From wlkngowl at i-2000.com Thu Apr 1 14:22:04 2004 From: wlkngowl at i-2000.com (Robert Rothenberg) Date: Mon Aug 2 21:37:44 2004 Subject: [sb.pm] When should we meet next? In-Reply-To: <406269D3.4060504@i-2000.com> References: <406269D3.4060504@i-2000.com> Message-ID: <406C79EC.4060005@i-2000.com> The questions are still out there: When is a good time for everybody to meet in April? What weeks are the students on the list less bogged-down with papers, mid-terms, and other projects? Also, what topics could we discuss? If there's no specific topics, maybe we could meet informally at a local pub. Comments? On 3/25/2004 12:10 AM Robert Rothenberg wrote: > > Attendance at tonight's meeting was a bit sparse. We assume it was due > to midterms. > > So when is a good time next month for everybody to meet? (Days of the > week and times of day are helpful.) From basu at pharm.sunysb.edu Mon Apr 5 10:01:30 2004 From: basu at pharm.sunysb.edu (Siddhartha Basu) Date: Mon Aug 2 21:37:44 2004 Subject: [sb.pm] When should we meet next? In-Reply-To: <406C79EC.4060005@i-2000.com> References: <406269D3.4060504@i-2000.com> <406C79EC.4060005@i-2000.com> Message-ID: <407174CA.60102@pharm.sunysb.edu> Hi, Robert Rothenberg wrote: > > The questions are still out there: > > When is a good time for everybody to meet in April? What weeks are the > students on the list less bogged-down with papers, mid-terms, and other > projects? > > Also, what topics could we discuss? If there's no specific topics, > maybe we could meet informally at a local pub. Here are some topic i can think of.. * Working with databases. (both relational and dbm based). * Object oriented perl programming introduction. (what i am trying to learn right now). * I/O with perl, working with files. Anyway, thanks for putting up the slides. -sidd > > Comments? > > On 3/25/2004 12:10 AM Robert Rothenberg wrote: > >> >> Attendance at tonight's meeting was a bit sparse. We assume it was >> due to midterms. >> >> So when is a good time next month for everybody to meet? (Days of the >> week and times of day are helpful.) > > > > _______________________________________________ > StonyBrook-PM mailing list > StonyBrook-PM@mail.pm.org > http://mail.pm.org/mailman/listinfo/stonybrook-pm From wlkngowl at i-2000.com Wed Apr 7 10:55:54 2004 From: wlkngowl at i-2000.com (Robert Rothenberg) Date: Mon Aug 2 21:37:44 2004 Subject: [sb.pm] When should we meet next? In-Reply-To: <407174CA.60102@pharm.sunysb.edu> References: <406269D3.4060504@i-2000.com> <406C79EC.4060005@i-2000.com> <407174CA.60102@pharm.sunysb.edu> Message-ID: <4074248A.5060003@i-2000.com> We still need to figure out *when* we want to meet, particularly as we near the end of the semester. The last Wednesdays in April (21 and 28) are actually bad for me. How's Tuesday April 27 or Thursday April 29? Also, if you need help with a specific Perl question, why not post it to the list? Rob On 4/5/2004 11:01 AM Siddhartha Basu wrote: > Here are some topic i can think of.. > > * Working with databases. (both relational and dbm based). DBI and DBM files (using tie?) are separate topics. Which do people on the list prefer? I'm willing to do something on DBI, although I might not have time to get a presentation ready for the next meeting. > * Object oriented perl programming introduction. (what i am trying to > learn right now). That's quite a topic. Have you tried Damien Conway's "Object Oriented Perl" book? It's an excellent book on object-oriented programming (in general, not just for Perl). > * I/O with perl, working with files. That's an easier topic to lecture about. From kostas at cs.sunysb.edu Tue Apr 13 23:50:31 2004 From: kostas at cs.sunysb.edu (Kostas Pentikousis) Date: Mon Aug 2 21:37:45 2004 Subject: [sb.pm] When should we meet next? In-Reply-To: <4074248A.5060003@i-2000.com> References: <406269D3.4060504@i-2000.com> <406C79EC.4060005@i-2000.com> <407174CA.60102@pharm.sunysb.edu> <4074248A.5060003@i-2000.com> Message-ID: On Wed, 7 Apr 2004, Robert Rothenberg wrote: | How's Tuesday April 27 or Thursday April 29? I would prefer 4/29. |> Here