一些脚本

1. 统计fasta文件序列条数（Shell）

grep -c ">" x.fasta

2. fastq转换成fasta格式（Shell）

gzip -dc BGIseq500.fq.gz | awk 'NR%4==1{printf ">%s\n",substr($0,2)} NR%4==2{print}' > BGIseq500.fa

3. 统计read数目和read长度（Shell）

readNum=`gzip -dc BGIseq500_1.fq.gz | wc -l | awk '{print $1/4}'`
echo read number:$readNum
readLen=`less newBGIseq500_1.fq.gz | head -2 | awk -F"\n" '{if($1 !~ /^@/) { print length($1)}}'`
echo read length:$readLen
totalBase=`echo "$readNum $readLen" | awk '{ print $1*$2*2} '`
echo total base number:$totalBase

4. coverage乘数概率问题（R）

totalBp <- 1599999*100*2
print(totalBp)
deepth <- totalBp/6000000
print(deepth)
ppois(40, deepth, lower=FALSE)
qpois(0.99, deepth, lower=FALSE)

 5. SOAPdenovo组装

　　config文件

# config文件
#maximal read length
max_rd_len=100
[LIB]
#average insert size
avg_ins=450
#if sequence needs to be reversed
reverse_seq=0
#in which part(s) the reads are used
asm_flags=3
#use only first 100 bps of each read
rd_len_cutoff=100
#in which order the reads are used while scaffolding
rank=1
# cutoff of pair number for a reliable connection (at least 3 for short insert size)
pair_num_cutoff=3
#minimum aligned length to contigs for a reliable read location (at least 32 for short insert size)
map_len=32
#a pair of fastq file, read 1 file should always be followed by read 2 file
q1=newBGIseq500_1.fq.gz
q2=newBGIseq500_2.fq.gz

　　SOAPdenovo命令（Shell）

SOAPdenovo-63mer all -s my.cfg -K 35 -D 1 -o new 1>new.log 2>new.err

6. 统计fasta文件中每一条序列的长度（Perl）

use strict;

my $num = 0;
my @lengthList = ();
my $len = undef;

open(OUT, ">scanffoldLength.list") or die ("can't open file!\n");

while(<>) {
        chomp;
        if (/^>/) {
                if ($len == undef) {
                        $len = 0;
                        next;
                } else {
                        $lengthList[$num] = $len;
                        $num += 1;
                        $len = 0;
                }
        } else {
                $len += length($_);
        }
}
$lengthList[$num] = $len;
$num += 1;
print "num: $num\n";
print "num2: ", scalar @lengthList, "\n";
foreach (@lengthList) {
        print OUT "$_\n";
}
close(OUT);

7. 按数字从大到小排序（Shell）

sort -r -g scanffoldLength.list > scanffoldLength.sort.list

8. 统计scanffold序列累积长度，计算N50，并画图（R）

lengthList <- read.table("scanffoldLength.sort.list")
lengthList <- lengthList[,1]
head(lengthList)
length(lengthList)
accLen <- numeric(length(lengthList))
totLen <- lengthList[1];
accLen[1] <- lengthList[1];
for (i in (2:length(lengthList))) {
        accLen[i] <- (accLen[i-1] + lengthList[i])
        totLen <- totLen + lengthList[i];
}
head(accLen)
length(accLen)
totLen
N50 <- 0
index <- 0
accLen[length(lengthList)]
for (i in (1:length(lengthList))) {
        if (accLen[i] > totLen/2) {
                N50 <- lengthList[i]
                index <- i
                break
        }
}
N50
pdf("length.pdf")
plot(x=(1:length(lengthList)), y=accLen, type="l", xlab="l", ylab="accLen")
print(index)
#lines(c(index,index), c(0,accLen[index]), col="blue")
#lines(c(0,index), c(accLen[index],accLen[index]), col="blue")
text <- paste("(", as.character(index), "," , as.character(N50), ")", sep = "")
points(index, accLen[index], col="red")
text(x=index+200, y=accLen[index], labels=text, col="red")
dev.off()

9. vcftools的一些使用（Shell）

# get Qual
./vcftools --gzvcf chr17.vcf.gz --site-quality --out Qual
# get interval
./vcftools --gzvcf chr17.vcf.gz --chr chr17 --from-bp 7661779 --to-bp 7687550 --remove-indels --out TP53 --recode

10. 画数据分布Hist图（R）

data <- read.table("Qual.lqual", header=TRUE)
pdf("Qual.pdf")
hist(data[,3], breaks=100 , main="Qual Hist", freq=F)
dev.off()

11. 统计vcf文件中样本的genotype（Perl）

use strict;

my @samples = ();
my %statTable = ();

while (<>) {
        chomp;
        next if(/^##/);
        if(/^#CHROM/) {
                my @labels = split;
                for my $index (9..@labels-1) {
                        push(@samples, $labels[$index]);
                }
                #print "@samples\n";
                for (0..@samples-1) {
                        my %subTab = ();
                        $statTable{$samples[$_]}{"0/0"} = 0;
                        $statTable{$samples[$_]}{"0/1"} = 0;
                        $statTable{$samples[$_]}{"1/1"} = 0;
                }
                #print %statTable;
                next;
        }
        my @vcfData = split;
        for my $index (9..@vcfData-1) {
                my @values = split /:/, $vcfData[$index];
                if($values[0] eq "0/0") {
                        $statTable{$samples[$index-9]}{"0/0"} += 1;
                } elsif($values[0] eq "0/1") {
                        $statTable{$samples[$index-9]}{"0/1"} += 1;
                } elsif($values[0] eq "1/1") {
                        $statTable{$samples[$index-9]}{"1/1"} += 1;
                } else {
                        die("error~");
                }
        }
        #print "\n";
}

foreach my $sampleName (keys %statTable) {
        print "$sampleName:\n";
        foreach my $gt (keys $statTable{$sampleName}) {
                print "$gt\t$statTable{$sampleName}{$gt}\n";
        }
}