1536 days ago
Python script to check sequence length in multifasta file
#!/usr/bin/python from Bio import SeqIO import sys cmdargs = str(sys.argv) for seq_record in SeqIO.parse(str(sys.argv[1]), "fasta"): output_line = '%s\t%i' % \ (seq_record.id, len(seq_record)) print(output_line)1242 days ago
Onliner to split the multifasta to singlefasta files !
#Split the multifasta to singlefasta # Multi fasta #Single fasta awk '$0 ~ "^>" { match($1, /^>([^:]+)/, id); filename=id[1]} {print >> filename".fa"}' sequence.fasta1427 days ago
1429 days ago
Sequence Ids conversion files !
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ Name Size Date Modified ARCHIVE/ 02/01/2020, 05:30:00 ASN_BINARY/ 03/07/2020, 07:49:00 GENE_INFO/ 03/07/2020, 07:48:00 0...1429 days ago
Reformat the multifasta for sequence length !
#awk oneliner to reformat the multifasta sequences awk '!/^>/ {printf "%s", $0; n = "\n"} /^>/ {print n $0; n = ""}' file.fasta | fold -w 1001419 days ago
Bash script to handle Multifasta files
#Convert all lowercase residues to uppercase in a FASTA sequence file $ awk 'BEGIN{FS=" "}{if(!/>/){print toupper($0)}else{print $1}}' input.fasta > output.fasta #Rearrange FASTA sequences...1384 days ago
1367 days ago
1230 days ago
Install and set up i-adhore for synteny and wgd analysis ! -- step by step --
#Need to download i-adhore-3.0.01.tar.gz from https://wdiceryfd4rjn74bjhhtz2k5di--bioinformatics-psb-ugent-be.translate.goog/webtools/i-adhore/licensing/ #Follow the...1230 days ago