aindex2 1.0.1

Perfect hash based index for genome data.

aindex

Perfect hash based index for text data.

Installation

git clone https://github.com/ad3002/aindex.git
cd aindex
make
pip install build installer
python -m build && python -m installer dist/aindex-1.0.0-py3-none-any.whl

This will create the necessary executables in the bin directory.

To clean up the compiled files, run:

make clean

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

time python ~/Dropbox/workspace/aindex/scripts/compute_aindex.py -i $FASTQ1,$FASTQ2 -t fastq -o $OUTPUT_PREFIX --lu 2 -P 30

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 from Python

You can simply run demo.py or:

from aindex import *

settings = {
  "index_prefix": "tests/raw_reads.101bp.IS350bp25.23",
  "aindex_prefix": "tests/raw_reads.101bp.IS350bp25.23",
  "reads_file": "tests/raw_reads.101bp.IS350bp25.reads",
}

index = load_aindex(settings)

k = 23
sequence = "TAAGTTATTATTTAGTTAATACTTTTAACAATATTATTAAGGTATTTAAAAAATACTATTATAGTATTTAACATAGTTAAATACCTTCCTTAATACTGTTAAATTATATTCAATCAATACATATATAATATTATTAAAATACTTGATAAGTATTATTTAGATATTAGACAAATACTAATTTTATATTGCTTTAATACTTAATAAATACTACTTATGTATTAAGTAAATATTACTGTAATACTAATAACAATATTATTACAATATGCTAGAATAATATTGCTAGTATCAATAATTACTAATATAGTATTAGGAAAATACCATAATAATATTTCTACATAATACTAAGTTAATACTATGTGTAGAATAATAAATAATCAGATTAAAAAAATTTTATTTATCTGAAACATATTTAATCAATTGAACTGATTATTTTCAGCAGTAATAATTACATATGTACATAGTACATATGTAAAATATCATTAATTTCTGTTATATATAATAGTATCTATTTTAGAGAGTATTAATTATTACTATAATTAAGCATTTATGCTTAATTATAAGCTTTTTATGAACAAAATTATAGACATTTTAGTTCTTATAATAAATAATAGATATTAAAGAAAATAAAAAAATAGAAATAAATATCATAACCCTTGATAACCCAGAAATTAATACTTAATCAAAAATGAAAATATTAATTAATAAAAGTGAATTGAATAAAATTTTGAAAAAAATGAATAACGTTATTATTTCCAATAACAAAATAAAACCACATCATTCATATTTTTTAATAGAGGCAAAAGAAAAAGAAATAAACTTTTATGCTAACAATGAATACTTTTCTGTCAAATGTAATTTAAATAAAAATATTGATATTCTTGAACAAGGCTCCTTAATTGTTAAAGGAAAAATTTTTAACGATCTTATTAATGGCATAAAAGAAGAGATTATTACTATTCAAGAAAAAGATCAAACACTTTTGGTTAAAACAAAAAAAACAAGTATTAATTTAAACACAATTAATGTGAATGAATTTCCAAGAATAAGGTTTAATGAAAAAAACGATTTAAGTGAATTTAATCAATTCAAAATAAATTATTCACTTTTAGTAAAAGGCATTAAAAAAATTTTTCACTCAGTTTCAAATAATCGTGAAATATCTTCTAAATTTAATGGAGTAAATTTCAATGGATCCAATGGAAAAGAAATATTTTTAGAAGCTTCTGACACTTATAAACTATCTGTTTTTGAGATAAAGCAAGAAACAGAACCATTTGATTTCATTTTGGAGAGTAATTTACTTAGTTTCATTAATTCTTTTAATCCTGAAGAAGATAAATCTATTGTTTTTTATTACAGAAAAGATAATAAAGATAGCTTTAGTACAGAAATGTTGATTTCAATGGATAACTTTATGATTAGTTACACATCGGTTAATGAAAAATTTCCAGAGGTAAACTACTTTTTTGAATTTGAACCTGAAACTAAAATAGTTGTTCAAAAAAATGAATTAAAAGATGCACTTCAAAGAATTCAAACTTTGGCTCAAAATGAAAGAACTTTTTTATGCGATATGCAAATTAACAGTTCTGAATTAAAAATAAGAGCTATTGTTAATAATATCGGAAATTCTCTTGAGGAAATTTCTTGTCTTAAATTTGAAGGTTATAAACTTAATATTTCTTTTAACCCAAGTTCTCTATTAGATCACATAGAGTCTTTTGAATCAAATGAAATAAATTTTGATTTCCAAGGAAATAGTAAGTATTTTTTGATAACCTCTAAAAGTGAACCTGAACTTAAGCAAATATTGGTTCCTTCAAGATAATGAATCTTTACGATCTTTTAGAACTACCAACTACAGCATCAATAAAAGAAATAAAAATTGCTTATAAAAGATTAGCAAAGCGTTATCACCCTGATGTAAATAAATTAGGTTCGCAAACTTTTGTTGAAATTAATAATGCTTATTCAATATTAAGTGATCCTAACCAAAAGGAAAAATATGATTCAATGCTGAAAGTTAATGATTTTCAAAATCGCATCAAAAATTTAGATATTAGTGTTAGATGACATGAAAATTTCATGGAAGAACTCGAACTTCGTAAGAACTGAGAATTTGATTTTTTTTCATCTGATGAAGATTTCTTTTATTCTCC

ATTTACAAAAA"
test_kmer = "TAAGTTATTATTTAGTTAATACT"
right_kmer = "AGTTAATACTTTTAACAATATTA"

print "Task 1. Get kmer frequency"
raw_input("\nReady?")
for i in xrange(len(sequence)-k+1):
    kmer = sequence[i:i+k]
    print "Position %s kmer %s freq = %s" % (i, kmer, index[kmer])

print "Task 2. Iter read by read, print the first 20 reads"
raw_input("\nReady?")
for i, read in enumerate(index.iter_reads()):
    if i == 20:
        break
    print i, read

print "Task 3. Iter reads by kmer, returs (start, next_read_start, read, pos_if_uniq|None, all_poses)"
raw_input("\nReady?")
for read in iter_reads_by_kmer(test_kmer, index):
    print read

print "Task 4. Get distances in reads for two kmers, returns a list of (rid, left_kmer_pos, right_kmer_pos) tuples."
raw_input("\nReady?")
print get_left_right_distances(test_kmer, right_kmer, index)

print "Task 5. Get layout for kmer, returns (max_pos, reads, lefts, rights, rids, starts), for details see source code"
raw_input("\nReady?")
max_pos, reads, lefts, rights, rids, starts = get_layout_for_kmer(right_kmer, index)
print "Central layout:"
for read in reads:
    print read
print "Left flanks:"
print lefts
print "Right flanks:"
print rights

print "Task 6. Iter reads by sequence, returns (start, next_read_start, read, pos_if_uniq|None, all_poses)"
raw_input("\nReady?")
sequence = "AATATTATTAAGGTATTTAAAAAATACTATTATAGTATTTAACATA"
for read in iter_reads_by_sequence(sequence, index):
    print read