I'm trying to process a DOS text file (with DOS CRLF line terminations)
and translate from one database export format into another database
input format. I've pasted in my program and a short example file of data
at the end of this message. If the program is named 'medline2popline.pl'
and the data file is named 't.txt', the program is run with
'./medline2popline.pl t.txt'.
In the data file, fields start with 2-4 uppercase letters or spaces,
followed by a dash and a space, followed by the data. They end with
CRLF. Records are separated by two consecutive CRLF combinations.
I think my problem is caused by the DOS line terminations and the way
I'm trying to handle them in my overall program. My problem is lines
that look like this:
AD - Department of Family and Community Medicine, College of Medicine,
King Faisal^M$
University, Dammam, Saudi Arabia. [EMAIL PROTECTED]
(This should be just two lines; my email program is wrapping them.) I'm
trying to capture everything from the first 'AD - ' to the next set of
four characters that are either upper-case letters or blanks, followed
by a dash and a blank. I tried to use this:
my($ad) = /AD - (.*?)\015\012([A-Z]|\s){4}-\s/;
This regex only matches the one address in my sample data that consists
of just one line. It fails to match anything for the multi-line
addresses. Any suggestions on how I could capture both (or however many
lines used) lines in $ad?
Thanks for your advice and help.
-Kevin
Kevin Zembower
Internet Services Group manager
Center for Communication Programs
Bloomberg School of Public Health
Johns Hopkins University
111 Market Place, Suite 310
Baltimore, Maryland 21202
410-659-6139
============================
My complete program so far:
#! /usr/bin/perl -w
#
#medline2popline.pl written 7-Jan-2008 by Kevin Zembower
#
# This program converts medline records into POPLINE InMagic
importable records.
#
# It reads the medline records from STDIN and output POPLINE import
records to STDOUT
use strict;
$/="\015\012\015\012"; # Read a whole records (separated by a blank
line) at a time.
$\="\015\012"; # Output line termination is CRLF (for DOS)
while (<>) {
chomp;
#print "Record: $_";
my($ad) = /AD - (.*?)\015\012([A-Z]|\s){4}-\s/;
my($au) = /AU - (.*?)\015\012/;
my($dp) = /DP - (.*?)\015\012/;
my($ip) = /IP - (.*?)\015\012/;
my($pg) = /PG - (.*?)\015\012/;
my($pl) = /PL - (.*?)\015\012/;
my($tt) = /TT - (.*?)\015\012/;
my($vi) = /VI - (.*?)\015\012/;
print "AuthorAddress $ad" if ($ad);
print "Author $au" if ($au);
print "DateofPub $dp" if ($dp);
print "Issue $ip" if ($ip);
print "Pagination $pg" if ($pg);
print "JournalCountry $pl" if ($pl);
print "TT $tt" if ($tt);
print "Volume $vi" if ($vi);
print ""; #Blank line between records
}# while there are more lines to input
==============================================
short data file (in cat -vet output format):
[EMAIL PROTECTED]:~/medline2popline$ cat -vet t.txt
PMID- 17991957^M$
OWN - NLM^M$
STAT- MEDLINE^M$
DA - 20071109^M$
DCOM- 20071126^M$
PUBM- Print^M$
IS - 1468-5833 (Electronic)^M$
VI - 335^M$
IP - 7627^M$
DP - 2007 Nov 10^M$
TI - Faulty government condoms threaten South Africa's AIDS
programme.^M$
PG - 957^M$
FAU - Moszynski, Peter^M$
AU - Moszynski P^M$
LA - eng^M$
PT - News^M$
PL - England^M$
TA - BMJ^M$
JT - BMJ (Clinical research ed.)^M$
JID - 8900488^M$
SB - AIM^M$
SB - IM^M$
MH - Acquired Immunodeficiency Syndrome/*prevention & control^M$
