bioinformatics perl useful
发布时间:2020-12-16 00:31:09 所属栏目:大数据 来源:网络整理
导读: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(); wh
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
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,$hmm_start,$hmm_end,$hmm_length,$bit_score,$evalue,$significance,$clan)=split /s+/; mumer my %aln; open(F,'<',$file_nucmer) or die("$!: $file_nucmern"); while (<F>) { next unless(m/^d+/); chomp; my($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}},[$start1,$id_query]); } close(F); (编辑:李大同) 【声明】本站内容均来自网络,其相关言论仅代表作者个人观点,不代表本站立场。若无意侵犯到您的权利,请及时与联系站长删除相关内容! |