are some topic i can think of.. I'm sure there are a lot of topics we can discuss. For example, I could review "Perl Medic", a rather interesting book. I don't mind presenting again, and I guess Rob would not have a problem as well. However, we would like to see significant participation in the next meeting. If the date/time/topics we will decide is not of your liking and you will not make the meeting please do let us know. We can always skip preparing a formal presentation with slides, etc. and discuss the topic, and more, in a cosier setting with some good food and drinks ;) |DBI and DBM files (using tie?) are separate topics. Which do people on the |list prefer? I'm willing to do something on DBI, although I might not have |time to get a presentation ready for the next meeting. I'm using a hash tied to DB_File for one of my research projects. I could explain why and how to use such a tool. I'm also interested in listening to a presentation on DBI, I'm sure there will many new things to learn :). But wouldn't you be more interested in a dry run on SkipLists? ;) Best regards, Kostas __________________________________________________________________ Kostas Pentikousis www.cs.stonybrook.edu/~kostas From wlkngowl at i-2000.com Wed Apr 14 00:32:59 2004 From: wlkngowl at i-2000.com (Robert Rothenberg) Date: Mon Aug 2 21:37:45 2004 Subject: [sb.pm] When should we meet next? In-Reply-To: References: <406269D3.4060504@i-2000.com> <406C79EC.4060005@i-2000.com> <407174CA.60102@pharm.sunysb.edu> <4074248A.5060003@i-2000.com> Message-ID: <407CCD0B.2000307@i-2000.com> On 4/14/2004 12:50 AM Kostas Pentikousis wrote: > On Wed, 7 Apr 2004, Robert Rothenberg wrote: > > > | How's Tuesday April 27 or Thursday April 29? > > I would prefer 4/29. I just realized that 4/29 is bad for me. (I'll be on my way down to Kentucky, http://www.kentuckyderby.com/2004/). Should we just post-pone it the first week of May? If there's not going to be a presentation, I'm fine with a purely social meeting over a few drinks. > ... However, we would like to see significant participation in > the next meeting. ... Yes. I don't want to work on a presentation for just a couple of people. > I'm using a hash tied to DB_File for one of my research projects. > I could explain why and how to use such a tool. I'm also > interested in listening to a presentation on DBI, I'm sure there > will many new things to learn :). But wouldn't you be more > interested in a dry run on SkipLists? ;) Would be a very dry run on skip lists, as I'm not done on the presentation for YAPC::NA, which brings me to another topic (next post).... From wlkngowl at i-2000.com Wed Apr 14 00:39:19 2004 From: wlkngowl at i-2000.com (Robert Rothenberg) Date: Mon Aug 2 21:37:45 2004 Subject: [sb.pm] YAPC::NA - carpooling? Message-ID: <407CCE87.5090307@i-2000.com> YAPC::NA (Yet Another Perl Conference, North America) is happening in Buffalo, June 16-18. Is anybody up for carpooling there? More info at http://www.yapc.org/America/ From basu at pharm.sunysb.edu Wed Apr 14 10:13:41 2004 From: basu at pharm.sunysb.edu (Siddhartha Basu) Date: Mon Aug 2 21:37:45 2004 Subject: [sb.pm] When should we meet next? In-Reply-To: <407CCD0B.2000307@i-2000.com> References: <406269D3.4060504@i-2000.com> <406C79EC.4060005@i-2000.com> <407174CA.60102@pharm.sunysb.edu> <4074248A.5060003@i-2000.com> <407CCD0B.2000307@i-2000.com> Message-ID: <407D5525.80509@pharm.sunysb.edu> Hi, Robert Rothenberg wrote: > > > On 4/14/2004 12:50 AM Kostas Pentikousis wrote: > >> On Wed, 7 Apr 2004, Robert Rothenberg wrote: >> >> >> | How's Tuesday April 27 or Thursday April 29? >> >> I would prefer 4/29. > > > I just realized that 4/29 is bad for me. (I'll be on my way down to > Kentucky, http://www.kentuckyderby.com/2004/). > > Should we just post-pone it the first week of May? > First week of may is good for me. However, after 6:30 will be prefarable . I will be able to wrap my labwork around then. > If there's not going to be a presentation, I'm fine with a purely social > meeting over a few drinks. > >> ... However, we would like to see significant