纯Python read_counts 转FPKM v2

重新写了一个由reads_counts转FPKM矩阵的脚本，之前的那一般只适用于18个样本的，这里更新了一下，没有样本限制了。
还是分为3步：

grep "exon" genome.gtf > genome_exon.gtf
python count_genelen_from_gft.py genome_exon.gtf gene.len
python Caculate_FPKM.py mapped_gene_number.txt gene.len raw_counts.matrix FPKM.matrix

第一步：把gtf文件中的exon抓取出来
第二步：计算每条基因的exon长度和
第三步：基于每个样本匹配到的reads总数、每个基因的长度、read_counts矩阵得到FPKM矩阵

第一步：
直接运行上面脚本的第一行就行了，记得更改输入的gtf的文件的文件名为你的文件名。
gtf范例

Morimp01GS001   AUGUSTUS        start_codon     47156   47158   .       -       0       gene_id "MIM04M26Gene00002"; transcript_id "MIM04M26Gene00002.t1"; gene_name "MIM04M26Gene00002";
Morimp01GS001   AUGUSTUS        exon    47073   47158   .       -       .       gene_id "MIM04M26Gene00002"; transcript_id "MIM04M26Gene00002.t1"; gene_name "MIM04M26Gene00002";
Morimp01GS001   AUGUSTUS        CDS     47073   47158   0.6     -       0       gene_id "MIM04M26Gene00002"; transcript_id "MIM04M26Gene00002.t1"; gene_name "MIM04M26Gene00002";
Morimp01GS001   AUGUSTUS        exon    46887   46999   .       -       .       gene_id "MIM04M26Gene00002"; transcript_id "MIM04M26Gene00002.t1"; gene_name "MIM04M26Gene00002";
Morimp01GS001   AUGUSTUS        CDS     46887   46999   0.92    -       1       gene_id "MIM04M26Gene00002"; transcript_id "MIM04M26Gene00002.t1"; gene_name "MIM04M26Gene00002";
Morimp01GS001   AUGUSTUS        exon    46644   46784   .       -       .       gene_id "MIM04M26Gene00002"; transcript_id "MIM04M26Gene00002.t1"; gene_name "MIM04M26Gene00002";
Morimp01GS001   AUGUSTUS        CDS     46644   46784   0.91    -       2       gene_id "MIM04M26Gene00002"; transcript_id "MIM04M26Gene00002.t1"; gene_name "MIM04M26Gene00002";
Morimp01GS001   AUGUSTUS        exon    45970   46559   .       -       .       gene_id "MIM04M26Gene00002"; transcript_id "MIM04M26Gene00002.t1"; gene_name "MIM04M26Gene00002";
Morimp01GS001   AUGUSTUS        CDS     45970   46559   0.92    -       2       gene_id "MIM04M26Gene00002"; transcript_id "MIM04M26Gene00002.t1"; gene_name "MIM04M26Gene00002";
Morimp01GS001   AUGUSTUS        stop_codon      45970   45972   .       -       0       gene_id "MIM04M26Gene00002"; transcript_id "MIM04M26Gene00002.t1"; gene_name "MIM04M26Gene00002";

Morimp01GS001   AUGUSTUS        start_codon     54027   54029   .       +       0       gene_id "MIM04M26Gene00003"; transcript_id "MIM04M26Gene00003.t1"; gene_name "MIM04M26Gene00003";
Morimp01GS001   AUGUSTUS        exon    54027   54291   .       +       .       gene_id "MIM04M26Gene00003"; transcript_id "MIM04M26Gene00003.t1"; gene_name "MIM04M26Gene00003";
Morimp01GS001   AUGUSTUS        CDS     54027   54291   0.59    +       0       gene_id "MIM04M26Gene00003"; transcript_id "MIM04M26Gene00003.t1"; gene_name "MIM04M26Gene00003";
Morimp01GS001   AUGUSTUS        exon    54361   54689   .       +       .       gene_id "MIM04M26Gene00003";