读存Fa文件

InAndOutFa.cpp

// C++ read fa-sequence
void ReadFaSeq(const char *file, map<string, string> &fa) {

    ifstream I(file);
    if (!I){
        cerr << "Cannot open file : " << file << endl;
        exit(1);
    }

    string tmp, refId;
    while (1) {

        I >> tmp;
        if (I.eof()) break;
        if (tmp[0] != '>') {

            fa[refId] += tmp;
        } else {
            refId.assign (tmp, 1, string::npos);
            fa[refId].clear();
        }
        getline(I, tmp, '\n');
    }
    I.close();
}


void OutputFa(string id, int lineLength, string &seq) {

    cout << id << endl;
    for (size_t i(0); i < seq.size(); ++i) {

        cout << seq[i];
        if ((i + 1) % lineLength == 0) cout << endl;
    }
    if (seq.length() % lineLength > 0) cout << endl;


    return;
}

InAndOutFa.pl

### Read Fa sequence ###
sub ReadFaSeq {

    my ( $file, $fa ) = @_;

    my ( $refId, $seq );
    open I, $file or die "Cannot open file : $file\n";

    $/ = ">"; <I>; $/ = "\n";
    while ( <I> ) {
        chomp;
        $refId = ( split /\s+/ )[0];
        $/ = ">"; chomp( $seq = <I> ); $/ = "\n";
        $seq =~ s/\s+//g;
        $$fa{$refId} = $seq;
    }
    close I;
}


### Output Fa Sequence ####
sub OutputFa {

    my ( $id, $lineLength, $seq ) = @_;

    my $i= 0;
    print "$id\n";
    for (; $i < length( $$seq ); $i += $lineLength ) {

        print substr($$seq, $i, $lineLength );
        print "\n";
    }
}