Add some missing sources for tests

#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)

>Seq0

ACCTATAAGGATCCACGTCTTGATGTGACCGACGATGTTATCTGCCTATAGCGAACATTTCCTGGTAGGAATACTATTATATTACCTAAATTCTCCGGATTTCCGTGTTCTTCGGAAGCTTAGGTCACGCGCGTCATACTACAGTAAGTTACTGAATTTTGGAGTAATGCATATCGACCGAGTCCGGGGAATCGTCCGTATCCCCGCCAGGCGTATCCAATAATTAGGTCGGACCCCTAGCGCGTACGAGTCCTATAGCTGACATGCGAATTGGCCGTGCATCGAGCTCAAATGTCCTAGCTTGAGAGTGCGTATCTCACCGATCCCCTGGCTATGCTCCGCGATTCACTAGTAGTTTCACGCCGACAGAGCGAAACCGTGATAGGTCATCATGCCGGTCTGCAGTCACGTGCCCAGCAGTCTCCAATATAGCCACTTATGTCGGAATGTAATCGGCTCCAAATTACTGTGAACCTGATGATCGACGACGCGCTGGGTGCGGGATAGTGTAACTGTCCCGTATAAGGCTTAAATTGAGTATGCAGGATACACTTTTAGTATGACTCGGAAAATCCCACTACAGTATGAACCGTGACTGTCGTTGGGCGGTGCTTGTTGCTATTAACTGGATGGTAAGTCAATTTTAAGTGGAGCCCCCTGCAAGATGGAAGAGAACTATATGTGGAACCGGATGTCACGTCAAGACCACCGCGCACGCTTAACACAACGCATGGTTCGGCGACTGCTCCGGTTCTGGAATTCCTCTTTTTTATCGAGATTAGCATCTCATTAGCGCGCAGTGTGTCCTAGTGTCCCAGAACGTAAAGACCAGATTTGACATTAGTAAGTTGCATTCGCGGGTCTTTAGAGCTCCTACTAAGCCCATTCAGATTGAAAAAGGCGCGCCTGCGGTTCCATGTCATAGTTTAACTTGGTTGAGACGGCGCACGAAAGCATACTACCACCATCCATGTCAAAACTGGCGACGATCTTGCTGGGT

>Seq1

GTTTTATAACAAGTGAAGAAAGAACAGTCATTAGGCCCGAAGGCGTACACGGAATCCGCCTAAACTAATGCTTATGGTCCCTCGTAGGCCCCGACGGCATAGGGTGCCCCGTAATTGCGTAGACAGCGAAAGGAAAGTGTACCGACGACGAGATCAAGTGGCAGTGAACCCCTTGGAAAACTTCATATCGACAGACACTGTCCGAGTGATAAATCTACTATTCGCGGAACGGCTCCATAAACGGTGACTATGACCTCATCAGTTAAATTCATTAACCTATAGATGTTGAGAATCCGCCTAAATTGGAGGACGCCGCGCAAAGCCGGTCAACAGCGTTAGTATGTTGAAAGTTTACTCAGATCGCTTCTGTCGGCCTAAGTTATGAATACAGTCAGGGGTTTTCCTGGATACAGATCTTCGGAAGTCTGCTAGTGCCGGTCACGCCACGTATAAGACTAGAGACCTGACACTCATCTCGGACTGTAATTATTTTCTAAGCTAGCTGTCCTATTGTAAGGTAAGTCGGGGTGCCGGACCTTGGCAGCCGTCCGTACGTACATTAATGCATCAGACCAGTAATCTTGCTCGCTAGAGTCGGATCGGCGAGGTCCTCTCAGCTATGAAAAGTAGAATTCAGTCTTGCCCGGGGTAGGGCTAGAGACAAGGGTTGATATTGTCTGAAATGGCGCTCCCATCCGATAACTAAACTACCGTACGGGTGCACGCGAGTAGCCTTAATCCTGTTGGGAAGGAATTGCAATACTCTCCGAACCAGCTTAGGGCCCCCCGCCGCCGCAATTCGAGCGTTATGCCCGGAGCATTTGCACGATGCCATTAAACTATATCAACTACATATACTAGACTATCATCCTAGGGCGTAGAACTCCCTTTGCGTTACCACTCACAACGCGTGTGTTTCTCGTGCGGTGATCCCGGGAGTATTTTATCGGCGCCCCAACTGCCGGCAACTCGAGTGCACCGGAGCTGAGGAACGCTTCAC

>Seq2

TGCTGCCGATCGCTACGACGTCCTACCTTACACACAACGGGCCGCGTTCATACCCACGTATGAAGACATGCGGTTATCCGTTAGTTGGGGCCCGCGATGGCTGTTGTATGTAATGAGTGGAGTAAAAGAACACGGGAGATGTTCAATTAGGCTCAACCATTTGTATTGAAGGGGTCAAAACCCACCTGTGTAAGTAGCATTGAGTGCTGCTCATGGCCGATTCTCTTACTTTATTTAAGCCCATACCACTGATGGAGGAGACTCCAAGGAATAGTCCAACCGTTGTTCCGGGAAAAACGAACTCGGTCCGCTAGCGTGCTTGTCGTCGCAGCGCAGATTCCCTCCTAAGTTATTTTACCGGTTGACTCAGTCGCAGGGGTGCTGAACGCCATGGGGCGGACCGAGCGGAGATCTTTCAGGTGTAATTGGATGATCTTCACCCTAAGGAGGGAGCGGGTTATTGGGCAGGCCCGACCGCCGCTGGAAAGATGCAAGTATGAACAAGGCATGCGTAAGTTATCGTGAAACCATGATGGCCCCTTACTAGACCAAATGTACTGAATGCGTCTTGATTAGACCCCGAAAAGGCATATCACATCAACTTGTCGTGTTAGAGATGTCGCGAGAACCCTCGCCTATTCACGAAGTGCCCATGAGCCTTTGGGCCTGGTTGACAATATGCGCACCCTGTAGCCTACCAACCCTTCATAATCTATCTTCAATTTAGCCTGTCGAGAACGTCCTAACAAGGCTTTTGGCGCTCCAGATGGGACAGTCACTCTCTAGCATCAACCCATAGTTTTTGAGCTACCCGCCCTCGGTGAGAAGGTAGTATACCCAAACGCGTCCTATGCAGTTTTGGGCTTGAGGAACTAAAATCAATTCGTTAAGTCCAGTAGTCCTTATGTGTGGCCGTTCCAAGAATTAATCATATCGCGGAATCACCGGCGATTCATTTTCCGCACCAGAGCTTTCAGGTGCGGCGCGGCCCTAAAAGGTC

