Adding parser for contrast information

.tests/contrasts.tsv

@@ -0,0 +1 @@
+T2	T1

src/files.py

@@ -0,0 +1,120 @@
+#!/usr/bin/env python3
+# -*- coding: UTF-8 -*-
+
+# Python standard library
+from __future__ import print_function
+import sys
+
+# Local imports
+from utils import (
+    Colors,
+    err,
+    fatal
+)
+
+
+def clean(s, remove=['"', "'"]):
+    """Cleans a string to remove any defined leading or trailing characters.
+    @param s <str>:
+        String to clean.
+    @param remove list[<str>]:
+        List of characters to remove from beginning or end of string 's'.
+    @return s <str>:
+        Cleaned string
+    """
+    for c in remove:
+        s = s.strip(c)
+    return s
+
+
+def contrasts(file, groups, delim='\t'):
+    """Reads and parses the group comparison file, contrasts.tsv, into a 
+    dictionary. This file acts as a config file to setup contrasts between
+    two groups, where groups of samples are defined in the groups.tsv file.
+    This information is used in differential analysis, like differential 
+    gene expression, etc. 
+    @Example: contrasts.tsv
+        G2  G1
+        G4  G3
+        G5  G1
+    >> contrasts = contrasts('contrasts.tsv', groups = ['G1', 'G2', 'G3', 'G4', 'G5'])
+    >> contrasts
+    [
+        ["G2",  "G1"],
+        ["G4",  "G3"],
+        ["G5",  "G1"]
+    ]
+    @param file <str>:
+        Path to contrasts TSV file.
+    @param groups list[<str>]:
+        List of groups defined in the groups file, enforces groups exist.
+    @return comparisons <list[list[str, str]]>:
+        Nested list contain comparsions of interest.  
+    """
+
+    c = Colors()
+    errors = []
+    comparsions = []
+    line_number = 0
+    with open(file) as fh:
+        for line in fh:
+            line_number += 1
+            linelist = [clean(l.strip()) for l in line.split(delim)]
+            try:
+                g1 = linelist[0]
+                g2 = linelist[1]
+                if not g1 or not g2: continue # skip over empty lines
+            except IndexError:
+                # Missing a group, need two groups to tango
+                # This can happen if the file is NOT a TSV file,
+                # and it is seperated by white spaces, :(  
+                err(
+                '{}{}Warning: {} is missing at least one group on line {}: {}{}'.format(
+                    c.bg_yellow,
+                    c.black,
+                    file,
+                    line_number,
+                    line.strip(),
+                    c.end
+                    )
+                )
+                err('{}{}\t  └── Skipping over line, check if line is tab seperated... {}'.format(
+                    c.bg_yellow,
+                    c.black,
+                    c.end)
+                )
+                continue
+            # Check to see if groups where defined already,
+            # avoids user errors and spelling errors
+            for g in [g1, g2]:
+                if g not in groups:
+                    # Collect all error and report them at end
+                    errors.append(g)
+
+            # Add comparsion to list of comparisons
+            if [g1, g2] not in comparsions:
+                comparsions.append([g1, g2])
+
+    if errors:    
+        # One of the groups is not defined in groups file
+        err('{}{}Error: the following group(s) in "{}" are not defined in --groups file! {}'.format(
+            c.bg_red, 
+            c.white,
+            file,
+            c.end)
+        )
+        fatal('{}{}\t  └── {} {}'.format(
+            c.bg_red,
+            c.white,
+            ','.join(errors),
+            c.end)
+        )
+
+    return comparsions
+
+
+if __name__ == '__main__':
+    # Testing TSV parser
+    groups = {"T1": ["A","B"], "T2": ["C","D"]}
+    comparsions = contrasts(sys.argv[2], groups=groups.keys())
+    print(comparsions)