Input text file
LID - E164 [pii]
LID - 10.3390/antiox9020164 [doi]
AB - Although prickly pear fruits have become an important part of the Canary diet,
their native varieties are yet to be characterized in terms of betalains and
phenolic compounds.
FAU - Gomez-Maqueo, Andrea
AU - Gomez-Maqueo A
AUID- ORCID: 0000-0002-0579-1855
PG - 1-13
LID - 10.1007/s00442-020-04624-w [doi]
AB - Recent observational evidence suggests that nighttime temperatures are increasing
faster than daytime temperatures, while in some regions precipitation events are
becoming less frequent and more intense.
CI - (c) 2020 Production and hosting by Elsevier B.V. on behalf of Cairo University.
FAU - Farag, Mohamed A
AU - Farag MA
PG - 3044
LID - 10.3389/fmicb.2019.03044 [doi]
AB - Microbial symbionts account for survival, development, fitness and evolution of
eukaryotic hosts. These microorganisms together with their host form a biological
unit known as holobiont.
AU - Flores-Nunez VM
AD - Departamento de Ingenieria Genetica, Centro de Investigacion y de Estudios
Avanzados del Instituto Politecnico Nacional, Irapuato, Mexico.
I'm trying to extract the abstracts denoted by AB in the text. I'm iterating through each line, checks whether the key is that of the abstract. If so I'm setting a flag and appending the subsequent lines separated by space. Is there a better way to do this?
f = "sample.txt"
abstracts = []
flag = False
with open(f) as myfile:
for line in myfile:
# append subsequent lines if flag is set
if flag:
if line.startswith(" "):
req_line = req_line + " " + line.strip()
else:
abstracts.append(req_line)
req_line = ""
flag = False
# find beginning of abstract
if line.startswith("AB - "):
req_line = line.replace("AB - ", "", 1)
flag = True
Output:
[
"Although prickly pear fruits have become an important part of the Canary diet, their native varieties are yet to be characterized in terms of betalains and phenolic compounds.",
"Recent observational evidence suggests that nighttime temperatures are increasing faster than daytime temperatures, while in some regions precipitation events are becoming less frequent and more intense.",
"Microbial symbionts account for survival, development, fitness and evolution of eukaryotic hosts. These microorganisms together with their host form a biological unit known as holobiont."
]
Do it with regex (assuming your input string is s read via open("file.txt").read()):
import re
matches = re.findall("AB\W*-\W*([^-]*(?=\n))", s)
output = [" ".join(map(str.strip, i.split("\n"))) for i in matches]
gives
['Although prickly pear fruits have become an important part of the Canary diet, their native varieties are yet to be characterized in terms of betalains and phenolic compounds.',
'Recent observational evidence suggests that nighttime temperatures are increasing faster than daytime temperatures, while in some regions precipitation events are becoming less frequent and more intense.',
'Microbial symbionts account for survival, development, fitness and evolution of eukaryotic hosts. These microorganisms together with their host form a biological unit known as holobiont.']