perl语言提取DNA序列

hubenxia

我想提取DNA序列contig的序列


>contig00010
AGCTAGCTTCGGCTATCGCTGGTCTCGGCACTCTGCTGCTGCCGTCTTTTTTTTTTTTTTTGCGATGTCTTACCCCCATACTTAATCTGTGTGCGTAGTCATCCTCCTGTACGTGTCAGTATGCTATACTGTCATCTTCTCATTCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGCAGTTTTTTTTTTTTTTCGTAAAAAAAAAAAAAAAAAAACTGATCATCATCATCTGCATGCTGGTCTGAC

请高手赐教

金刚狼2

发帖辛苦了,楼主 支持

mcshell

回复 1# hubenxia


    亲，，，不学生物真看不懂你在说啥

gaoyang636

我是生物出身的，呃～也看不懂lz想说啥～～

hubenxia

#!/usr/bin/perl -w
open DATA,"<seq.fna";
open SEQUENCE,">result.txt";
my %hash;
my $last;
while (<DATA> {
if (/^\>/) {
$last = $_ ;
}
else {
$hash{$last} = $_;
}
open DABA, "<list.txt";
while ($line=<DABA> {
($number) = $line =~/^(\S+)\s+/;
if ($last =~/$number/) {
print SEQUENCE $last;
print SEQUENCE $hash{$last};
print $last;
print $hash{$last};
}
}
close DABA;
}
close DATA;
close SEQUENCE;

hubenxia

我需要提取这个编号的contig00139 4963 138  序列


我的序列是这个：>contig00139  length=4963   numreads=1960
CGGTGCCcGGCGGCCAGTGCCTGGCGGGCGATGTCGGTGCCGAGTCCGCGCCCGGCGCCG
GTGATGAAGAACACCTTGCTCATCAGACGGATCCTCCGTAGGGGTGGTGGGGTCACGCGG
CGTTGCGGGCGTCGACGATCTTCTTGAGCTGCGTGATCGCGGTGACGGCGTTGGGCCAGC
CCGCGTAGAACGCCAGATGGGTGATCGCCTCGGACAGCTCCTCCACCGTGAGCCCGTTGT
CCAGGGCGACACCGAGGTGGTAACCGAGCTGCTCGTTGCGGTAGAGGGCGGACAGCACAC
TCACTGTGACCAGACTGCGATCCCGCGGAGACAGCCCCGGACGCTCCCAGACATCACCGA
ACAGGACGTCGTCGGTGAGCGCGACGAGCTTGGGCGCGATCTCGGCAAGTTCCTGCGGGG
CGGACTGCTCAGGCATACGAACAACTCCTTGATCAACACGGGCGGACCGGTCACCTCCAC
CGTGGGGTGCGGGCGGCTCTCCGGCAGCACCACGGCTCGTCTCCCGGGTCGTTTCCGGCA
GCcTCAGCCGCTGACGCCTTCGAGGAAACCGCAGCTCAAAGGGGTGCGGAAGGGACTGTT
GTCACAGGTACTGACAGGCCCCCCCACATCTGCGCTGTCCGGCTTAGCGTGGAAGGCGTG
AGCATCGAGAGCGACATCCGCGAGTTCCTGGCCTCCCACCGCGCCAAGATCACCCCCCAG
CAGGCCGGGCTGCCCGCCTACGGCACCAACCGCCGGGTAAAGGGCCTGCGCCGCGAGGAA
GTCGCCATGCTCGCCGGCGTCAGCGTCGACTACTACGTCCGCCTGGAACGCGGCCGCATC
GCCGGGGCCTCGGAAGAAGTCCTCGACGCCGTCGCCAACGCCCTCCATCTCGACGAGGCC
GAACGCGCCCACCTCTACGACCTGGCCCGCGCCGCcGCCAAACgCCCAGCCCACCGCAGG
CGCGCCCGCGGCCcACTCCCCGACAGCATCCTGCGCGTCCTGCGCTCCATGACCGACTCC

longbow0

用emboss的 extractseq程序；或者Bio::Seq的subseq()