【问题】

have a file with annotations in the following format:

XS-5236245.2_hypothetical_protein

and a tab delimited blast report with only the accession id in the second column:

transcript1 XS-5236245.2 94.3 35 0 245 356 789 896 1e-230 6.3

I want to replace the accession_id from the blast report with the whole line from the annotations file when there is a match. This is my attempt and as you can see I use very basic python. If you give me a more complex solution I would appreciate some explanation. Thank you for your help.

Linu

#!/usr/bin/python``#import sys

#input1 = sys.argv[1] --> file with annoations``#input2 = sys.argv[2] --> file with blast report``#output = sys.argv[3] --> modified blast report with annotations

f1 = open(sys.argv[1],"r")``f2 = open(sys.argv[2],"r")``f3 = open(sys.argv[3],"w")

#open and read line by line:
for line in f1:
 # break line by '_'
splitline = line.split("_")
# define search_id as the first element of the line
searchid = splitline[0]
# open blast report and read line by line
 for row in f2:
# split columns by tab separator
col = row.split("\t")
# define target_id as the content of the second column
targetid = col[1]
# when target_id matches search_id replace content with the whole line
 if searchid == targetid:
f3.write(targetid.replace(searchid, splitline))
 else:
 pass
f1.close()
f2.close()
f3.close()

【回答】

perl 对结构化计算支持有限，代码也比较难写。完成这类需求用 SPL 更方便：