基因資料處理123之SSW程式碼不正確，到時比SparkSW時間長
阿新 • • 發佈：2018-12-25
基因資料處理系列
1.解釋
由於要生成新的score matrix：blosum50，第一次使用靜態方法，直接傳給align，到時每次執行都需要進行一次score matrix的計算，而這個是將blosum50的矩陣轉換成128*128的矩陣，當計算Q0,即8個字串的query時，顯然時間佔比大，本來序列比對時間就不長，所以比sparkSW慢
2.程式碼：
優化：將靜態方法傳給靜態矩陣，然後再給align方法，這樣在類載入的時候靜態矩陣就計算好的，多次呼叫的時候也就只計算了一次，而不需要每次都計算。
DSW: ssw.SSW
3.結果：
2.01611E+16 SparkSW D1Line.fasta 0P18691.file 128 1 5 18.679 /xubo/project/SparkSW/output/time/20161127200906643SparkSW_queryFile_0P18691.file_dbFile_D1Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSW D1Line.fasta 0P18691.file 128 1 5 18.594 /xubo/project/SparkSW/output/time/20161127200931088SparkSW_queryFile_0P18691.file_dbFile_D1Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSW D1Line.fasta 0P18691.file 128 1 5 17.815 /xubo/project/SparkSW/output/time/20161127200955742SparkSW_queryFile_0P18691.file_dbFile_D1Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSWSSW D1Line.fasta 0P18691.file 128 1 5 22.759 /xubo/project/SparkSW/output/time/20161127201019619SparkSWSSW_queryFile_0P18691.file_dbFile_D1Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSWSSW D1Line.fasta 0P18691.file 128 1 5 22.801 /xubo/project/SparkSW/output/time/20161127201048357SparkSWSSW_queryFile_0P18691.file_dbFile_D1Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSWSSW D1Line.fasta 0P18691.file 128 1 5 21.942 /xubo/project/SparkSW/output/time/20161127201117262SparkSWSSW_queryFile_0P18691.file_dbFile_D1Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSW D2Line.fasta 0P18691.file 128 1 5 25.162 /xubo/project/SparkSW/output/time/20161127201145181SparkSW_queryFile_0P18691.file_dbFile_D2Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSW D2Line.fasta 0P18691.file 128 1 5 24.905 /xubo/project/SparkSW/output/time/20161127201216281SparkSW_queryFile_0P18691.file_dbFile_D2Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSW D2Line.fasta 0P18691.file 128 1 5 24.998 /xubo/project/SparkSW/output/time/20161127201246764SparkSW_queryFile_0P18691.file_dbFile_D2Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSWSSW D2Line.fasta 0P18691.file 128 1 5 33.404 /xubo/project/SparkSW/output/time/20161127201317724SparkSWSSW_queryFile_0P18691.file_dbFile_D2Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSWSSW D2Line.fasta 0P18691.file 128 1 5 33.419 /xubo/project/SparkSW/output/time/20161127201357058SparkSWSSW_queryFile_0P18691.file_dbFile_D2Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSWSSW D2Line.fasta 0P18691.file 128 1 5 33.071 /xubo/project/SparkSW/output/time/20161127201436498SparkSWSSW_queryFile_0P18691.file_dbFile_D2Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSW D3Line.fasta 0P18691.file 128 1 5 35.385 /xubo/project/SparkSW/output/time/20161127201515580SparkSW_queryFile_0P18691.file_dbFile_D3Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSW D3Line.fasta 0P18691.file 128 1 5 35.632 /xubo/project/SparkSW/output/time/20161127201557039SparkSW_queryFile_0P18691.file_dbFile_D3Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSW D3Line.fasta 0P18691.file 128 1 5 36.336 /xubo/project/SparkSW/output/time/20161127201638723SparkSW_queryFile_0P18691.file_dbFile_D3Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSWSSW D3Line.fasta 0P18691.file 128 1 5 54.668 /xubo/project/SparkSW/output/time/20161127201720962SparkSWSSW_queryFile_0P18691.file_dbFile_D3Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSWSSW D3Line.fasta 0P18691.file 128 1 5 54.857 /xubo/project/SparkSW/output/time/20161127201821633SparkSWSSW_queryFile_0P18691.file_dbFile_D3Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSWSSW D3Line.fasta 0P18691.file 128 1 5 53.338 /xubo/project/SparkSW/output/time/20161127201922460SparkSWSSW_queryFile_0P18691.file_dbFile_D3Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSW D4Line.fasta 0P18691.file 128 1 5 45.174 /xubo/project/SparkSW/output/time/20161127202021797SparkSW_queryFile_0P18691.file_dbFile_D4Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSW D4Line.fasta 0P18691.file 128 1 5 42.346 /xubo/project/SparkSW/output/time/20161127202112921SparkSW_queryFile_0P18691.file_dbFile_D4Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSW D4Line.fasta 0P18691.file 128 1 5 44.676 /xubo/project/SparkSW/output/time/20161127202201329SparkSW_queryFile_0P18691.file_dbFile_D4Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSWSSW D4Line.fasta 0P18691.file 128 1 5 66.426 /xubo/project/SparkSW/output/time/20161127202252059SparkSWSSW_queryFile_0P18691.file_dbFile_D4Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSWSSW D4Line.fasta 0P18691.file 128 1 5 69.492 /xubo/project/SparkSW/output/time/20161127202405206SparkSWSSW_queryFile_0P18691.file_dbFile_D4Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSWSSW D4Line.fasta 0P18691.file 128 1 5 67.195 /xubo/project/SparkSW/output/time/20161127202520291SparkSWSSW_queryFile_0P18691.file_dbFile_D4Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSW D5Line.fasta 0P18691.file 128 1 5 55.823 /xubo/project/SparkSW/output/time/20161127202633365SparkSW_queryFile_0P18691.file_dbFile_D5Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSW D5Line.fasta 0P18691.file 128 1 5 56.501 /xubo/project/SparkSW/output/time/20161127202735122SparkSW_queryFile_0P18691.file_dbFile_D5Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSW D5Line.fasta 0P18691.file 128 1 5 55.71 /xubo/project/SparkSW/output/time/20161127202837220SparkSW_queryFile_0P18691.file_dbFile_D5Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSWSSW D5Line.fasta 0P18691.file 128 1 5 102.413 /xubo/project/SparkSW/output/time/20161127202939014SparkSWSSW_queryFile_0P18691.file_dbFile_D5Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSWSSW D5Line.fasta 0P18691.file 128 1 5 93.266 /xubo/project/SparkSW/output/time/20161127203127477SparkSWSSW_queryFile_0P18691.file_dbFile_D5Line.fasta_splitNum_128_taskNum_1_topK_5 2.01611E+16 SparkSWSSW D5Line.fasta 0P18691.file 128 1 5 104.084 /xubo/project/SparkSW/output/time/20161127203306305SparkSWSSW_queryFile_0P18691.file_dbFile_D5Line.fasta_splitNum_128_taskNum_1_topK_5
參考
【1】https://github.com/xubo245
【2】http://blog.csdn.net/xubo245/