MH - Condoms/*standards^M$
MH - Humans^M$
MH - South Africa^M$
EDAT- 2007/11/10 09:00^M$
MHDA- 2007/12/06 09:00^M$
12/7/2007 1:36PM335/7627/957 [pii]^M$
AID - 10.1136/bmj.39388.651308.DB [doi]^M$
PST - ppublish^M$
SO - BMJ. 2007 Nov 10;335(7627):957.^M$
^M$
PMID- 17983999^M$
OWN - NLM^M$
STAT- MEDLINE^M$
DA - 20071106^M$
DCOM- 20071129^M$
PUBM- Print^M$
IS - 1542-2011 (Electronic)^M$
VI - 52^M$
IP - 6^M$
DP - 2007 Nov-Dec^M$
TI - Contraception and lactation.^M$
PG - 614-20^M$
AB - The benefits of breastfeeding for both the infant and the mother
are undisputed. ^M$
Longer intervals between births decrease fetal/infant and maternal
complications.^M$
Lactation is an effective contraceptive for the first 6 months
postpartum only if^M$
women breastfeed exclusively and at regular intervals, including
nighttime.^M$
Because a high percentage of women in the United States supplement
breastfeeding,^M$
it is important for these women to choose a method of
contraception to prevent^M$
unintended pregnancies. Both the method of contraception and the
timing of the^M$
initiation of contraceptives are important decisions that a
clinician must help^M$
the breastfeeding woman make. Ideally, the chosen method of
contraception should ^M$
not interfere with lactation. This article reviews the research on
the effect of ^M$
contraceptives, including hormonal contraceptives, on
lactation.^M$
AD - Emory University School of Nursing, Atlanta, GA 30322, USA.
[EMAIL PROTECTED]
FAU - King, Joyce^M$
AU - King J^M$
LA - eng^M$
LA - fre^M$
PT - Journal Article^M$
PT - Review^M$
PL - United States^M$
TA - J Midwifery Womens Health^M$
JT - Journal of midwifery & women's health^M$
JID - 100909407^M$
RN - 0 (Contraceptive Agents, Female)^M$
SB - IM^M$
SB - N^M$
MH - Contraception/*methods^M$
MH - Contraception Behavior^M$
MH - *Contraceptive Agents, Female^M$
MH - *Contraceptive Devices, Female^M$
MH - Evidence-Based Medicine^M$
MH - Female^M$
MH - Health Knowledge, Attitudes, Practice^M$
MH - Humans^M$
MH - Infant Welfare^M$
MH - Infant, Newborn^M$
MH - *Lactation^M$
MH - Maternal Welfare^M$
MH - Mothers/education^M$
MH - *Patient Education as Topic^M$
MH - *Postpartum Period^M$
RF - 37^M$
EDAT- 2007/11/07 09:00^M$
MHDA- 2007/12/06 09:00^M$
AID - S1526-9523(07)00355-8 [pii]^M$
AID - 10.1016/j.jmwh.2007.08.012 [doi]^M$
PST - ppublish^M$
SO - J Midwifery Womens Health. 2007 Nov-Dec;52(6):614-20.^M$
^M$
PMID- 17955772^M$
OWN - NLM^M$
STAT- MEDLINE^M$
DA - 20071024^M$
DCOM- 20071120^M$
PUBM- Print^M$
IS - 1020-3397 (Print)^M$
VI - 13^M$
IP - 4^M$
DP - 2007 Jul-Aug^M$
TI - Birth interval: perceptions and practices among urban-based Saudi
Arabian women.^M$
PG - 881-92^M$
AB - To determine perceptions towards birth spacing, actual birth
interval and^M$
associated sociodemographic factors, we carried out a
cross-sectional study on^M$
436 mothers aged 15-50 years in Al-Khobar. All had had > or = 2
children within^M$
the previous 10 years. Only 5.2% preferred a birth interval of < 2
years, 28.2%^M$
preferred a 2 -< 3-year interval, while the rest favoured > or = 3
years.^M$
Education and employment status were predictors of birth spacing
preference.^M$
About half were not aware of the physical benefits associated with
longer birth^M$
interval. Only 26.3% had mean birth interval < 2 years. Age and
employment status^M$
were significant positive predictors of longer birth interval.
