[med-svn] [Git][med-team/mcl][master] 2 commits: Add test data files
Saira Hussain
gitlab at salsa.debian.org
Thu Jul 11 12:51:22 BST 2019
Saira Hussain pushed to branch master at Debian Med / mcl
Commits:
8405acbe by Saira Hussain at 2019-07-11T11:48:08Z
Add test data files
- - - - -
1fcdcc18 by Saira Hussain at 2019-07-11T11:50:50Z
Add scripts to document the data file generation
- - - - -
8 changed files:
- + debian/tests/data/LMCLUST.sh
- + debian/tests/data/diamond_result.txt
- + debian/tests/data/genome_graphs.txt
- + debian/tests/data/hypergeom.py
- + debian/tests/data/orfs.gff
- + debian/tests/data/predicted_prot.faa
- + debian/tests/data/protein_graphs.txt
- + debian/tests/data/proteins_database.dmnd
Changes:
=====================================
debian/tests/data/LMCLUST.sh
=====================================
@@ -0,0 +1,52 @@
+#!/bin/bash
+
+# Implementation of Lima-Mendez et al. (DOI: 10.1093/molbev/msn023)
+# method of clustering of bacteriophages based on gene shared content.
+#
+# Used a FASTA sequence from NCBI and Skunavirus inclusive
+#
+# Requirements:
+# * Prodigal - ORFs caller (DOI: 10.1186/1471-2105-11-119)
+# * Diamond- - homology search engine (DOI: https://doi.org/10.1038/nmeth.3176)
+# * MCL - clustering algorithm (DOI: https://doi.org/10.1137/040608635)
+
+# Modified implementation of the above paper in the public domain (scientific)
+# Original file by kseniaarkhipova
+
+threads=$(nproc)
+
+prodigal='prodigal'
+diamond='/usr/lib/debian-med/bin/diamond'
+LM_scripts='./'
+mcl=''
+
+fasta=${1}
+
+#Predicting ORFs, diamond all-vs-all
+${prodigal} -i ${fasta} -a predicted_prot.faa -o orfs.gff -p meta -q -f gff
+
+"$diamond" makedb --in predicted_prot.faa -d proteins_database.dmnd
+"$diamond" blastp --db proteins_database.dmnd -q predicted_prot.faa -o diamond_result.txt --quiet
+
+#Filtering of an alignment result, proteins with hits with bitscore > 50 considered as related
+awk -F'\t' -v OFS='\t' '($1 != $2) && $12 > 50 {print $1, $2, $11}' diamond_result.txt > protein_graphs.txt
+
+#Generation of protein families
+"$mcl"mcxload -abc protein_graphs.txt --stream-mirror --stream-neg-log10 -stream-tf 'ceil(200)' -o protein_graphs.mci -write-tab protein_graphs.tab
+"$mcl"mcl protein_graphs.mci -I 2
+"$mcl"mcxdump -icl out.protein_graphs.mci.I20 -tabr protein_graphs.tab -o clusters.protein_graphs.mci.I20
+
+#Pairwise comparison of contigs and assessment of shared gene content
+"$LM_scripts"hypergeom.py clusters.protein_graphs.mci.I20
+
+#Building clusters of genomes
+"$mcl"mcxload -abc genome_graphs.txt --stream-mirror -o genome_graphs.mci -write-tab genome_graphs.tab
+
+"$mcl"mcl genome_graphs.mci -I 1.2
+"$mcl"mcl genome_graphs.mci -I 2
+"$mcl"mcl genome_graphs.mci -I 4
+"$mcl"mcl genome_graphs.mci -I 6
+"$mcl"mcxdump -icl out.genome_graphs.mci.I12 -tabr genome_graphs.tab -o clusters.genome.mci.I12
+"$mcl"mcxdump -icl out.genome_graphs.mci.I20 -tabr genome_graphs.tab -o clusters.genome.mci.I20
+"$mcl"mcxdump -icl out.genome_graphs.mci.I40 -tabr genome_graphs.tab -o clusters.genome.mci.I40
+"$mcl"mcxdump -icl out.genome_graphs.mci.I60 -tabr genome_graphs.tab -o clusters.genome.mci.I60
=====================================
debian/tests/data/diamond_result.txt
=====================================
The diff for this file was not included because it is too large.
