Snippet revisions — Bitbucket

+#!/usr/bin/env python

+# -*- coding: utf-8 -*-

+# Denes Turei EMBL 2018

+# turei.denes@gmail.com

+import os

+import itertools

+from lipyd import sample

+basedir = ('/', 'home', 'denes' , 'archive', 'cihan')

+mgfpath = ('data', 'mgf')

+skip = {'blanks and standards'}

+fractions = [

+    (('A8', 'A9', 'A10'),             ('A11', 'A12')),

+    (('A6', 'A7', 'A8', 'A9', 'A12'), ('A10', 'A11')),

+    (('A6', 'A7', 'A8', 'A9', 'A10'), ('A11', 'A12')),

+    (('A9', 'A10', 'B2'),             ('A11', 'A12', 'B1')),

+]

+fractions = [

+    (('A8', 'A9'),             ('A11', 'A12')),

+    (('A6', 'A7', 'A8'),       ('A10', 'A11')),

+    (('A6', 'A7', 'A8', 'A9'), ('A11', 'A12')),

+    (('A9', ),                 ('A11', 'A12', 'B1')),

+]

+experiments = [

+    os.path.join(*(basedir + (dir0, dir1)))

+    for dir0 in os.listdir(os.path.join(*basedir))

+    for dir1 in os.listdir(os.path.join(*(basedir + (dir0,))))

+    if dir0 not in skip

+]

+peaksfiles = [

+    os.path.join(expdirs, 'feature.csv')

+    for expdirs in experiments

+]

+mgfdirs = [

+    os.path.join(*((expdirs,) + mgfpath))

+    for expdirs in experiments

+]

+for i in range(len(peaksfiles)):

+    reader = sample.SampleReader(

+        input_type = 'peaks',

+        fname = peaksfiles[i]

+    )

+    samples = reader.get_sampleset(

+        sampleset_args = {

+            'ms2_param': {

+                'mgfdir': mgfdirs[i]

+            },

+            'ms2_format': 'mgf',

+        }

+    )

+    samples.basic_filters()

+    samples.peak_size_filter(*fractions[i // 2])

+    samples.database_lookup()

+    samples.ms2_identify()

+    samples.export_table(

+        fname = '%s.results.tsv' % peaksfiles[i],

+        variables = ['peaksize']

+    )

+    for f in range(len(samples)):

+        if any(

+            ms2i.hg.main in {'BMP', 'PG'}

+            for ms2iii in samples.feattrs.ms2_identities[f]

+            for ms2ii in ms2iii.values()

+            for ms2i in ms2ii

+        ):

+            print(peaksfiles[i])

+            print(samples.mzs[f])

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