Oral contraception^M$
was the most popular method adopted for child spacing.^M$
AD - Department of Family and Community Medicine, College of Medicine,
King Faisal^M$
University, Dammam, Saudi Arabia. [EMAIL PROTECTED]
FAU - Rasheed, P^M$
AU - Rasheed P^M$
FAU - Al-Dabal, B K^M$
AU - Al-Dabal BK^M$
LA - eng^M$
PT - Journal Article^M$
PL - Egypt^M$
TA - East Mediterr Health J^M$
JT - Eastern Mediterranean health journal = La revue de sante de la
Mediterranee^M$
orientale = al-Majallah al-sihhiyah li-sharq al-mutawassit^M$
JID - 9608387^M$
SB - IM^M$
MH - Adolescent^M$
MH - Adult^M$
MH - *Attitude to Health^M$
MH - *Birth Intervals/psychology/statistics & numerical data^M$
MH - Choice Behavior^M$
MH - Contraception/methods/psychology/statistics & numerical data^M$
MH - Contraception Behavior/psychology/statistics & numerical data^M$
MH - Cross-Sectional Studies^M$
MH - Educational Status^M$
MH - Family Characteristics^M$
MH - Female^M$
MH - *Health Knowledge, Attitudes, Practice^M$
MH - Humans^M$
MH - Intention^M$
MH - Linear Models^M$
MH - Maternal Age^M$
MH - *Mothers/education/psychology/statistics & numerical data^M$
MH - Multivariate Analysis^M$
MH - Occupations/statistics & numerical data^M$
MH - Questionnaires^M$
MH - Saudi Arabia^M$
MH - Socioeconomic Factors^M$
MH - Urban Population^M$
EDAT- 2007/10/25 09:00^M$
MHDA- 2007/12/06 09:00^M$
PST - ppublish^M$
SO - East Mediterr Health J. 2007 Jul-Aug;13(4):881-92.^M$
^M$
PMID- 17955618^M$
OWN - NLM^M$
STAT- MEDLINE^M$
DA - 20071005^M$
DCOM- 20071113^M$
PUBM- Print^M$
IS - 1181-7186 (Print)^M$
VI - 19^M$
IP - 5^M$
DP - 2007 Jul-Aug^M$
TI - Infections. Sex and hepatitis C infection in Germany.^M$
PG - 9-10^M$
LA - eng^M$
PT - Newspaper Article^M$
PL - Canada^M$
TA - TreatmentUpdate^M$
JT - TreatmentUpdate^M$
JID - 100891076^M$
SB - X^M$
MH - Adult^M$
MH - Condoms^M$
MH - Germany/epidemiology^M$
MH - Hepatitis C/*epidemiology/prevention & control/transmission^M$
MH - Humans^M$
MH - Male^M$
MH - Risk Factors^M$
MH - *Sexual Behavior^M$
MH - Substance-Related Disorders^M$
MH - Surgical Procedures, Operative/adverse effects^M$
EDAT- 2007/10/25 09:00^M$
MHDA- 2007/11/14 09:00^M$
PST - ppublish^M$
SO - TreatmentUpdate. 2007 Jul-Aug;19(5):9-10.^M$
^M$
PMID- 17952213^M$
OWN - NLM^M$
STAT- MEDLINE^M$
DA - 20071022^M$
DCOM- 20071106^M$
LR - 20071115^M$
PUBM- Print^M$
IS - 0256-9574 (Print)^M$
VI - 97^M$
IP - 8^M$
DP - 2007 Aug^M$
TI - Emergency contraception--lack of awareness among women presenting
for termination^M$
of pregnancy.^M$
PG - 584-5^M$
FAU - Moodley, Jennifer^M$
AU - Moodley J^M$
FAU - Morroni, Chelsea^M$
AU - Morroni C^M$
LA - eng^M$
PT - Letter^M$
PL - South Africa^M$
TA - S Afr Med J^M$
JT - South African medical journal = Suid-Afrikaanse tydskrif vir