=====================================
debian/tests/data/genome_graphs.txt
=====================================
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+NC_028900 NC_001909 6.49974988877
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+NC_028900 FJ848885 14.2618364821
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+NC_028900 FJ848883 11.7240154761
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+NC_028900 NC_021853 11.5864022412
+NC_028900 NC_021852 8.99488930586
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+NC_028900 JQ740788 10.328475258
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+NC_028900 NC_021854 7.83090736181
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+NC_028900 NC_042024 8.14207528933
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+NC_028900 NC_008370 6.7692488724
+NC_028900 NC_008363 9.79385612425
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+NC_028900 KC182547 7.83090736181
+NC_028900 NC_013155 15.589866952
+NC_028900 NC_013154 14.2618364821
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+NC_028900 NC_017698 12.6095013991
+NC_028900 JQ740804 12.6095013991
+NC_028900 NC_017695 10.328475258
+NC_017698 EU221285 5.87403039039
+NC_017698 NC_021860 6.40834951499
+NC_017698 NC_017702 22.0189113619
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+NC_017698 NC_001909 4.69641683593
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+NC_017698 FJ848885 8.84049208947
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+NC_017698 AF011378 5.29069576887
+NC_017698 NC_013153 8.84049208947
+NC_017698 KF676640 5.29069576887
+NC_017698 GQ979703 7.30063982941
+NC_017698 JQ740787 6.35644280183
+NC_017698 NC_017696 19.5417653095
+NC_017698 NC_001835 5.29069576887
+NC_017698 NC_021853 9.59527458747
+NC_017698 NC_021852 6.49307743671
+NC_017698 NC_017688 6.35644280183
+NC_017698 JQ740789 22.0189113619
+NC_017698 JQ740788 9.556231789
+NC_017698 NC_021855 6.40834951499
+NC_017698 NC_021854 6.40834951499
+NC_017698 JQ740813 19.5417653095
+NC_017698 NC_042024 7.30063982941
+NC_017698 DQ227764 7.85585376493
+NC_017698 NC_011046 5.87403039039
+NC_017698 DQ054536 7.04295318766
+NC_017698 NC_008370 3.27751731014
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+JQ740804 NC_042024 7.30063982941
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+JQ740804 DQ054536 7.04295318766
+JQ740804 NC_008370 3.27751731014
+JQ740804 NC_008363 7.04295318766
+JQ740804 KC182546 6.40834951499
+JQ740804 KC182547 6.40834951499
+JQ740804 NC_013155 9.04627220543
+JQ740804 NC_013154 8.84049208947
+JQ740804 KC182542 9.59527458747
+JQ740804 NC_013152 8.04044219212
+JQ740804 NC_028900 12.6095013991
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+JQ740804 NC_017695 9.556231789
+NC_017695 EU221285 3.3611629708
+NC_017695 NC_021860 7.0185855513
+NC_017695 NC_017702 8.19247862484
+NC_017695 AF009630 6.28289499654
+NC_017695 NC_001909 6.28289499654
+NC_017695 FJ848884 8.29655262048
+NC_017695 FJ848885 8.29655262048
+NC_017695 DQ227763 2.00194711411
+NC_017695 FJ848881 10.328475258
+NC_017695 FJ848882 11.3386024209
+NC_017695 FJ848883 8.85329867668
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+NC_017695 NC_008371 3.97653944456
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+NC_017695 NC_013153 8.29655262048
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+NC_017695 GQ979703 3.55929351936
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+NC_017695 NC_021854 5.85056651973
+NC_017695 JQ740813 6.93440042858
+NC_017695 NC_042024 3.55929351936
+NC_017695 DQ227764 3.97653944456
+NC_017695 NC_011046 3.3611629708
+NC_017695 DQ054536 5.34829041569
+NC_017695 NC_008370 2.00194711411
+NC_017695 NC_008363 5.34829041569
+NC_017695 KC182546 7.0185855513
+NC_017695 KC182547 5.85056651973
+NC_017695 NC_013155 11.3386024209
+NC_017695 NC_013154 8.29655262048
+NC_017695 KC182542 6.37848115086
+NC_017695 NC_013152 8.85329867668
+NC_017695 NC_028900 10.328475258
+NC_017695 NC_017698 9.556231789
+NC_017695 JQ740804 9.556231789
=====================================
debian/tests/data/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()
=====================================
debian/tests/data/orfs.gff
=====================================
The diff for this file was not included because it is too large.
=====================================
debian/tests/data/predicted_prot.faa
=====================================
The diff for this file was not included because it is too large.
=====================================
debian/tests/data/protein_graphs.txt
=====================================
The diff for this file was not included because it is too large.
=====================================
debian/tests/data/proteins_database.dmnd
=====================================
Binary files /dev/null and b/debian/tests/data/proteins_database.dmnd differ
View it on GitLab: https://salsa.debian.org/med-team/mcl/compare/da5f490229c7199efcbb674592d8b39f3c98c225...1fcdcc18d4e6c1bef15c3a1726f64f7746a21d93
--
View it on GitLab: https://salsa.debian.org/med-team/mcl/compare/da5f490229c7199efcbb674592d8b39f3c98c225...1fcdcc18d4e6c1bef15c3a1726f64f7746a21d93
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