Hi I have this uniprot gff data that looks like
+--------+--------+-------+------+------------------------------------------------------------------------------------------------------+
| Entry | check | start | end | Domains |
+--------+--------+-------+------+------------------------------------------------------------------------------------------------------+
| O75581 | Repeat | 63 | 106 | Note=LDL-receptor class B 1 |
| O75581 | Repeat | 150 | 193 | Note=LDL-receptor class B 3 |
| O75581 | Domain | 282 | 324 | Note=EGF-like 1 |
| O75581 | Domain | 1248 | 1286 | Note=LDL-receptor class A 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00124 |
| O75581 | Domain | 1287 | 1323 | Note=LDL-receptor class A 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00124 |
| O75581 | Domain | 1325 | 1361 | Note=LDL-receptor class A 3;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00124 |
| P13688 | Domain | 35 | 142 | Note=Ig-like V-type;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P31997 |
| P13688 | Domain | 145 | 232 | Note=Ig-like C2-type 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00114 |
| P13688 | Domain | 237 | 317 | Note=Ig-like C2-type 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00114 |
| P13688 | Domain | 323 | 413 | Note=Ig-like C2-type 3;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00114 |
| P19022 | Domain | 160 | 267 | Note=Cadherin 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00043 |
| P19022 | Domain | 268 | 382 | Note=Cadherin 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00043 |
| P19022 | Domain | 383 | 497 | Note=Cadherin 3;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00043 |
| Q13586 | Domain | 132 | 200 | Note=SAM;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00184 |
| P04629 | Repeat | 90 | 113 | Note=LRR 1 |
| P04629 | Repeat | 116 | 137 | Note=LRR 2 |
+--------+--------+-------+------+------------------------------------------------------------------------------------------------------+
I am trying to extract the domain names column df['Domains]. With the following code, I am close to getting the first 2 3 words of the domain name but doesn't work universally.
for row in df['Domains']:
print(re.findall(r'Note=(\w*)(.?)(\w*)', row))
which gives something like this
[('LDL', '-', 'receptor')]
[('LDL', '-', 'receptor')]
[('EGF', '-', 'like')]
[('Ig', '-', 'like')]
[('Ig', '-', 'like')]`
So, I wish to change my approach and get everything starting after Note= and ends before ; or end of line. How may I get this?
Could you please try following.
for row in df['Domains']:
print(re.findall(r'Note=([^;]*)', row))