How to use perl to realize ncbi Genome data format conversion
Editor to share with you how to use perl to achieve ncbi genome data format conversion, I hope you will learn something after reading this article, let's discuss it together!
Format conversion of ncbi Genome data
We all know that the genomic data downloaded from ncbi is different from the normal genomic data, and the ID of all gene transcripts CDS is restarted, which is very inconvenient to use, so we write a perl script to convert its ID back.
The usage is as follows:
UsageForced parameter:-gff genoma gff file must be given-fa genoma fasta file must be given-o output gff file must be given-out output fasta file must be givenOther parameter:-h Help document
The code is as follows:
Use Getopt::Long;use strict;use Bio::SeqIO;use Bio::Seq;#get optsmy% opts;GetOptions (\% opts, "gff=s", "oaths", "fa=s", "out=s", "h"); if (! defined ($opts {gff}) | |! defined ($opts {o}) | |! defined ($opts {fa}) | |! defined ($opts {out}) | | defined ($opts {h}) {print new (- file = > "$opts {fa}",-format = > 'Fasta')) My $out = Bio::SeqIO- > new (- file = > "> $opts {out}",-format = > 'fasta'); while (my $seq = $in- > next_seq ()) {# my ($id,$sequence) = ($seq- > id,$seq- > seq); my ($id,$sequence,$desc) = ($seq- > id,$seq- > seq,$seq- > desc); my $newSeqobj = Bio::Seq- > new (- seq = > $sequence,-desc = > $desc,-id = > $chr {$id},) $out- > write_seq ($newSeqobj);} after reading this article, I believe you have some understanding of "how to use perl to convert ncbi genomic data format". If you want to know more about it, please follow the industry information channel. Thank you for reading!
