[med-svn] [Git][med-team/bcalm][master] Add some missing sources for tests

[Shayan Doust]

Shayan Doust pushed to branch master at Debian Med / bcalm


Commits:
f299ab0a by Shayan Doust at 2019-09-23T07:14:15Z
Add some missing sources for tests

- - - - -


4 changed files:

- + debian/missing-sources/compare_fasta.py
- + debian/missing-sources/reference.fasta
- + debian/missing-sources/simple_test.sh
- + debian/source/include-binaries


Changes:

=====================================
debian/missing-sources/compare_fasta.py
=====================================
@@ -0,0 +1,36 @@
+#very basic, one seq per line only, no pysam for max portability
+#doesn't care if sequences are in revcomp or forward order
+import sys
+
+fasta1 = sys.argv[1]
+fasta2 = sys.argv[2]
+
+revcomp = lambda x: ''.join([{'A':'T','C':'G','G':'C','T':'A'}[B] for B in x][::-1])
+def normalize(seq):
+    rev = revcomp(seq)
+    return min(rev,seq)
+
+def read_seqs(fasta):
+    seqs = set()
+    for  line in open(fasta):
+        if line[0] == '>': continue
+        seqs.add(normalize(line.strip()))
+    return seqs
+
+s1 = read_seqs(fasta1)
+s2 = read_seqs(fasta2)
+
+if s1 == s2:
+    sys.exit(0)
+
+if len(s1) == len(s2) and len(s1) == 1:
+    # special case, e.g. for read50 and genome10k, let's see if one is included in the other
+    seq1= s1.copy().pop()
+    seq2= s2.copy().pop()
+    if seq1 in seq2 or seq2 in seq1:
+        print("one seq is perfectly included in the other")
+    else:
+        print("BAD: one sequence doesn't exactly match the other")
+
+print("NOT EQUAL: %d sequence(s) in %s not in %s" % (len(s1.difference(s2)), fasta1, fasta2))
+sys.exit(1)


