Text Replacement after Multi-file Association
【Answer】
I 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 explanations. 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()
【Answer】
Perl gives weak support for structured data processing. So it’s hard to code your question in the high-level language. It’s much easier to get it done in SPL (Structured Process Language):
A |
|
1 |
=file("annotations.txt").import().derive(left(_1,pos(_1,"_")-1):key) |
2 |
=file("blastreport.txt").import() |
3 |
>A2.switch(_2,A1:key) |
4 |
=A2.new(_1,_2._1,_3,_4,_5,_6,_7,_8,_9,_10,_11) |
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