feat: illumnia sample sheet parser

scripts/ss.py

@@ -0,0 +1,126 @@
+from csv import DictReader
+from io import StringIO
+from datetime import datetime
+from operator import itemgetter
+from dateutil import parser as dateparser
+
+
+class IllumniaSampleSheet():
+    """Class to parse illumnia sample sheet information according to the
+    sample sheet format specified by [Illumina](https://support-docs.illumina.com/SHARE/SampleSheetv2/Content/SHARE/SampleSheetv2/SampleSheetStructure.htm)
+
+    Properties:
+        pairedend(bool): True for paired end seqencing data, False for single end sequencing data
+        project(str): Title of the project for this sequencing run
+        run(str): Run Identifer this single sequencing run
+
+    """
+
+    def __init__(self, samplesheet, end=None):
+        self.sheet = self.parse_sheet(samplesheet)
+        self.force_endedness = end
+
+    def parse_sheet(self, sheet):
+        sheet_sections = dict()
+        with open(sheet) as opensheet:
+            this_section = None
+            for _line in opensheet:
+                line = _line.strip()
+                first = _line.split(',')[0]
+                if first.startswith('[') and first.endswith(']'):
+                    sheet_sections[first[1:-1]] = []
+                    this_section = first[1:-1]
+                else:
+                    sheet_sections[this_section].append(line)
+
+        if 'Header' in sheet_sections:
+            self.process_simple_section(sheet_sections['Header'])
+
+        if 'Settings' in sheet_sections:
+            self.process_simple_section(sheet_sections['Settings'])
+
+        if 'Reads' in sheet_sections:
+            self.process_simple_section(sheet_sections['Reads'])
+
+        assert 'Data' in sheet_sections, 'No sample data within this sample sheet'
+        self.process_csv_section(sheet_sections['Data'])
+
+
+    def process_simple_section(self, section):
+        """Simple section processing for Illumnia sample sheet. 
+
+        Objective:
+            Disgard rows of all commas, collect rows with single values into self attributes which 
+            are 
+
+        """
+        for _line in section:
+            index = _line.split(',')[0]
+            if ' ' in index:
+                index = index.replace(' ', '_')
+            if "\n" in _line:
+                _line = _line.replace("\n", ' ')
+            rest = ','.join(_line.split(',')[1:])
+            if set(list(rest)) == ',':
+                continue
+            else:
+                second = _line.split(',')[1]
+                if index == 'Date':
+                    setattr(self, index, dateparser.parse(second))
+                else:
+                    setattr(self, index, second)
+        return
+
+    def process_csv_section(self, section):
+        section_io = StringIO("\n".join(section))
+        section_csv = DictReader(section_io, delimiter=',')
+        setattr(self, 'data', list(section_csv))
+
+
+    @property
+    def samples(self):
+        return getattr(self, 'data', None)
+
+    @property
+    def project(self):
+        sheet_projects = list(set(map(itemgetter('Sample_Project'), self.data)))
+        assert len(sheet_projects) == 1, 'Sample sheet containers multiple project, please limit to single project per sheet.'
+        return sheet_projects[0]
+
+    @property
+    def instrument(self):
+       return getattr(self, 'Instrument', None)
+
+    @property
+    def adapters(self):
+        r1 = getattr(self, 'Read01', None)
+        r2 = getattr(self, 'Read02', None)
+        return list(map(int, filter(None, [r1, r2])))
+
+    @property
+    def indexes(self):
+        i1 = getattr(self, 'Index01', None)
+        i2 = getattr(self, 'Index02', None)
+        return list(map(int, filter(None, [i1, i2])))
+
+    @property
+    def is_paired_end(self):
+        if len(self.adapters) == 1:
+            return False
+        elif len(self.adapters) == 2:
+            return True
+        else:
+            raise ValueError('Unknown endedness from sample sheet')
+
+    @property
+    def is_single_end(self):
+        if len(self.adapters) == 1:
+            return True
+        elif len(self.adapters) == 2:
+            return False
+        else:
+            raise ValueError('Unknown endedness from sample sheet')
+
+
+
+