bioinformatics perl useful
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BLAST
use Bio::SearchIO;my $searchio=Bio::SearchIO->new(-file=>$file_blast,-format=>'blast');while( my $result = $searchio->next_result ) { my $qid = $result->query_name(); my $qlen= $result->query_length(); my $did = $result->database_name(); while( my $hit = $result->next_hit ) { my $hit_name = $hit->name(); my $hit_len = $hit->length; while( my $hsp = $hit->next_hsp ) { my $qs=$hsp->start('query'); my $qe=$hsp->end('query'); my $ds=$hsp->start('subject'); my $de=$hsp->end('subject'); }#hsp }#hit}#result
FASTA
use Bio::SeqIO;my $in=Bio::SeqIO->new(-file=>$fa_add,-format=>'fasta');while(my $s=$in->next_seq){ my $id=$s->id; my $seq=$s->seq;}
GFF3
my($seqid,$source,$type,$start,$end,$score,$strand,$phase,$attribute)=split /\t/;
Pfam
my($seqid,$alignment_start,$alignment_end,$envelope_start,$envelope_end,$hmm_acc,$hmm_name,$type,$hmm_start,$hmm_end,$hmm_length,$bit_score,$evalue,$significance,$clan)=split /\s+/;
mumer
my %aln; open(F,'<',$file_nucmer) or die("$!: $file_nucmer\n"); while (<F>) { next unless(m/^\d+/); chomp; my($start1,$end1,$start2,$end2,$len1,$len2,$identity,$length_reference,$length_query,$coverage_reference,$coverage_query,$id_reference,$id_query)=split /\t/; push(@{$aln{$id_reference}},[$start1,$end1,$start2,$end2,$len1,$len2,$identity,$length_reference,$length_query,$coverage_reference,$coverage_query,$id_reference,$id_query]); } close(F);
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