=====================================
debian/missing-sources/reference.fasta
=====================================
@@ -0,0 +1,10 @@
+>Seq0
+ACCTATAAGGATCCACGTCTTGATGTGACCGACGATGTTATCTGCCTATAGCGAACATTTCCTGGTAGGAATACTATTATATTACCTAAATTCTCCGGATTTCCGTGTTCTTCGGAAGCTTAGGTCACGCGCGTCATACTACAGTAAGTTACTGAATTTTGGAGTAATGCATATCGACCGAGTCCGGGGAATCGTCCGTATCCCCGCCAGGCGTATCCAATAATTAGGTCGGACCCCTAGCGCGTACGAGTCCTATAGCTGACATGCGAATTGGCCGTGCATCGAGCTCAAATGTCCTAGCTTGAGAGTGCGTATCTCACCGATCCCCTGGCTATGCTCCGCGATTCACTAGTAGTTTCACGCCGACAGAGCGAAACCGTGATAGGTCATCATGCCGGTCTGCAGTCACGTGCCCAGCAGTCTCCAATATAGCCACTTATGTCGGAATGTAATCGGCTCCAAATTACTGTGAACCTGATGATCGACGACGCGCTGGGTGCGGGATAGTGTAACTGTCCCGTATAAGGCTTAAATTGAGTATGCAGGATACACTTTTAGTATGACTCGGAAAATCCCACTACAGTATGAACCGTGACTGTCGTTGGGCGGTGCTTGTTGCTATTAACTGGATGGTAAGTCAATTTTAAGTGGAGCCCCCTGCAAGATGGAAGAGAACTATATGTGGAACCGGATGTCACGTCAAGACCACCGCGCACGCTTAACACAACGCATGGTTCGGCGACTGCTCCGGTTCTGGAATTCCTCTTTTTTATCGAGATTAGCATCTCATTAGCGCGCAGTGTGTCCTAGTGTCCCAGAACGTAAAGACCAGATTTGACATTAGTAAGTTGCATTCGCGGGTCTTTAGAGCTCCTACTAAGCCCATTCAGATTGAAAAAGGCGCGCCTGCGGTTCCATGTCATAGTTTAACTTGGTTGAGACGGCGCACGAAAGCATACTACCACCATCCATGTCAAAACTGGCGACGATCTTGCTGGGT
+>Seq1
+GTTTTATAACAAGTGAAGAAAGAACAGTCATTAGGCCCGAAGGCGTACACGGAATCCGCCTAAACTAATGCTTATGGTCCCTCGTAGGCCCCGACGGCATAGGGTGCCCCGTAATTGCGTAGACAGCGAAAGGAAAGTGTACCGACGACGAGATCAAGTGGCAGTGAACCCCTTGGAAAACTTCATATCGACAGACACTGTCCGAGTGATAAATCTACTATTCGCGGAACGGCTCCATAAACGGTGACTATGACCTCATCAGTTAAATTCATTAACCTATAGATGTTGAGAATCCGCCTAAATTGGAGGACGCCGCGCAAAGCCGGTCAACAGCGTTAGTATGTTGAAAGTTTACTCAGATCGCTTCTGTCGGCCTAAGTTATGAATACAGTCAGGGGTTTTCCTGGATACAGATCTTCGGAAGTCTGCTAGTGCCGGTCACGCCACGTATAAGACTAGAGACCTGACACTCATCTCGGACTGTAATTATTTTCTAAGCTAGCTGTCCTATTGTAAGGTAAGTCGGGGTGCCGGACCTTGGCAGCCGTCCGTACGTACATTAATGCATCAGACCAGTAATCTTGCTCGCTAGAGTCGGATCGGCGAGGTCCTCTCAGCTATGAAAAGTAGAATTCAGTCTTGCCCGGGGTAGGGCTAGAGACAAGGGTTGATATTGTCTGAAATGGCGCTCCCATCCGATAACTAAACTACCGTACGGGTGCACGCGAGTAGCCTTAATCCTGTTGGGAAGGAATTGCAATACTCTCCGAACCAGCTTAGGGCCCCCCGCCGCCGCAATTCGAGCGTTATGCCCGGAGCATTTGCACGATGCCATTAAACTATATCAACTACATATACTAGACTATCATCCTAGGGCGTAGAACTCCCTTTGCGTTACCACTCACAACGCGTGTGTTTCTCGTGCGGTGATCCCGGGAGTATTTTATCGGCGCCCCAACTGCCGGCAACTCGAGTGCACCGGAGCTGAGGAACGCTTCAC
+>Seq2
+TGCTGCCGATCGCTACGACGTCCTACCTTACACACAACGGGCCGCGTTCATACCCACGTATGAAGACATGCGGTTATCCGTTAGTTGGGGCCCGCGATGGCTGTTGTATGTAATGAGTGGAGTAAAAGAACACGGGAGATGTTCAATTAGGCTCAACCATTTGTATTGAAGGGGTCAAAACCCACCTGTGTAAGTAGCATTGAGTGCTGCTCATGGCCGATTCTCTTACTTTATTTAAGCCCATACCACTGATGGAGGAGACTCCAAGGAATAGTCCAACCGTTGTTCCGGGAAAAACGAACTCGGTCCGCTAGCGTGCTTGTCGTCGCAGCGCAGATTCCCTCCTAAGTTATTTTACCGGTTGACTCAGTCGCAGGGGTGCTGAACGCCATGGGGCGGACCGAGCGGAGATCTTTCAGGTGTAATTGGATGATCTTCACCCTAAGGAGGGAGCGGGTTATTGGGCAGGCCCGACCGCCGCTGGAAAGATGCAAGTATGAACAAGGCATGCGTAAGTTATCGTGAAACCATGATGGCCCCTTACTAGACCAAATGTACTGAATGCGTCTTGATTAGACCCCGAAAAGGCATATCACATCAACTTGTCGTGTTAGAGATGTCGCGAGAACCCTCGCCTATTCACGAAGTGCCCATGAGCCTTTGGGCCTGGTTGACAATATGCGCACCCTGTAGCCTACCAACCCTTCATAATCTATCTTCAATTTAGCCTGTCGAGAACGTCCTAACAAGGCTTTTGGCGCTCCAGATGGGACAGTCACTCTCTAGCATCAACCCATAGTTTTTGAGCTACCCGCCCTCGGTGAGAAGGTAGTATACCCAAACGCGTCCTATGCAGTTTTGGGCTTGAGGAACTAAAATCAATTCGTTAAGTCCAGTAGTCCTTATGTGTGGCCGTTCCAAGAATTAATCATATCGCGGAATCACCGGCGATTCATTTTCCGCACCAGAGCTTTCAGGTGCGGCGCGGCCCTAAAAGGTC
+>Seq3
+TATTGCGCCCTTCAAGAAGCTTCTGCTGACCGTAGGCGTCTCGGCGGTTTGTACTTTGAAAAATTAGCTGCACTACATCCGATGGGTATCCCTCCTCAATCTCAGCAGACCCGGAAAGCGATAGAATCAGCCACGCGGTCGTCCGGGCTAGGGGCCCTGCGCAAGGAAGGTTGGACAGGGCTAGACCCGGAAGCATCGGCTTTTCCTAAATGGTGACGGAGTTATATAGGGTAAGCCTGATAGCGCGGTAGGTGTAATGGCCATCCCCTCGCCTAGCGTGCGCGCAGACAAGTCCAGTCCCGGAGGAGGCATAGGCCTCATTATCATTTCCCTAGAATCGCTCTTGACATCTAGGTTGTACTAGGGACCAGGCGCCCAAAGCGGACGGTTCTCCGTGCTTTCGTGCCGTTTCAGCGTAAGATGCTATTTTTTGGGGAAATGGTCGGCGTGTGCGGGGGAGAACCACGGTACCAACTACGATAAGTCCGTCGTGTAACTTACGTGAAGGTGCTGTGAAGCAGGAATCCGTGCCAAAATGTCCGTGCGATATCCAACTTTCATAGTATTACACGAGAGCCTATGATTTGCCCAGGCGCGACCCGTGAATCGAGGTAATCGCCGACCAGATATTGCGAAACACCACATTACATGACTACTGTCCGCTTGAAGAGTTATATACTTGACAGTCCTGGTTGACGGCACAGCATATCTCCAATGTGTGGTTTAAAGTCTCACGTTCTTCATGCGCGCCGGCCCATGGGAACAGGTATCCTTACTTTCGGTACAAATGAGGCTCCAAAATAGCACGCTTGCAGCAGTCAAGTTGAACGCCTTAAAAGGCACCGCCGCTCGTTCATTGGGATTCCTTGAGAATCGTGACTTGTTACACTATAAGATCATGGATTGGACAAAATAGGCCAACTCCCGCACGCTGTGGCTATTCTTAAGTTGCATAGGTGGGAGTAGCCTTATACTCGATTTCTAAAAAGAGTAGGTGAGC
+>Seq4
+TTCCGGCGCCGCACTAATTGAAGTGGTGAGCTGACCAGTCGTTCAGGATCCGAAGGCGGGGATGGCGCTATAGGAGCCGGCAGGTATGCTTTGCCGCAAAATTTCGGGGTGGTGGAACCGTCTTACCGAAAGTTAGCTACAGCCTGGAATGTGAAATTCCATGACCTGCCCGTCCTGTGTCCACAGGGCGACATTTGCCACGTAGGTAGGGCGACCATTAGAATGCTGCATTATCGGGCGATAAAAAGTTTTATACCCAAGAATCCTACAAAGATGAAAATTTCGAAGAGCTGCACGCAGTTGTAAGTTGCTTTTCTGGGGTAATCGAGATTCTCCACCATAACCTGCGCAATGCATCGTGAAGCTTTACCGCGCCCAAGGGGAGCGTCTCAGTGGGGTTGCCTCCAGGGATATATTGAAAGTTGAAGAAGAAGATCACAGGTTAAGCGGTATGTTAAGTTAGAACTCACGGGGAGCCGCCTTGATTTTGTTCGACATGAACCAGAGACCAAGTGTGTTATGTTCTGGAACCTTAATACGTACGTCGCCAGCACCGAGCCGGCACTCCATCTCTTTTGGGTGCGCAACATTGCTATACTTAGGATCCATTGACATCTGTCAGCCGTCTTTCCAGAACGTTATAAGACTCGTGAGGAAATTATACAAATCGTTGCCATCATCCAAAGCAAAGTACTTCCGCTTAGGAGTGCCTTGAAGAACCGATTATCTCTGACAATGTAATGCCACAGCACCCTCGACAAAGTTCTACATTCGTTCCAGGTCATGATACAGCGCGCTAAATTACCGCTACGAGCCATACCCCGAACATTGAGACCTGGCCAGTAGGTAGGTGTCAAATCGATATCCACACCTGTCGAAGCAGCTAGGGACCTAGACGCAACAGTAACCGCCTCGGAGTAAGCCCTGGTAAAGATCGGTTGCGGCGGGAGTCCTCCATTCAGGCCAAACGTGCAGTGCTCGATGTGCTTCCTATCGCTCT


