[med-svn] [Git][med-team/mcl][master] Add python script for pairwise comparison

[Saira Hussain]

Saira Hussain pushed to branch master at Debian Med / mcl


Commits:
da5f4902 by Saira Hussain at 2019-07-11T11:39:18Z
Add python script for pairwise comparison

It performs pairwise copmarison of contigs and assesment of shared
gene content.

- - - - -


1 changed file:

- + debian/tests/hypergeom.py


Changes:

=====================================
debian/tests/hypergeom.py
=====================================
@@ -0,0 +1,50 @@
+#!/usr/bin/env python2
+# Pairwise comparison of contigs and assessment of shared gene content
+
+from __future__ import division
+import scipy.stats as stats
+import re
+import math
+import sys
+
+clusters = sys.argv[1]
+
+families = {}
+names2 = []
+with open(clusters) as file2:
+    for line in file2:
+        dat = line.strip().split('\t')
+        for i in dat:
+            contig = re.search('(\S+)_\d+', i).group(1)
+            families[contig] = set()
+            names2.append(contig)
+
+names = list(set(names2))
+
+with open(clusters) as file1:
+    count = 1
+    for line in file1:
+        dat = line.strip().split('\t')
+        for i in dat:
+            k = re.search('(\S+)_\d+', i).group(1)
+            if k in families:
+                families[k].add('family_' + str(count))
+        count += 1
+total = []
+file_out = open('genome_graphs.txt', 'w')
+for i in range(len(names)):
+    for j in range(len(names)):
+        if names[i] != names[j]:
+            common = len(families[names[i]].intersection(families[names[j]]))
+            c = max(len(families[names[i]]), len(families[names[j]]))
+            b = min(len(families[names[i]]), len(families[names[j]]))
+            p = stats.hypergeom.sf(common - 1, count - 1, c, b)
+            if p != 0:
+                link_strength = - math.log10(p * (len(names) * (len(names) - 1) / 2))
+                if link_strength > 0 and names[i] != names[j]:
+                    l = [names[i], names[j], str(link_strength)]
+                    file_out.write('\t'.join(l) + '\n')
+            else:
+                l = [names[i], names[j], "100"]
+                file_out.write('\t'.join(l) + '\n')
+file_out.close()



View it on GitLab: https://salsa.debian.org/med-team/mcl/commit/da5f490229c7199efcbb674592d8b39f3c98c225

-- 
View it on GitLab: https://salsa.debian.org/med-team/mcl/commit/da5f490229c7199efcbb674592d8b39f3c98c225
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