Results for "input"
Bio-Scripts
Rules to run fastp / Snakemake !
rule fastp: input: fwd=INPUT + "/{sample}-read_1.fq", rev=INPUT + "/{sample}-read_2.fq" output: fwd=RESULTS...sample}.preprocess.log" shell: "fastp --in1 {input.fwd} --in2 {input.rev} "...935 days ago
- ...command keeps a current count of the number of input records. Remember that record...unt of the number of fields within the current input record. #FS: FS command c...ord separator character. Since, by default, an input line is the input record, the...
928 days ago
bash script to extract sequence by ids !
Use a Perl one-liner, grep and seqtk subseq to extract the desired fasta sequences: # Create test input: cat > in.fasta BGI_novel_T016313 Solyc03g025570.2.1 TTCAAGTGTTAGTTTCAC...857 days ago
Perl script for six frame translation !
...strict; use warnings; use Bio::SeqIO; # Path to your input nucleotide sequence file in FASTA format my $input_fasta = 'path/to/your/input.f...he input FASTA file my $seqio = Bio::SeqIO->new(-file => $input_fasta, -format => 'fasta');...128 days ago
Python script for six frame translation of sequences !
...Reverse" print(f"Frame {frame_type} {abs(frame)} Translation:\n{protein_sequence}\n") # Replace 'path/to/your/input.fasta' with the actual path to your input nucleotide sequence in FASTA...128 days ago
Perl script to parse VCF file !
#!/usr/bin/perl use strict; use warnings; # Usage: ./parse_vcf.pl input.vcf die "Usage: ./parse_vcf.pl input.vcf\n" unless @ARGV; my $vcf_file = shift @ARGV; my @vcf_entries = parse_vcf($v...128 days ago
Perl script to calculate the basic stats of the assembled genome !
...use warnings; use Bio::SeqIO; # Input file containing the genome assembly in FASTA format my $input_file = 'genome_assembly.fasta...y $seqio = Bio::SeqIO->new(-file => $input_file, -format => 'fasta');...$gc_content = calculate_gc_content($input_file); # Print the compute...128 days ago
Python script for basic stats of the assembled genome !
...import SeqIO import statistics # Input file containing the genome assembly in FASTA format input_file = 'genome_assembly.fasta...assembly for record in SeqIO.parse(input_file, 'fasta'): length =...(f"GC Content: {calculate_gc_content(input_file)}%") print("\nContig Le...128 days ago
Python script to convert fastq to fasta
...o the FASTA file fa.write('>' + header[1:] + '\n') fa.write(sequence + '\n') # Usage example fastq_to_fasta('input.fastq', 'output.fasta')72 days ago
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