=====================================
debian/missing-sources/simple_test.sh
=====================================
@@ -0,0 +1,19 @@
+#!/bin/bash
+    
+rm -f reference.fasta
+#wget https://raw.githubusercontent.com/GATB/MindTheGap/f5cb0fec816686c7393772787d736565c4f056a4/test/full_test/reference.fasta >& /dev/null
+../build/bcalm -in reference.fasta -abundance-min 1 > /dev/null >& /dev/null
+rm -rf reference.unitigs.fa.glue*
+rm -f compare_fasta.py
+#wget https://raw.githubusercontent.com/GATB/minia/master/test/compare_fasta.py >& /dev/null
+python3 compare_fasta.py reference.fasta reference.unitigs.fa
+res=$?
+rm -f reference.fasta reference.h5 reference.unitigs.fa compare_fasta.py 
+if [ "$res" = "0" ]
+then
+    echo "test OK"
+    exit 0
+else
+    echo "test KO"
+    exit 1
+fi


=====================================
debian/source/include-binaries
=====================================
@@ -0,0 +1,3 @@
+debian/missing-sources/compare_fasta.py
+debian/missing-sources/reference.fasta
+debian/missing-sources/simple_test.sh



View it on GitLab: https://salsa.debian.org/med-team/bcalm/commit/f299ab0a3e8cb8aee0c733992af698ed94abbff1

-- 
View it on GitLab: https://salsa.debian.org/med-team/bcalm/commit/f299ab0a3e8cb8aee0c733992af698ed94abbff1
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