participation in >> the next meeting. ... > I agree with you. It's a waste to prepare only for few people. And if we are not expecting a lot of people before the meeting then the social meeting with food and drink is the way to go :-). Now, what about also having an informal discussion about increasing attendance in our group meeting. Last year we had also seen this problem of low attendance with lugsb group meeting too. The problem seems to be less this year though probably it has taken some time for that group to be known among the students. > > Yes. I don't want to work on a presentation for just a couple of people. > >> I'm using a hash tied to DB_File for one of my research projects. >> I could explain why and how to use such a tool. I'm also >> interested in listening to a presentation on DBI, I'm sure there >> will many new things to learn :). But wouldn't you be more >> interested in a dry run on SkipLists? ;) > > > Would be a very dry run on skip lists, as I'm not done on the > presentation for YAPC::NA, which brings me to another topic (next post).... > I am interested in going to the conference and want to help with carpooling anyway i can. We can also hash this out in the next social meet. -sidd Siddhartha Basu Post-Doctoral Research fellow Department of Pharmacology. > > > > _______________________________________________ > StonyBrook-PM mailing list > StonyBrook-PM@mail.pm.org > http://mail.pm.org/mailman/listinfo/stonybrook-pm From basu at pharm.sunysb.edu Wed Apr 14 14:11:57 2004 From: basu at pharm.sunysb.edu (Siddhartha Basu) Date: Mon Aug 2 21:37:45 2004 Subject: [sb.pm] When should we meet next? In-Reply-To: <4074248A.5060003@i-2000.com> References: <406269D3.4060504@i-2000.com> <406C79EC.4060005@i-2000.com> <407174CA.60102@pharm.sunysb.edu> <4074248A.5060003@i-2000.com> Message-ID: <407D8CFD.1090308@pharm.sunysb.edu> Hi, Robert Rothenberg wrote: > > Also, if you need help with a specific Perl question, why not post it to > the list? Most definitely. But at this moment i am facing more of a design problem rather than code related. I think i can discuss it here so that i can ge some help with a better approach. I work with making biological databases, mainly stroing metadata/annotation about genes/proteins in mysql. So, in most of the cases the inputs has different formats including non-standard ones.Naturally, the parsing routines also differs according to the inputs. So,... * What will be a good approach for taking inputs for a program specially if i want to run it from a cron job. * From the command line by using @ARGV or Getopt::Long. * Or by setting environmental variables and accessing from $ENV hash. Right now, i have mix of both but it is becoming cumbersome and i am thinking about having settling down with one approach. * Sometimes i have do read a flat text file line by line, split the column and then check whether the data in that column is present in another text file. So, my approach is to either read the second text file to a dbm hash or to mysql database. The downside what i am facing is that i have to write a script for every possible text file to be searched. Text files with varying format also compounds the problem. Nothing else comes to my mind at this moment so i am dealing with a bunch of scattared scripts. * What kind of format should i use for writing log file. Flat text file or xml format. > > Rob > > On 4/5/2004 11:01 AM Siddhartha Basu wrote: > >> Here are some topic i can think of.. >> >> * Working with databases. (both relational and dbm based). > > > DBI and DBM files (using tie?) are separate topics. Which do people on > the list prefer? I'm willing to do something on DBI, although I might > not have time to get a presentation ready for the next meeting. > >> * Object oriented perl programming introduction. (what i am trying to >> learn right now). > > > That's quite a topic. Have you tried Damien Conway's "Object Oriented > Perl" book? It's an excellent book on object-oriented programming (in > general, not just for Perl). > Yes, i am trying to grasp the ideas from the book. I am also