[med-svn] [Git][med-team/mcl][master] Move documentation script location

[Saira Hussain]

Saira Hussain pushed to branch master at Debian Med / mcl


Commits:
09270883 by Saira Hussain at 2019-07-11T11:51:27Z
Move documentation script location

- - - - -


2 changed files:

- − debian/tests/hypergeom.py
- debian/tests/run-unit-tests


Changes:

=====================================
debian/tests/hypergeom.py deleted
=====================================
@@ -1,50 +0,0 @@
-#!/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()


=====================================
debian/tests/run-unit-tests
=====================================
@@ -26,3 +26,15 @@ mcl protein_graphs.mci -I 2
 
 mcxdump -icl out.protein_graphs.mci.I20 -tabr protein_graphs.tab -o clusters.protein_graphs.mci.I20
 
+#Building clusters of genomes
+mcxload -abc genome_graphs.txt --stream-mirror -o genome_graphs.mci -write-tab genome_graphs.tab
+
+mcl genome_graphs.mci -I 1.2
+
+mcl genome_graphs.mci -I 2
+mcl genome_graphs.mci -I 4
+mcl genome_graphs.mci -I 6
+mcxdump -icl out.genome_graphs.mci.I12 -tabr genome_graphs.tab -o clusters.genome.mci.I12
+mcxdump -icl out.genome_graphs.mci.I20 -tabr genome_graphs.tab -o clusters.genome.mci.I20
+mcxdump -icl out.genome_graphs.mci.I40 -tabr genome_graphs.tab -o clusters.genome.mci.I40
+mcxdump -icl out.genome_graphs.mci.I60 -tabr genome_graphs.tab -o clusters.genome.mci.I60



View it on GitLab: https://salsa.debian.org/med-team/mcl/commit/09270883e5b4b4658093a59ed9d77ee62a8755f5

-- 
View it on GitLab: https://salsa.debian.org/med-team/mcl/commit/09270883e5b4b4658093a59ed9d77ee62a8755f5
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