geneeskunde^M$
JID - 0404520^M$
RN - 0 (Contraceptives, Postcoital)^M$
SB - IM^M$
MH - *Abortion, Legal^M$
MH - Adolescent^M$
MH - Adult^M$
MH - *Awareness^M$
MH - Contraception/*methods^M$
MH - Contraceptives, Postcoital/*therapeutic use^M$
MH - *Emergencies^M$
MH - Female^M$
MH - *Health Knowledge, Attitudes, Practice^M$
MH - Health Surveys^M$
MH - Humans^M$
MH - *Patient Education as Topic^M$
MH - Pregnancy^M$
EDAT- 2007/10/24 09:00^M$
MHDA- 2007/11/07 09:00^M$
PST - ppublish^M$
SO - S Afr Med J. 2007 Aug;97(8):584-5.^M$
^M$
PMID- 17949389^M$
OWN - NLM^M$
STAT- MEDLINE^M$
DA - 20071022^M$
DCOM- 20071108^M$
PUBM- Print^M$
IS - 1471-0528 (Electronic)^M$
VI - 114^M$
IP - 11^M$
DP - 2007 Nov^M$
TI - The feasibility, success and patient satisfaction associated with
outpatients^M$
hysteroscopic sterilisation.^M$
PG - 1449; author reply 1449-50^M$
FAU - Qureshi, N S^M$
AU - Qureshi NS^M$
LA - eng^M$
PT - Comment^M$
PT - Letter^M$
PL - England^M$
TA - BJOG^M$
JT - BJOG : an international journal of obstetrics and gynaecology^M$
JID - 100935741^M$
SB - AIM^M$
SB - IM^M$
CON - BJOG. 2007 Jun;114(6):676-83. PMID: 17516957^M$
MH - Ambulatory Surgical Procedures/*methods^M$
MH - Catheter Ablation/methods^M$
MH - Feasibility Studies^M$
MH - Female^M$
MH - Humans^M$
MH - Magnetic Resonance Imaging^M$
MH - Microwaves/therapeutic use^M$
MH - *Patient Satisfaction^M$
MH - Sterilization, Reproductive^M$
EDAT- 2007/10/24 09:00^M$
MHDA- 2007/11/09 09:00^M$
AID - BJO1494 [pii]^M$
AID - 10.1111/j.1471-0528.2007.01494.x [doi]^M$
PST - ppublish^M$
SO - BJOG. 2007 Nov;114(11):1449; author reply 1449-50.^M$
^M$
PMID- 17948764^M$
OWN - NLM^M$
STAT- MEDLINE^M$
DA - 20071022^M$
DCOM- 20071113^M$
PUBM- Print^M$
IS - 0895-3988 (Print)^M$
VI - 20^M$
IP - 4^M$
DP - 2007 Aug^M$
TI - Power relation and condom use in commercial sex behaviors.^M$
PG - 302-6^M$
AB - OBJECTIVE: To explore whether condom use is influenced by power
relation in^M$
commercial sex behaviors. METHODS: Variables were designed to
measure the power^M$
relation in commercial sex behaviors based on the theory of gender
and power^M$
relation and data were collected from male sexually transmitted
diseases (STD)^M$
patients and female commercial sex workers (FSWs) working at
recreation centers^M$
or being detained in a women education center to identify the
relationship^M$
between condom use and power relation in male and female
respondents using^M$
bivariate and multiple regression analysis. RESULTS: A significant
relationship^M$
was identified between power relation and female condom use, the
higher the score^M$
of power relations, the higher frequency the condom use, but no
similar result^M$
was found in males. Females got a higher score of power relation
