我想對兩個文件執行一些區間範圍操作,並且出現以下條件 檢查chrom是否相等,然後檢查我的co0rdinatefile的開始和結束是否在相等或相等開始和結束gene_annotation文件(條件如果鏈是「+」,開始和結束將是例如10-20,如果它的「 - 」將是20-10),如果匹配打印開始末尾鏈從座標和來自geneannotation文件的gene_id,gene_name。 (用於表示目的,我有頭annoataion文件)使用熊貓或枚舉查找兩個數據集之間的重疊/範圍
中的行數註釋文件〜50000 數協調的文件中的行〜200000
gene_annotationfile
chrom start end gene_id gene_name strand
17 71223692 71274336 ENSMUSG00000085299 Gm16627 -
17 18186448 18211184 ENSMUSG00000067978 Vmn2r-ps113 +
11 84645863 84684319 ENSMUSG00000020530 Ggnbp2 -
7 51097639 51106551 ENSMUSG00000074155 Klk5 +
13 31711037 31712238 ENSMUSG00000087276 Gm11378 +
coordinates_file
chrom start end strand
1 4247322 4247912 -
1 4427449 4432604 +
1 4763414 4764404 -
1 4764597 4767606 -
1 4764597 4766491 -
1 4766882 4767606 -
1 4767729 4772649 -
1 4767729 4768829 -
1 4767729 4775654 -
1 4772382 4772649 -
1 4772814 4774032 -
1 4772814 4774159 -
1 4772814 4775654 -
1 4772814 4774032 +
1 4774186 4775654 -
1 4774186 4775654
1 4774186 4775699 -
想要的輸出
chrom, start, end,strand, gene_id, gene_name
1 4427432 4432686 + ENSMUSG0001 abcd
另一個問題是,在某些情況下,如果有匹配它可以映射到在這種情況下,gene_id我還想寫
chrom, start, end,strand, gene_id, gene_name
1 4427432 4432686 + ENSMUSG0001,ENSMUSG0002 abcd,efgh
我迄今爲止代碼:
import csv
with open('coordinates.txt', 'r') as source:
coordinates = list(csv.reader(source, delimiter="\t"))
with open('/gene_annotations.txt', 'rU') as source:
#if i do not use 'rU' i get this error Error: new-line character seen in unquoted field - do you need to open the file in universal-newline mode?
annotations = list(csv.reader(source, delimiter="\t"))
for index,line in enumerate(coordinates):
for index2, line2 in enumerate(annotations):
if coordinates[line][0] == annotations[line2][0] and coordinates[line][1] <= annotations[line2][1] and annotations[line2][2] >= coordinates[line][2] :
print "%s\t%s\t%s\t%s\t%s" % (coordinates[line][0],coordinates[line][1],coordinates[line][2], annotations[line2][3], annotations[line2][4])
break
錯誤我得到
---> 15 if coordinates[line][0] == annotations[line2][0] and coordinates[line][1] <= annotations[line2][1] and annotations[line2][2] >= coordinates[line][2] :
16 print "%s\t%s\t%s\t%s\t%s" % (coordinates[line][0],coordinates[line][1],coordinates[line][2], annotations[line2][3], annotations[line2][4])
17 break
TypeError: list indices must be integers, not list
大熊貓會是一個很好的方法嗎?