>Seq3

TATTGCGCCCTTCAAGAAGCTTCTGCTGACCGTAGGCGTCTCGGCGGTTTGTACTTTGAAAAATTAGCTGCACTACATCCGATGGGTATCCCTCCTCAATCTCAGCAGACCCGGAAAGCGATAGAATCAGCCACGCGGTCGTCCGGGCTAGGGGCCCTGCGCAAGGAAGGTTGGACAGGGCTAGACCCGGAAGCATCGGCTTTTCCTAAATGGTGACGGAGTTATATAGGGTAAGCCTGATAGCGCGGTAGGTGTAATGGCCATCCCCTCGCCTAGCGTGCGCGCAGACAAGTCCAGTCCCGGAGGAGGCATAGGCCTCATTATCATTTCCCTAGAATCGCTCTTGACATCTAGGTTGTACTAGGGACCAGGCGCCCAAAGCGGACGGTTCTCCGTGCTTTCGTGCCGTTTCAGCGTAAGATGCTATTTTTTGGGGAAATGGTCGGCGTGTGCGGGGGAGAACCACGGTACCAACTACGATAAGTCCGTCGTGTAACTTACGTGAAGGTGCTGTGAAGCAGGAATCCGTGCCAAAATGTCCGTGCGATATCCAACTTTCATAGTATTACACGAGAGCCTATGATTTGCCCAGGCGCGACCCGTGAATCGAGGTAATCGCCGACCAGATATTGCGAAACACCACATTACATGACTACTGTCCGCTTGAAGAGTTATATACTTGACAGTCCTGGTTGACGGCACAGCATATCTCCAATGTGTGGTTTAAAGTCTCACGTTCTTCATGCGCGCCGGCCCATGGGAACAGGTATCCTTACTTTCGGTACAAATGAGGCTCCAAAATAGCACGCTTGCAGCAGTCAAGTTGAACGCCTTAAAAGGCACCGCCGCTCGTTCATTGGGATTCCTTGAGAATCGTGACTTGTTACACTATAAGATCATGGATTGGACAAAATAGGCCAACTCCCGCACGCTGTGGCTATTCTTAAGTTGCATAGGTGGGAGTAGCCTTATACTCGATTTCTAAAAAGAGTAGGTGAGC

>Seq4

TTCCGGCGCCGCACTAATTGAAGTGGTGAGCTGACCAGTCGTTCAGGATCCGAAGGCGGGGATGGCGCTATAGGAGCCGGCAGGTATGCTTTGCCGCAAAATTTCGGGGTGGTGGAACCGTCTTACCGAAAGTTAGCTACAGCCTGGAATGTGAAATTCCATGACCTGCCCGTCCTGTGTCCACAGGGCGACATTTGCCACGTAGGTAGGGCGACCATTAGAATGCTGCATTATCGGGCGATAAAAAGTTTTATACCCAAGAATCCTACAAAGATGAAAATTTCGAAGAGCTGCACGCAGTTGTAAGTTGCTTTTCTGGGGTAATCGAGATTCTCCACCATAACCTGCGCAATGCATCGTGAAGCTTTACCGCGCCCAAGGGGAGCGTCTCAGTGGGGTTGCCTCCAGGGATATATTGAAAGTTGAAGAAGAAGATCACAGGTTAAGCGGTATGTTAAGTTAGAACTCACGGGGAGCCGCCTTGATTTTGTTCGACATGAACCAGAGACCAAGTGTGTTATGTTCTGGAACCTTAATACGTACGTCGCCAGCACCGAGCCGGCACTCCATCTCTTTTGGGTGCGCAACATTGCTATACTTAGGATCCATTGACATCTGTCAGCCGTCTTTCCAGAACGTTATAAGACTCGTGAGGAAATTATACAAATCGTTGCCATCATCCAAAGCAAAGTACTTCCGCTTAGGAGTGCCTTGAAGAACCGATTATCTCTGACAATGTAATGCCACAGCACCCTCGACAAAGTTCTACATTCGTTCCAGGTCATGATACAGCGCGCTAAATTACCGCTACGAGCCATACCCCGAACATTGAGACCTGGCCAGTAGGTAGGTGTCAAATCGATATCCACACCTGTCGAAGCAGCTAGGGACCTAGACGCAACAGTAACCGCCTCGGAGTAAGCCCTGGTAAAGATCGGTTGCGGCGGGAGTCCTCCATTCAGGCCAAACGTGCAGTGCTCGATGTGCTTCCTATCGCTCT

#!/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/missing-sources/compare_fasta.py

debian/missing-sources/reference.fasta

debian/missing-sources/simple_test.sh