impressed with the new book by "Randal Schwartz's" entitled "Perl objects, references, and modules". The style and flow of writing is excellent. -sidd Siddhartha Basu Post-doc research fellow. Dept. of Pharmacology. From wlkngowl at i-2000.com Thu Apr 15 16:54:51 2004 From: wlkngowl at i-2000.com (Robert Rothenberg) Date: Mon Aug 2 21:37:45 2004 Subject: [sb.pm] When should we meet next? In-Reply-To: <407D8CFD.1090308@pharm.sunysb.edu> References: <406269D3.4060504@i-2000.com> <406C79EC.4060005@i-2000.com> <407174CA.60102@pharm.sunysb.edu> <4074248A.5060003@i-2000.com> <407D8CFD.1090308@pharm.sunysb.edu> Message-ID: <407F04AB.3020208@i-2000.com> On 4/14/2004 3:11 PM Siddhartha Basu wrote: > Most definitely. But at this moment i am facing more of a design problem > rather than code related. I think i can discuss it here so that i can ge > some help with a better approach. ... > * What will be a good approach for taking inputs for a program specially > if i want to run it from a cron job. > * From the command line by using @ARGV or Getopt::Long. > * Or by setting environmental variables and accessing from $ENV > hash. > Right now, i have mix of both but it is becoming cumbersome and i am > thinking about having settling down with one approach. I'd use command-line arguments, since it's easier to pass arguments to when running the scripts as one-shots. > * Sometimes i have do read a flat text file line by line, split the > column and then check whether the data in that column is present in > another text file. So, my approach is to either read the second text BioPerl has some flat database file drivers. DBD::CSV, DBD::Sprite or DBD::File might provide some DBI drivers to handle flat files and simplify your work. > file to a dbm hash or to mysql database. The downside what i am facing > is that i have to write a script for every possible text file to be > searched. Text files with varying format also compounds the problem. > Nothing else comes to my mind at this moment so i am dealing with a > bunch of scattared scripts. Where are these text files coming from that they are in different formats? > * What kind of format should i use for writing log file. Flat text file > or xml format. I'd avoid XML like the plague, unless you need to pass the logs to a program which requires it in XML. Do you really need sophisticated markup for a log file? Another alternative is YAML, which is more human-readable. See http://yaml.org/ for more information. From jkeen at verizon.net Fri Apr 16 18:08:15 2004 From: jkeen at verizon.net (James E Keenan) Date: Mon Aug 2 21:37:45 2004 Subject: [sb.pm] In NYC Tuesday Night? Message-ID: <200441619815.014542@crc3> In case you're in New York City this coming Tuesday night ... Our next Perl Seminar NY meeting will be Tuesday, April 20, 6:15 pm at: NYPC Users Group office suite 481 8 Ave (Ramada New Yorker hotel) Suite 1560 between West 34 & 35 Sts, Manhattan Here's what scheduled so far: Using Perl for Math Kurt Starsinic Creating Financial Charts for the Web Using GD Martin Heinsdorf Jim Keenan From wlkngowl at i-2000.com Mon Apr 19 12:25:55 2004 From: wlkngowl at i-2000.com (Robert Rothenberg) Date: Mon Aug 2 21:37:45 2004 Subject: [sb.pm] Next Meeting? Message-ID: <40840BA3.6050205@i-2000.com> Let's say we make the next meeting a social one rather than with a technical presentation. We could also discuss carpooling plans for YAPC Buffalo. We'll meet at a local at local food/drinking establishment some time after 6 or 7. Dates that are good for me: Wed 4/21, Thu 4/22, or Tue 4/27. I'm partial to getting together this week. The University Cafe (http://universitycafe.org/) is on campus and they have wraps and tapas. Off campus but walkable includes Full Moon Cafe (Pizza) and Velvet Lounge (Indian). We could also choose a further off-campus venue and arrange lifts for those on campus without cars. Some decent places are Marios (Italian) or Country Corner (Burgers & Armenian) in East Setauket. From kostas at cs.sunysb.edu Mon Apr 19 20:47:01 2004 From: kostas at cs.sunysb.edu (Kostas Pentikousis) Date: Mon Aug 2 