aindex: perfect hash based index for genomic data

Installation

Requirements:

jellyfish 2

(easy to install with apt install jellyfish or with conda install bioconda::jellyfish)

Installation with pip:

pip install aindex2

If you want to install the package from source or you don't have pip version for your system, you can do so by running the following commands:

git clone https://github.com/ad3002/aindex.git
cd aindex
make
pip install .

This will create the necessary executables in the bin directory.

To uninstall:

pip uninstall aindex2
pip uninstall clean

To clean up the compiled files, run:

make clean

Mac Compilation Command

Currently unsupported in Makefile. But you can try to compile the Python wrapper on MacOs manually with the following command:

g++ -c -std=c++11 -fPIC python_wrapper.cpp -o python_wrapper.o && g++ -c -std=c++11 -fPIC kmers.cpp kmers.hpp debrujin.cpp debrujin.hpp hash.cpp hash.hpp read.cpp read.hpp settings.hpp settings.cpp && g++ -shared -Wl,-install_name,python_wrapper.so -o python_wrapper.so python_wrapper.o kmers.o debrujin.o hash.o read.o settings.o

Usage

Compute all binary arrays:

FASTQ1=./tests/raw_reads.101bp.IS350bp25_1.fastq
FASTQ2=./tests/raw_reads.101bp.IS350bp25_2.fastq
OUTPUT_PREFIX=./tests/raw_reads.101bp.IS350bp25

compute_aindex.py -i $FASTQ1,$FASTQ2 -t fastq -o $OUTPUT_PREFIX --lu 2 -P 30

Usage from Python

You can simply run demo.py or:

import aindex

prefix_path = "tests/raw_reads.101bp.IS350bp25"
kmer2tf = aindex.get_aindex(prefix_path)

kmer = "A"*23
rkmer = "T"*23
kid = kmer2tf.get_kid_by_kmer(kmer)
print(kmer2tf.get_kmer_info_by_kid(kid))
print(kmer2tf[kmer], kid, kmer2tf.get_kmer_by_kid(kid), len(kmer2tf.pos(kmer)), kmer2tf.get_strand(kmer), kmer2tf.get_strand(rkmer))
kmer = kmer2tf.get_read(0, 23, 0)
pos = kmer2tf.pos(kmer)[0]
print(pos)

print(kmer2tf.get_kid_by_kmer(kmer), kmer2tf.get_kid_by_kmer(rkmer))

print(kmer2tf.get_hash_size())

print(kmer2tf.get_read(0, 123, 0))

print(kmer2tf.get_read(0, 123, 1))


k = 23
for p in kmer2tf.pos(kmer):
  print(kmer2tf.get_read(p, p+k))
  
test_kmer = "TAAGTTATTATTTAGTTAATACT"
right_kmer = "AGTTAATACTTTTAACAATATTA"

print(kmer2tf[kmer])

sequence = kmer2tf.get_read(0, 1023, 0)

print("Task 1. Get kmer frequency")
for i, (kmer, tf) in enumerate(kmer2tf.iter_sequence_kmers(sequence)):
    print(f"Position {i} kmer {kmer} freq = {tf}")
  
print("Task 2. Iter read by read, print the first 20 reads")
for rid, read in kmer2tf.iter_reads():
    if rid == 20:
        break
    print(rid, read)

print("Task 3. Iter reads by kmer, returs (read id, position in read, read, all_positions)")
for rid, pos, read, poses in aindex.iter_reads_by_kmer(test_kmer, kmer2tf):
  print(read[pos:pos+k])


print("Task 4. Iter reads by sequence, returns (read, position in read, read, all_positions ")
sequence = "AATATTATTAAGGTATTTAAAAAATACTATTATAGTATTTAACATA"
for read in aindex.iter_reads_by_sequence(sequence, kmer2tf):
    print(read)

print("Task 5. Iter reads by sequence over hamming distance, returns (read, position in read, read, all_positions, hamming distance). Note that the first kmer used as seed.")
sequence = "AATATTATTAAGGTATTTAAAAAATACTATTATAGTATTTAACATA"
for read in aindex.iter_reads_by_sequence(sequence, kmer2tf, hd=10):
    print(read)

print("Task 6. Iter reads by sequence over hamming distance or edit distance, returns (read, position in read, read, all_positions, hamming distance). Note that the first kmer used as seed")
sequence = "AATATTATTAAGGTATTTAAAAAATACTATTATAGTATTTAACATA"
for read in aindex.iter_reads_by_sequence(sequence, kmer2tf, hd=10):
    print(read)

for read in aindex.iter_reads_by_sequence(sequence, kmer2tf, ed=10):
    print(read)


print("Task 7. Get distances in reads for two kmers, returns a list of (rid, left_kmer_pos, right_kmer_pos) tuples.")
for rid, start, end, length, fragment, is_gapped, is_reversed in aindex.get_left_right_distances(test_kmer, right_kmer, kmer2tf):
    print(rid, start, end, length, fragment, is_gapped, is_reversed)

print("Task 8. Get layout for kmer, returns (max_pos, reads, lefts, rights, rids, starts), for details see source code")
max_pos, reads, lefts, rights, rids, starts = aindex.get_layout_from_reads(right_kmer, kmer2tf)
print("Central layout:")
for read in reads:
    print(read)
print("Left flanks:")
print(lefts)
print("Right flanks:")
print(rights)