题目:hg19基因组序列的一些探究
具体题目详情请参考生信技能树论坛
数据来源:http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz 下载.gz数据后解压
代码地址:https://raw.githubusercontent.com/x2yline/courseranotes/master/myscript/class2/fastafileGCandN.R
代码内容:
setwd('E:\\r\\biotrainee_demo\\class 2')# 读入数据t1 <- Sys.time()df <- read.csv('chr1.fa', header=F, stringsAsFactors=F)# index_df 为chr所在的位置index_df <- data.frame(begin=which(sapply(df[,1], function(x){ substr(x, start=1, stop=1)=='>'})))# index_df1 为string所在的位置+1index_df1 <- data.frame(rbind(matrix(index_df[-1,1]),dim(df)[1]+1))# 把index_start和index_end存入data.frameindex_df2 <- cbind(index_df, index_df1)remove(index_df1, index_df)# 得出每个染色体对应string后计算其N与GC百分比result <- apply(index_df2, 1, function(x) { # 把提取字符串后把字符串变为大写 y <- toupper(paste(df[(x[1]+1):(x[2]-1),1], collapse='')) y <- strsplit(y, split=character(0))[[1]] N <- length(y[y =='N'])/length(y) GC <- length(y[y =='G' | y == 'C'])/(length(y)-length(y[y =='N'])) c(N,GC)})# 把行名改为N和GC并转秩rownames(result) = c('N','GC')result <- t(result)# 取结果前几行head(result)difftime(Sys.time(), t1, units = 'secs')
由于电脑问题,试了一下1号染色体,电脑卡住了,于是又试了一下Y染色体,跑出来结果如下:
耗时:41.44945 secs
电脑配置信息:
数据来源: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz
数据下载时间:2017-01-10 23:08
运行消耗时间:309 seconds
未优化速度的代码如下
import osimport timebegin = time.time()os.chdir(r'F:\tmp\chromFa')def count_n_and_gc(file): content = [] chromsome = [] g = 0; c = 0; n = 0; a = 0; t = 0 with open(file) as f: raw_list = f.readlines() for i in raw_list: if not i.startswith('>'): i = i.upper() n += i.count('N') g += i.count('G') c += i.count('C') a += i.count('A') t += i.count('T') else: if chromsome: content.append((n ,a, t, c, g)) g = 0; c = 0; n = 0; a = 0; t = 0 chromsome.append(i.strip()) content.append(( n ,a, t, c, g)) return (content,chromsome)content = []chromsome = []for i in (list(range(1,23)) + ['X','Y']): file = 'chr'+ str(i) + '.fa' print('Start dealing with ' + file) m, n = count_n_and_gc(file) content += m chromsome += nall_info = 'chr,GC_ratio,N_ratio,Length,N,A,T,C,G'for i in range(len(chromsome)): data = '\n'+str(chromsome[i]) +',' + "%.5f"%((content[i][-1]+content[i][-2])/sum(content[i][1:])) +',' + "%.5f" %(content[i][0]/(sum(content[i]))) +',' +str((sum(content[i]))) +',' +str((content[i][0])) + ',' +str(content[i][1])+',' +str(content[i][2])+',' +str(content[i][3])+',' +str(content[i][4]) all_info += datawith open('hg19_analysis.csv','w') as f: f.write(all_info)print('Time using:'+ str(time.time() - begin) + ' seconds\n')
shell +python3(最快)
先使用shell脚本把所有chromFa.tar.gz 中的所有.fa文件合并为一个hg19.fa文件
脚本如下:
tar zvfx chromFa.tar.gzcat *.fa > hg19.farm chr*.faless hg19.fa
按照老师的方法对python算法进行改良
改良后的代码如下:
代码地址:
import osimport timeimport reimport sysfrom collections import OrderedDictstart = time.clock()def count_fasta_atcgn(file_path, buffer_size=1024*1024): bases = ['N', 'A', 'T', 'C', 'G'] ATCG_analysis = OrderedDict() with open(file_path, 'r') as f: line1 = f.readline() chr_i = re.split('\s', line1)[0][1:] print(chr_i) ATCG_analysis[chr_i] = OrderedDict() for base in bases: ATCG_analysis[chr_i][base] = 0 while True: chunk = f.read(buffer_size).upper() if '>' in chunk: chromsome = re.split('>',chunk) if chromsome[0]: for base in bases: ATCG_analysis[chr_i][base] += chromsome[0].count(base) for i in chromsome[1:]: if i: chr_i = re.split('\s', i[0:i.index('\n')])[0] print(chr_i) strings_i = i[i.index('\n'):].upper() ATCG_analysis[chr_i] = OrderedDict() for base in bases: ATCG_analysis[chr_i][base] = strings_i.count(base) else: for base in bases: ATCG_analysis[chr_i][base] += chunk.count(base) if not chunk: break return ATCG_analysisdef write_atcg_to_csv(ATCG_analysis, file_path = '.'): file = os.path.join(file_path,'atcg_analysis.csv') csv_content = 'chromsome\tGC_content\tN_content\tLength\tN\tA\tT\tC\tG\n' for chr_id, atcg_count in ATCG_analysis.items(): GC = atcg_count['G'] + atcg_count['C'] N = atcg_count['N'] Length = sum(atcg_count.values()) GC_content = GC*1.0/(Length-N) N_content = N*1.0/Length csv_content += chr_id + '\t' + '%.4f'%GC_content + '\t' + '%.4f'%N_content + '\t' + str(Length) + '\t' + str(atcg_count['N']) +'\t' + str(atcg_count['A']) + '\t' + str(atcg_count['T']) + '\t' + str(atcg_count['C'])+'\t'+ str(atcg_count['G'])+ '\n' with open(file, 'w') as f: csv_file_content = re.sub('\t', ',', csv_content) f.write(csv_file_content) print(u'File have been saved in '+ file) return csv_contentif sys.argv: result = OrderedDict() for f in sys.argv: done = 0 f= f.strip(''''"''') if f.count('.') != 1 or f[-2:] == 'py' or not os.path.exists(f): continue print(f) try: done = 1 result = OrderedDict(count_fasta_atcgn(file_path = f, buffer_size = 1024*2048), **result) except Exception as e: if f.startswith('-'): pass else: print(type(e)) if done == 1: file = write_atcg_to_csv(result) print(file) print('used %.2f s'%(time.clock()-start)) else: print ('\n\nSorry! The command is invalid!\n')else: directory = input('Enter your file: ') start = time.clock() if directory.count('.') != 1 or directory[-2:] == 'py' or not os.path.exists(directory): print('Your file is invalid!') else: result = count_fasta_atcgn(file_path = directory, buffer_size = 1024*2048) file = write_atcg_to_csv(result) print('used %.2f s'%(time.clock()-start))
保存上述代码为 fasta_atcgn_summary.py
文件后
在命令行下输入:
python fasta_atcgn_summary.py F:\tmp\hg19.fa
部分输出结果如下
使用python进一步进行可视化处理
代码如下:
import osimport timeimport reimport sysfrom collections import OrderedDictstart = time.clock()def count_fasta_atcgn(file_path, buffer_size=1024*1024): bases = ['N', 'A', 'T', 'C', 'G'] ATCG_analysis = OrderedDict() with open(file_path, 'r') as f: line1 = f.readline().upper() chr_i = re.split('\s', line1)[0][1:] print(chr_i) ATCG_analysis[chr_i] = OrderedDict() for base in bases: ATCG_analysis[chr_i][base] = 0 while True: chunk = f.read(buffer_size).upper() if '>' in chunk: chromsome = re.split('>',chunk) if chromsome[0]: for base in bases: ATCG_analysis[chr_i][base] += chromsome[0].count(base) for i in chromsome[1:]: if i: chr_i = re.split('\s', i[0:i.index('\n')])[0] print(chr_i) strings_i = i[i.index('\n'):] ATCG_analysis[chr_i] = OrderedDict() for base in bases: ATCG_analysis[chr_i][base] = strings_i.count(base) else: for base in bases: ATCG_analysis[chr_i][base] += chunk.count(base) if not chunk: break return ATCG_analysisdef write_atcg_to_csv(ATCG_analysis, file_path = '.'): file = os.path.join(file_path,'atcg_analysis.csv') csv_content = 'chromsome\tGC_content\tN_content\tLength\tN\tA\tT\tC\tG\n' for chr_id, atcg_count in ATCG_analysis.items(): GC = atcg_count['G'] + atcg_count['C'] N = atcg_count['N'] Length = sum(atcg_count.values()) GC_content = GC*1.0/(Length-N) N_content = N*1.0/Length csv_content += chr_id + '\t' + '%.4f'%GC_content + '\t' + '%.4f'%N_content + '\t' + str(Length) + '\t' + str(atcg_count['N']) +'\t' + str(atcg_count['A']) + '\t' + str(atcg_count['T']) + '\t' + str(atcg_count['C'])+'\t'+ str(atcg_count['G'])+ '\n' with open(file, 'w') as f: csv_file_content = re.sub('\t', ',', csv_content) f.write(csv_file_content) print(u'File have been saved in '+ file) return csv_contentfile_path = 'F:\genome\chromFa\hg19.fa'ATCG_analysis = count_fasta_atcgn(file_path, buffer_size=1024*1024)cg_list = []chr_id_list = list(range(1,23)) + ['X','Y','M']for i in chr_id_list: cg_list.append((ATCG_analysis['CHR'+str(i)]['G']+ATCG_analysis['CHR'+str(i)]['C'])/(ATCG_analysis['CHR'+str(i)]['A']+ATCG_analysis['CHR'+str(i)]['T']+ATCG_analysis['CHR'+str(i)]['C']+ATCG_analysis['CHR'+str(i)]['G'])*100)import matplotlib.pyplot as pltplt.bar(left = range(25), height = cg_list, color='k')for i in range(len(cg_list)): plt.text( x=i-0.1, y=cg_list[i]+.35,s=str(round(cg_list[i])))plt.title('GC content for hg19 genome')plt.ylabel('GC content (%)')pos = []for i in range(len(chr_id_list)): pos.append(i + 0.35)plt.xticks(pos, list(range(1,23)) + ['X','Y','MT'], fontsize=8)plt.xlim(-0.2, )plt.ylim(0, 100)plt.savefig('F:\hg19_gc.png',dpi=600)plt.show()
本文编辑:思考问题的熊