than males.^M$
CONCLUSIONS: Power relation is one of the factors that influence
condom use,^M$
which should be considered when relevant theories are used to
study the rate of^M$
condom use. It is worthwhile exploring the relationship between
safe sex and^M$
power relation in spouses and regular sex partners when
interventions are adopted^M$
to prevent HIV/AIDS spreading from high risk groups to the general
population.^M$
AD - Institute of Viral Disease Prevention and Control, Chinese Center
for Disease^M$
Control and Prevention, Beijing 100050, China.^M$
FAU - Wang, Ying^M$
AU - Wang Y^M$
FAU - Li, Bing^M$
AU - Li B^M$
FAU - Song, Dong-Mei^M$
AU - Song DM^M$
FAU - Ding, Guang-Yan^M$
AU - Ding GY^M$
FAU - Cathy, Emric^M$
AU - Cathy E^M$
LA - eng^M$
PT - Journal Article^M$
PL - United States^M$
TA - Biomed Environ Sci^M$
JT - Biomedical and environmental sciences : BES^M$
JID - 8909524^M$
SB - IM^M$
MH - Adolescent^M$
MH - Adult^M$
MH - Condoms/*utilization^M$
MH - Female^M$
MH - Humans^M$
MH - Male^M$
MH - *Power (Psychology)^M$
MH - *Sexual Behavior^M$
EDAT- 2007/10/24 09:00^M$
MHDA- 2007/11/14 09:00^M$
PST - ppublish^M$
SO - Biomed Environ Sci. 2007 Aug;20(4):302-6.^M$
^M$
PMID- 17939181^M$
OWN - NLM^M$
STAT- MEDLINE^M$
DA - 20071015^M$
DCOM- 20071030^M$
PUBM- Print^M$
IS - 1473-3099 (Print)^M$
VI - 7^M$
IP - 10^M$
DP - 2007 Oct^M$
TI - Female-initiated prevention strategies key to tackling HIV.^M$
PG - 637^M$
FAU - Nelson, Roxanne^M$
AU - Nelson R^M$
LA - eng^M$
PT - News^M$
PL - United States^M$
TA - Lancet Infect Dis^M$
JT - The Lancet infectious diseases^M$
JID - 101130150^M$
RN - 0 (Anti-HIV Agents)^M$
RN - 0 (Phosphonic Acids)^M$
RN - 0 (Reverse Transcriptase Inhibitors)^M$
RN - 107021-12-5 (tenofovir)^M$
RN - 73-24-5 (Adenine)^M$
SB - IM^M$
MH - Adenine/analogs & derivatives/therapeutic use^M$
MH - Africa South of the Sahara^M$
MH - Anti-HIV Agents/therapeutic use^M$
MH - Condoms, Female/utilization^M$
MH - Diaphragm^M$
MH - Female^M$
MH - HIV Infections/*prevention & control^M$
MH - Humans^M$
MH - Phosphonic Acids/therapeutic use^M$
MH - Primary Prevention/*methods^M$
MH - Reverse Transcriptase Inhibitors/therapeutic use^M$
MH - Rwanda^M$
MH - Women/*education/*psychology^M$
EDAT- 2007/10/17 09:00^M$
MHDA- 2007/10/31 09:00^M$
PST - ppublish^M$
SO - Lancet Infect Dis. 2007 Oct;7(10):637.^M$
^M$
PMID- 17933635^M$
OWN - NLM^M$
STAT- MEDLINE^M$
DA - 20071015^M$
DCOM- 20071026^M$
PUBM- Print^M$
IS - 1474-547X (Electronic)^M$
VI - 370^M$
IP - 9595^M$
DP - 2007 Oct 13^M$
TI - Contraception, safe abortion, and maternal morbidity.^M$
PG - 1294-5^M$
AD - Department of Population, Family and Reproductive Health, Johns
Hopkins Bloomberg^M$
School of Public Health, Baltimore, MD 21205, USA.
