scan = lambda s: s['params']['scans']
if exts[0] == '.mzXML':
file = open(filepath, 'rb')
file_object = mzxml.MzXML(file)
Expand All @@ -289,8 +307,6 @@ def main():
file = open(filepath, 'rb')
file_object = mzml.PreIndexedMzML(file)
get_spectrum_func = get_mzml_spectrum
if exts[0] == '.mgf':
pass
if exts[0] == '.mzXML':
file = open(filepath, 'rb')
file_object = mzxml.MzXML(file,use_index = True)
Expand All @@ -299,7 +315,7 @@ def main():
if file:
if file_object and get_spectrum_func:
print("{}: Opened file {}, ready to load".format(datetime.now().strftime("%H:%M:%S"),filename))
if len(psms_to_consider[filename]) >= min_spectra_to_load_file:
if read_full_file:
file_cosine_to_synthetic, file_explained_intensity_per_spectrum = process_spectrum_read_file(psms_to_consider,filename,synthetic_scans,tol,args.low_mass_filter,args.min_snr,threshold,file_object,get_spectrum_func,read_scan)
else:
file_cosine_to_synthetic, file_explained_intensity_per_spectrum = process_spectrum(psms_to_consider,filename,synthetic_scans,tol,args.low_mass_filter,args.min_snr,threshold,file_object,get_spectrum_func)
Expand Down