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fix: change subsampling to always selects precursor table #139

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fix: change subsampling to always selects precursor table #139

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39 changes: 23 additions & 16 deletions pyprophet/levels_contexts.py
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Original file line number Diff line number Diff line change
Expand Up @@ -648,15 +648,15 @@ def infer_glycopeptides(infile, outfile, context,


def subsample_osw(infile, outfile, subsample_ratio, test):
if os.path.exists(outfile):
click.echo("Warning: Output file %s already exists. It will be overwritten." % outfile)
os.remove(outfile)

conn = sqlite3.connect(infile)
ms1_present = check_sqlite_table(conn, "FEATURE_MS1")
ms2_present = check_sqlite_table(conn, "FEATURE_MS2")
transition_present = check_sqlite_table(conn, "FEATURE_TRANSITION")
## Check if infile contains multiple entries for run table, if only 1 entry, then infile is a single run, else infile contains multiples run
n_runs = conn.cursor().execute("SELECT COUNT(*) AS NUMBER_OF_RUNS FROM RUN").fetchall()[0][0]
multiple_runs = True if n_runs > 1 else False
if multiple_runs:
click.echo("Warn: There are %s runs in %s" %(n_runs, infile))

conn.close()

conn = sqlite3.connect(outfile)
Expand Down Expand Up @@ -770,22 +770,27 @@ def subsample_osw(infile, outfile, subsample_ratio, test):
click.echo("Info: Subsampled MS2 features of file %s to %s." % (infile, outfile))

if transition_present:
input_conn = sqlite3.connect(infile)
columns = [i[1] for i in input_conn.execute("pragma table_info(FEATURE_TRANSITION)").fetchall()]
columns_to_select = ['FEATURE_ID', 'TRANSITION_ID', 'AREA_INTENSITY', 'APEX_INTENSITY'] + [ col for col in columns if 'VAR' in col]
columns_to_select = ', '.join(columns_to_select)
input_conn.close()
if subsample_ratio >= 1.0:
c.executescript('''
c.executescript(f'''
ATTACH DATABASE "%s" AS sdb;

CREATE TABLE FEATURE_TRANSITION AS
SELECT *
SELECT {columns_to_select}
FROM sdb.FEATURE_TRANSITION;

DETACH DATABASE sdb;
''' % infile)
else:
c.executescript('''
c.executescript(f'''
ATTACH DATABASE "%s" AS sdb;

CREATE TABLE FEATURE_TRANSITION AS
SELECT *
SELECT {columns_to_select}
FROM sdb.FEATURE_TRANSITION
WHERE sdb.FEATURE_TRANSITION.FEATURE_ID IN
(SELECT ID
Expand All @@ -795,8 +800,7 @@ def subsample_osw(infile, outfile, subsample_ratio, test):
''' % infile)
click.echo("Info: Subsampled transition features of file %s to %s." % (infile, outfile))

if multiple_runs:
c.executescript('''
c.executescript('''
PRAGMA synchronous = OFF;

ATTACH DATABASE "%s" AS sdb;
Expand All @@ -810,9 +814,9 @@ def subsample_osw(infile, outfile, subsample_ratio, test):

DETACH DATABASE sdb;
''' % infile)
click.echo("Info: Subsampled precursor table of file %s to %s. For scoring merged subsampled file." % (infile, outfile))
click.echo("Info: Subsampled precursor table of file %s to %s. For scoring merged subsampled file." % (infile, outfile))

c.executescript('''
c.executescript('''
PRAGMA synchronous = OFF;

ATTACH DATABASE "%s" AS sdb;
Expand All @@ -826,10 +830,10 @@ def subsample_osw(infile, outfile, subsample_ratio, test):

DETACH DATABASE sdb;
''' % infile)
click.echo("Info: Subsampled transition_precursor_mapping table of file %s to %s. For scoring merged subsampled file." % (infile, outfile))
click.echo("Info: Subsampled transition_precursor_mapping table of file %s to %s. For scoring merged subsampled file." % (infile, outfile))


c.executescript('''
c.executescript('''
PRAGMA synchronous = OFF;

ATTACH DATABASE "%s" AS sdb;
Expand All @@ -843,7 +847,7 @@ def subsample_osw(infile, outfile, subsample_ratio, test):

DETACH DATABASE sdb;
''' % infile)
click.echo("Info: Subsampled transition table of file %s to %s. For scoring merged subsampled file." % (infile, outfile))
click.echo("Info: Subsampled transition table of file %s to %s. For scoring merged subsampled file." % (infile, outfile))

conn.commit()
conn.close()
Expand All @@ -852,6 +856,9 @@ def subsample_osw(infile, outfile, subsample_ratio, test):


def reduce_osw(infile, outfile):
if os.path.exists(outfile):
click.echo("Warning: Output file %s already exists. It will be overwritten." % outfile)
os.remove(outfile)
conn = sqlite3.connect(infile)
if not check_sqlite_table(conn, "SCORE_MS2"):
raise click.ClickException("Apply scoring to MS2 data before reducing file for multi-run scoring.")
Expand Down
3 changes: 3 additions & 0 deletions pyprophet/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -420,6 +420,9 @@ def reduce(infile, outfile):
else:
outfile = outfile

if os.path.exists(outfile):
click.echo(click.style(f"Warn: {outfile} already exists, will overwrite", fg='yellow'))

reduce_osw(infile, outfile)


Expand Down