[EMAIL PROTECTED]
FAU - Hindin, Michelle J^M$
AU - Hindin MJ^M$
LA - eng^M$
PT - Comment^M$
PT - Journal Article^M$
PL - England^M$
TA - Lancet^M$
JT - Lancet^M$
JID - 2985213R^M$
SB - AIM^M$
SB - IM^M$
CON - Lancet. 2007 Oct 13;370(9595):1329-37. PMID: 17933647^M$
MH - Abortion, Induced/*statistics & numerical data/trends^M$
MH - Burkina Faso/epidemiology^M$
MH - Contraception/economics/*utilization^M$
MH - Female^M$
MH - Humans^M$
MH - *Maternal Mortality^M$
MH - Obstetric Labor Complications/*epidemiology/mortality/prevention &
control^M$
MH - Pregnancy^M$
EDAT- 2007/10/16 09:00^M$
MHDA- 2007/10/30 09:00^M$
AID - S0140-6736(07)61555-4 [pii]^M$
AID - 10.1016/S0140-6736(07)61555-4 [doi]^M$
PST - ppublish^M$
SO - Lancet. 2007 Oct 13;370(9595):1294-5.^M$
^M$
PMID- 17933295^M$
OWN - NLM^M$
STAT- MEDLINE^M$
DA - 20071015^M$
DCOM- 20071120^M$
PUBM- Print^M$
IS - 0039-3665 (Print)^M$
VI - 38^M$
IP - 3^M$
DP - 2007 Sep^M$
TI - Senegal 2005: results from the demographic and health survey.^M$
PG - 212-7^M$
LA - eng^M$
PT - Journal Article^M$
PL - United States^M$
TA - Stud Fam Plann^M$
JT - Studies in family planning^M$
JID - 7810364^M$
SB - IM^M$
MH - Adolescent^M$
MH - Adult^M$
MH - Birth Rate/trends^M$
MH - Breast Feeding/statistics & numerical data^M$
MH - Contraception/statistics & numerical data/utilization^M$
MH - *Demography^M$
MH - Female^M$
MH - Health Knowledge, Attitudes, Practice^M$
MH - Health Status^M$
MH - *Health Surveys^M$
MH - Humans^M$
MH - Infant^M$
MH - Infant Mortality/trends^M$
MH - Infant, Newborn^M$
MH - Middle Aged^M$
MH - Senegal/epidemiology^M$
EDAT- 2007/10/16 09:00^M$
MHDA- 2007/12/06 09:00^M$
PST - ppublish^M$
SO - Stud Fam Plann. 2007 Sep;38(3):212-7.^M$
^M$
PMID- 17933294^M$
OWN - NLM^M$
STAT- MEDLINE^M$
DA - 20071015^M$
DCOM- 20071120^M$
PUBM- Print^M$
IS - 0039-3665 (Print)^M$
VI - 38^M$
IP - 3^M$
DP - 2007 Sep^M$
TI - Guinea 2005: results from the demographic and health survey.^M$
PG - 206-11^M$
LA - eng^M$
PT - Journal Article^M$
PL - United States^M$
TA - Stud Fam Plann^M$
JT - Studies in family planning^M$
JID - 7810364^M$
SB - IM^M$
MH - Adolescent^M$
MH - Adult^M$
MH - Birth Rate/trends^M$
MH - Breast Feeding/statistics & numerical data^M$
MH - Contraception/statistics & numerical data/utilization^M$
MH - *Demography^M$
MH - Female^M$
MH - Guinea/epidemiology^M$
MH - Health Knowledge, Attitudes, Practice^M$
MH - Health Status^M$
MH - *Health Surveys^M$
MH - Humans^M$
MH - Infant^M$
MH - Infant Mortality/trends^M$
MH - Infant, Newborn^M$
MH - Middle Aged^M$
EDAT- 2007/10/16 09:00^M$
MHDA- 2007/12/06 09:00^M$
PST - ppublish^M$
SO - Stud Fam Plann. 2007 Sep;38(3):206-11.^M$
^M$
[EMAIL PROTECTED]:~/medline2popline$
====================================
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