根据FPKM将基因分组

来源：互联网发布：985贴吧知乎编辑：程序博客网时间：2024/05/23 11:45

基因表达量FPKM计算之后，可以根据其值分组。
输入格式：

Geneid  UN003324    UN004629    UN011750    UN013498    UN016818    UN018363    UN018537    UN019619    UN019632    UN026711    UN054416    UN056756    UN058273root_Z10_mean   0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00 root_Z13_mean   0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00 root_Z39_mean   0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00 stem_Z30_mean   0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00 stem_Z32_mean   0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00 stem_Z65_mean   0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00 leaf_Z10_mean   0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00 leaf_Z23_mean   0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00 leaf_Z71_mean   0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00 spike_Z32_mean  0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00 spike_Z39_mean  0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00 spike_Z65_mean  0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00 new_carpel  0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00 new_stamen  0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00 latet_lepto_mean    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00 diplo_dia_mean  0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00 zygo_pachy_mean 0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00 metaphaseI_mean 0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00 grain_Z71_mean  0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00 grain_Z75_mean  0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00 grain_Z85_mean  0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00

python代码：

#!/usr/bin/env python# -*- coding: utf-8 -*-with open('rna_seq.txt', 'r') as f:    print 'Tissue''\t''no''\t''low''\t''medium''\t''high'    for line in f:        if 'Geneid' not in line:            line = line.strip().split()            no = []            low = []            medium = []            high = []            for i in line[1:]:                if float(i) < 0.02:                    no.append(i)                if 0.02 <= float(i) < 20:                    low.append(i)                if 20 <= float(i) < 50:                    medium.append(i)                if float(i) >= 50:                    high.append(i)            print '%s\t%d\t%d\t%d\t%d' % (line[0], len(no), len(low), len(medium), len(high))

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