Results for "Python Classes"
Bio-Scripts
The following files for plugin example would go in /mod/example/ actions/ example/ action.php other_action.php classes/ VendorNamespace/...831 days ago
- (abhiENV) [abhi@hn1 output_OM824]$ conda create -n mgsc python=3.6 graphviz numpy Collecting package metadat...ted specs: - graphviz - numpy - python=3.6 The following packag...kgs/main/linux-64::pixman-0.40.0-h7f8727e_1 python...
819 days ago
Python script to convert Multi-line Fasta to Single-line Fasta
def multi_to_single_line_fasta(input_filename, output_filename): try: with open(input_filename, 'r') as input_file: with open(output_filename...89 days ago
- #You typically need the corresponding genome sequence file in FASTA format. The GFF file contains information a...anslate the DNA sequences into protein sequences. #Simple example using Python and Biopython...
88 days ago
Python script for six frame translation of sequences !
from Bio import SeqIO from Bio.Seq import Seq def translate_frame(sequence, frame): if frame > 0: translated_seq = sequence[frame-1:].translate()...88 days ago
Python script to find repeats in the DNA sequence !
def find_repeats(sequence, min_repeat_length=3): repeats = [] for i in range(len(sequence) - min_repeat_length + 1): substring = sequence[i:i+m...88 days ago
Python script for basic stats of the assembled genome !
from Bio import SeqIO import statistics # Input file containing the genome assembly in FASTA format input_file = 'genome_assembly.fasta' # Variables for computi...88 days ago
Python script to convert fastq to fasta
def fastq_to_fasta(fastq_file, fasta_file): with open(fastq_file, 'r') as fq: with open(fasta_file, 'w') as fa: while True:...32 days ago
Python script to parse GFF file
def parse_gff(gff_file): features = [] with open(gff_file, 'r') as f: for line in f: if not line.startswith('#'): # Ignore comment line...32 days ago
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