biofile-kit 0.1.0

Bioinformatics File Operations Toolkit.

Introduction

BioFileKit: A Python command-line toolkit dedicated to simplifying the reading, writing, conversion, parsing and basic operations of various biological data file formats.

Install

pip install biofile-kit --upgrade

Change log

v0.1.0

• New
  • Fasta file tools (fasta_tools):
    • change hard masked to soft masked
    • telomere finder
  • Gff file tools (gff_tools):
    • Statistical analysis of GFF file
  • Genotype file tools (gt_kit):
    • genotype consistency analysis
    • genotype file merging
    • statistical analysis of SNP loci
  • VCF file tools (vcf_tools):
    • convert the file format from VCF to Genotype (GT)
• Modified
  • Null
• Deleted
  • Null

Usage example

Generate random nucleotide sequences

fasta_tools random_nucl -n seq1,seq2 -l 1000,1200

>seq1 length=1000
CGCCAGGCCTGCCCTGCGACGGAGGTTCCCCGTATGACTGCCCTATATCATTCCTGCTAAACTCAATCCACAAGATCAATTCACTCCGGGGAACAACTGCCACTAGAAACCGTAGGTTACCATCAATAGTTCCCCACTTGGAGGAAGAAGTCTTTGAAGCAGGTTGTCATCCAGCATTCTTTCTAAACGTCATTGGACATAGGGGTAAGCTCATATCCTCTCCCAACCATTCAGAAGTCCATGACCATGTCCGGTGCAAATTTGAAAGTCATGATGGTGAGGGAGCAAGAGAGCGCAGATCACGGATAAGTATTAAAAAGTGCTGTCGAGGCCGCAGTGGAAGTGACTAATTGGCTGATGCACGGACCTCCAGTGTACAGCTCATGTTTCAGGTGCGTCGGACTGTCAGTGACTCAATTTTCTGGGCCCAACTCCGCGTTCGGTGGATTAGTAACTATAGTGGTTGCATGAGGTACTGAGATTGAGCCGTGAAAAGCATTCAAAGTGCGGTTCCTCAACCTATTATTATTAAGACATAAGTTTGCTAGCGCTTTGTTGCAATCGTGTCGTGGAATGCGATTGATGCTTAGCAGTTTCCGGGAAGTACGGACTCATGCCGTTATGTGCGCCAACAAACAGCGCGTGTTTCATTTCGCGCCGGTCGCCTGGCGCGTGTTATGGGATCGCACTTCACCGTGCTGATATCGCTGAGGCGAGGGTTCCTCGAGATATTGGCTTGGCTCGCCAGGCAGTAGTCGTGGTCAGCCCGACTTGGCACGCTAAAGACGAGCCCACGTGCATTCGGTCGGAATCAGTTAGACGTCGAACGATTCGATCCAGCGTGAGGCCTATCCTTTGCCCATTTAACTCCGTATTCACGGTCTCCTTGATACATAGTGTACTTAGTGTTACCAGCGAACTCCGACGCGGACAGTGTCCTCGGAGTATTACCTCCAAAGAAATTCTCGGGCCGAACAGCGTAGTCTATACCGCCTGGGTG
>seq2 length=1200
ATAGGTGTAGTGTGTCTTCATCTTGATGTAAGTTCGTTCACCCAGATCTGCTAAAACGCATGGCATTTTTTTCGCATACGGTCCACTGGCACTATATGATTCCCAGTACTTCGCAGATTTGGGGGGGTAAGAGTCCGCGGAAGCGTTGTTCTGACGCGTACGCATGTTCGGTATTTTTTACGGGTGAGTTGCATCGGTTGTGTATTGGTCCATGTTAAGACGGTTATCGGGCAGGCTTCTCAATGCGGTGAGTCGGGAAGACACTAGCCAGCGAAATTATGTGATCGCTGGAATAGGATCGATGTAGCAACGACACTTTCCTGGCCTACAGACGGACTTGGACCGGATCAATCGTCTTATATAATAATACACGTCGCAGAACGGTCTGTGTATAGGACCGGTAGAATGAGTAGTTCATACTCCGGCCCGCAGGTACCCCTGTACGCATGAAAGTCCAAGCTCTCGCTGAACCGACACCTCTAGCCGAGGTACGTATGCATGACCTGGTTGTTCTCTTCGGGTCACGACAGTTGCCTATTTACGCTCGGATACCAGGAAACTTTGCCGGGAGTTCGCCCCCAGTAGTTCCCGGGTTGGGGTCGGGGTGTTCTGCCGATTACCGGATGTATCTCACCTGAGATTCAGCATCGGTGCGAACATCGTGAATCCTAAAGGTTGAACAAAGGAAGGCCTCCATGCGTTGGAAAGTCCTCGAAGTGGAGAAGTCTATCGTAGATCAACCGATAGGCAATGAAAAGAAAAAGCGCAACAGACGCCACGCTTCTAGATCGCAGTTGGCCTTTTAATGGCGAATCCATTTACCGAGCGAAGAAAAAGCCTGGCTAGCTTGTTTAAAACTGGTAACACTGAATCTCCGAAAGAGTAGCTATAGGCTCCCAGCACAGCCTGCGGCTGGCGCCAACGCCTAACGAAAATGCCAATCCACTTAGTTGTGTTAACTGTCTCCCCACTATATGCGGCTTACCAGGGAGTGTAATTTCTGGCGATGACCAGCGTTTCCTTTGGGTTCCGTCGAATTCCTTAGATCTAGGACAGCAGTTCGAATTACTTGGCGTGGTCGCATCAGGACTTCGCGTAGTGGCTATCCAGATCATAGACTGAGTCACGTATTTGACGCCAGACCTAAGACCCCACGATGGTTTCTAGTCGTAACTTGAGTGAGCTAGCTCGCCTCGTGTC

ORF prediction

fasta_tools random_nucl -n seq1,seq2 -l 1000,1200 | fasta_tools ORF_finder -c -

>seq1 length=42 ORF_prediction
MRLMLSSFREVRTHAVMCANKQRVFHFAPVAWRVLWDRTSPC*
>seq2 length=87 ORF_prediction
MIWIATTRSPDATTPSNSNCCPRSKEFDGTQRKRWSSPEITLPGKPHIVGRQLTQLSGLAFSLGVGASRRLCWEPIATLSEIQCYQF*