通过正则表达式过滤txt文件的信息

Question

I have a file with information, this is how it looks like:

****ALIGNMENT****
Sequence:  gi|86755972|gb|ABD15130.1| cold acclimation protein COR413-PM1 [Chimonanthus praecox]
Length:  201
E-value:  2.66576e-82
KYLAMKTDQLAVANMIDSDINELKMATMRLINDASMLGHYGFGTHFLKWLACLAAIYLLILDRTNWRTNMLTSLL...
+YLAMKTD+ +   +I +D+ E+  A  +L+ DA+ LG  G GT  LKW+A  AAIYLLILDRTNW+TNMLT+LL...
EYLAMKTDEWSAQQLIQTDLKEMGKAAKKLVYDATKLGSLGVGTSILKWVASFAAIYLLILDRTNWKTNMLTALL...

Now I want to filter some information, and I want to use it as a variable. I think I should use a regular expression for this, but I don't know how to do that with lots of information of the second line, for example.

I need the hitsid , protein , organism , and evalue .

The corresponding data:

hitsid = 86755972
protein = cold acclimation protein COR413-PM1
organism = Chimonanthus praecox
evalue = 2.66576e-82

So I want that, when I ask for the hitsid , that Python prints ' 86755972 '.

Could anyone help me with this? Thanks!

Answer 1

Use a regex like

^Sequence:[^|]*\|(?P<hitsid>[^|]*)\|\S*\s*(?P<protein>[^][]*?)\s*\[(?P<organism>[^][]*)][\s\S]*?\nE-value:\s*(?P<evalue>.*)

See the regex demo

A sample Python code getting multiple values into a list of dictionaries:

import re
p = re.compile(r'^Sequence:[^|]*\|(?P<hitsid>[^|]*)\|\S*\s*(?P<protein>[^][]*?)\s*\[(?P<organism>[^][]*)][\s\S]*?\nE-value:\s*(?P<evalue>.*)', re.MULTILINE)
s = "****ALIGNMENT****\nSequence:  gi|86755972|gb|ABD15130.1| cold acclimation protein COR413-PM1 [Chimonanthus praecox]\nLength:  201\nE-value:  2.66576e-82\nKYLAMKTDQLAVANMIDSDINELKMATMRLINDASMLGHYGFGTHFLKWLACLAAIYLLILDRTNWRTNMLTSLL...\n+YLAMKTD+ +   +I +D+ E+  A  +L+ DA+ LG  G GT  LKW+A  AAIYLLILDRTNW+TNMLT+LL...\nEYLAMKTDEWSAQQLIQTDLKEMGKAAKKLVYDATKLGSLGVGTSILKWVASFAAIYLLILDRTNWKTNMLTALL..."
res = [m.groupdict() for m in p.finditer(s)]
for x in res:
    print(x['hitsid'])
    print(x['protein'])
    print(x['organism'])
    print(x['evalue'])