pybioinformatic 1.2.5

Bioinformatic python package.

This is a bioinformatic python package.

Install

pip install pybioinformatic --upgrade

Issue

ImportError: libffi.so.7: cannot open shared object file: No such file or directory

# First use the following command to verify that the file exists in that path.
ls /usr/lib/x86_64-linux-gnu/libffi.so.7

# If libffi.so.6 is present on your system but libffi.so.7 is missing, you can try creating a soft link to an existing libffi.so.6 file.
ln -s /usr/lib/x86_64-linux-gnu/libffi.so.6 /usr/lib/x86_64-linux-gnu/libffi.so.7

# You can also install libffi7 with sudo grant.
sudo apt-get install libffi7

Usage example

RNA secondary structure prediction.

from pybioinformatic import Nucleotide

# Generate random nucleic acid sequence.
random_nucl = Nucleotide.random_nucl(name='demo', length=[100, 150], bias=1.0)

# Secondary structure prediction
ss, mfe = random_nucl.predict_secondary_structure('test/structure.ps')
print(ss, mfe, sep='\n')

>demo length=135
CAAAAAAAAACCATAAGCCGCCATGTCTCACATCGCAACCGGCTCAAGTAGAGTGCCCCTAATAATATGATCTTCGCTACAGAAGTTCCCCCCCCGCTGCCGGCTAGATGCGAACTCCACGCCTGGATGGCTCAG
...............((((((((.((......(((((.(.((((...((((.................((.((((......)))).))........)))).)))).).))))).......)).))).)))))...
-27.299999237060547

Connect MySQL

from pybioinformatic import BioMySQL

with BioMySQL(
    mysql_host='192.168.1.110',
    mysql_port=3306,
    mysql_user='60533',
    mysql_password='NJFU',
    ssh_ip=None,
    ssh_port=None,
    ssh_user=None,
    ssh_password=None,
    remote_bind_ip=None,
    remote_bind_port=None,
    local_bind_ip=None,
    local_bind_port=None
) as connect:
    cur = connect.cursor()
    sql = 'use Ptrichocarpa;'
    cur.execute(sql)
    sql = 'select protein_id,sequence from protein where protein_id = "Potri.019G097720.1.p";'
    cur.execute(sql)
    for data in cur.fetchall():
        protein_id, sequence = data
        print(f'>{protein_id}\n{sequence}')

>Potri.019G097720.1.p
MESLQHLYLSKTGIKEIPSSFKHMISLITLKLDGTPIKELPLSIKDKVCLEYLTLHGTPIKALPELPPSLRFLTTHDCASLETVISIINISSLWFRRDFTNCFKLDQKPLVAAMHLKIQSGEETPHGTIQMVLLGSEIPEWFGDKGIGSSLTIQLPSNCHLLKGIAFCLVFLLPLPSQDMPCEVDDDSYVHVYFDCHVKSKNGESDGGDEIVFGSQERRALLYLLETCDSDHMFLHYELGLVNHLRKYSGNEVTFKFYHEVYNQGRKLGHEIRKPFKLKNCGVYLHFDENLPADTDLP*

Analysis of Phenotypic Differences by Genotype

from pybioinformatic import GenoType


with GenoType('E:/Desktop/GWAS/raw_data/BLINK.DBH4(NYC).GT.xls') as gt:
    gt.genotype_phenotype_analysis(
        trait_file='E:/Desktop/GWAS/raw_data/28clones_trait.txt',
        trait_name='DBH4',
        out_path='E:/Desktop/GWAS/test',
        mark_sample_list=['35_2', '35_3', '85_7']
    )