21:37:45 2004 Subject: [sb.pm] Next Meeting? In-Reply-To: <40840BA3.6050205@i-2000.com> References: <40840BA3.6050205@i-2000.com> Message-ID: On Mon, 19 Apr 2004, Robert Rothenberg wrote: | |Dates that are good for me: Wed 4/21, Thu 4/22, or Tue 4/27. I'm partial to |getting together this week. I'd prefer next Tue, 4/27 at 6.30, but Thu 4/22 at 6.30 is OK too. |The University Cafe (http://universitycafe.org/) is on campus and they have |wraps and tapas. I'd like to give the UC a chance :) Best regards, Kostas From wlkngowl at i-2000.com Mon Apr 19 23:06:29 2004 From: wlkngowl at i-2000.com (Robert Rothenberg) Date: Mon Aug 2 21:37:45 2004 Subject: [sb.pm] Next Meeting? In-Reply-To: References: <40840BA3.6050205@i-2000.com> Message-ID: <4084A1C5.60505@i-2000.com> I think the cafe is only open in the evenings on Wednesday through Saturday. So we'd have to meet there on a Thursday. So how's this Thursday at 6:30pm at the Cafe for everybody? On 4/19/2004 9:47 PM Kostas Pentikousis wrote: > On Mon, 19 Apr 2004, Robert Rothenberg wrote: > > | > |Dates that are good for me: Wed 4/21, Thu 4/22, or Tue 4/27. I'm partial to > |getting together this week. > > I'd prefer next Tue, 4/27 at 6.30, but Thu 4/22 at 6.30 is OK too. > > |The University Cafe (http://universitycafe.org/) is on campus and they have > |wraps and tapas. > > I'd like to give the UC a chance :) > > Best regards, > > Kostas > > From basu at pharm.sunysb.edu Thu Apr 22 08:53:53 2004 From: basu at pharm.sunysb.edu (Siddhartha Basu) Date: Mon Aug 2 21:37:45 2004 Subject: [sb.pm] Next Meeting? In-Reply-To: <4084A1C5.60505@i-2000.com> References: <40840BA3.6050205@i-2000.com> <4084A1C5.60505@i-2000.com> Message-ID: <4087CE71.6000902@pharm.sunysb.edu> I presume we are meeting today at 6:30PM at the Cafe. See you there. -sidd Robert Rothenberg wrote: > > I think the cafe is only open in the evenings on Wednesday through > Saturday. So we'd have to meet there on a Thursday. > > So how's this Thursday at 6:30pm at the Cafe for everybody? > > On 4/19/2004 9:47 PM Kostas Pentikousis wrote: > >> On Mon, 19 Apr 2004, Robert Rothenberg wrote: >> >> | >> |Dates that are good for me: Wed 4/21, Thu 4/22, or Tue 4/27. I'm >> partial to >> |getting together this week. >> >> I'd prefer next Tue, 4/27 at 6.30, but Thu 4/22 at 6.30 is OK too. >> >> |The University Cafe (http://universitycafe.org/) is on campus and >> they have >> |wraps and tapas. >> >> I'd like to give the UC a chance :) >> >> Best regards, >> >> Kostas >> >> > _______________________________________________ > StonyBrook-PM mailing list > StonyBrook-PM@mail.pm.org > http://mail.pm.org/mailman/listinfo/stonybrook-pm From wlkngowl at i-2000.com Thu Apr 22 10:24:04 2004 From: wlkngowl at i-2000.com (Robert Rothenberg) Date: Mon Aug 2 21:37:45 2004 Subject: [sb.pm] Today 6:30pm University Cafe In-Reply-To: <4087CE71.6000902@pharm.sunysb.edu> References: <40840BA3.6050205@i-2000.com> <4084A1C5.60505@i-2000.com> <4087CE71.6000902@pharm.sunysb.edu> Message-ID: <4087E394.4040703@i-2000.com> Yes. I was just about to post something. FYI, directions/info at http://universitycafe.org/ On 4/22/2004 9:53 AM Siddhartha Basu wrote: > I presume we are meeting today at 6:30PM at the Cafe. See you there. > > -sidd > Robert Rothenberg wrote: > >> >> I think the cafe is only open in the evenings on Wednesday through >> Saturday. So we'd have to meet there on a Thursday. >> >> So how's this Thursday at 6:30pm at the Cafe for everybody? >> [Snip!] From kostas at cs.sunysb.edu Thu Apr 22 16:51:01 2004 From: kostas at cs.sunysb.edu (Kostas Pentikousis) Date: Mon Aug 2 21:37:45 2004 Subject: [sb.pm] Reminder: University Cafe @ 6.30 In-Reply-To: <4087CE71.6000902@pharm.sunysb.edu> References: <40840BA3.6050205@i-2000.com> <4084A1C5.60505@i-2000.com> <4087CE71.6000902@pharm.sunysb.edu> Message-ID: Take a break and come join us for coffee or dinner. Best regards, Kostas From basu at pharm.sunysb.edu Thu Apr 22 19:34:08 2004 From: basu at pharm.sunysb.edu (Siddhartha Basu) Date: Mon Aug 2 21:37:45 2004 Subject: [sb.pm] Re: Today 6:30pm University Cafe In-Reply-To: <4087E394.4040703@i-2000.com> References: <40840BA3.6050205@i-2000.com> <4084A1C5.60505@i-2000.com> <4087CE71.6000902@pharm.sunysb.edu> <4087E394.4040703@i-2000.com> Message-ID: <40886480.2070209@pharm.sunysb.edu> I missed it today. I went to to wrong cafe and wandered around for half an hour. Maybe should have checked the direction earlier. Anyway, what happened in todays meeting. And of course when are we meeting again. -sidd Robert Rothenberg wrote: > > Yes. I was just about to post something. > > FYI, directions/info at http://universitycafe.org/ > > On 4/22/2004 9:53 AM Siddhartha Basu wrote: > >> I presume we are meeting today at 6:30PM at the Cafe. See you there. >> >> -sidd >> Robert Rothenberg wrote: >> >>> >>> I think the cafe is only open in the evenings on Wednesday through >>> Saturday. So we'd have to meet there on a Thursday. >>> >>> So how's this Thursday at 6:30pm at the Cafe for everybody? >>> > [Snip!] > From wlkngowl at i-2000.com Sun Apr 25 15:20:17 2004 From: wlkngowl at i-2000.com (Robert Rothenberg) Date: Mon Aug 2 21:37:45 2004 Subject: [sb.pm] May meeting... Message-ID: <408C1D81.8000702@i-2000.com> When is a good time to schedule a meeting in May? Should we wait until after final exams? Who will still be around? From kostas at cs.sunysb.edu Sun Apr 25 21:23:47 2004 From: kostas at cs.sunysb.edu (Kostas Pentikousis) Date: Mon Aug 2 21:37:45 2004 Subject: [sb.pm] May meeting... In-Reply-To: <408C1D81.8000702@i-2000.com> References: <408C1D81.8000702@i-2000.com> Message-ID: On Sun, 25 Apr 2004, Robert Rothenberg wrote: |When is a good time to schedule a meeting in May? Should we wait until after |final exams? Who will still be around? I'd prefer a meeting on Tue 5/25. It's after the exams and close enough to YAPC. Anything earlier than 5/25 is no good for me. It would be great to have another social meeting at the university cafe, though, before the formal May meeting. Best regards, Kostas From kostas at cs.sunysb.edu Thu Apr 29 18:52:30 2004 From: kostas at cs.sunysb.edu (Kostas Pentikousis) Date: Mon Aug 2 21:37:45 2004 Subject: [sb.pm] Design Issues (was: When should we meet next?) In-Reply-To: <407F04AB.3020208@i-2000.com> References: <406269D3.4060504@i-2000.com> <406C79EC.4060005@i-2000.com> <407174CA.60102@pharm.sunysb.edu> <4074248A.5060003@i-2000.com> <407D8CFD.1090308@pharm.sunysb.edu> <407F04AB.3020208@i-2000.com> Message-ID: On Thu, 15 Apr 2004, Robert Rothenberg wrote: |On 4/14/2004 3:11 PM Siddhartha Basu wrote: |> * What will be a good approach for taking inputs for a program specially |> if i want to run it from a cron job. |> * From the command line by using @ARGV or Getopt::Long. |> * Or by setting environmental variables and accessing from $ENV |> hash. |> Right now, i have mix of both but it is becoming cumbersome and i am |> thinking about having settling down with one approach. I do not use ENV variables. The main reason is that you need to document how and when they are used. And you pollute one's environment regardless if s/he uses the program or not. If you are concerned about code maintenance, in particular if you want other people use your code, avoid ENV variables. Command line arguments also need documentation, but if a new-comer in your lab asks to use your code, you do not need to start explaining ENV settings and such (what if bash, what if csh, what if windows?). With command line options, you only need to email her the command line. |I'd use command-line arguments, since it's easier to pass arguments to when |running the scripts as one-shots. If you have several true/false switches, command line arguments are probably the best way to go (esp. for a cron job). If you also assign default values in your code, then the switches are needed only for "exceptional cases" (possibly making the cron entry considerably shorter). If, on the other hand, each option needs a value, then having 8 switches and 10 value-pairs gets kind of ugly, no? I would consider using default values in the code and a configuration file. Configuration files are pretty standard in Unix/Linux, and you can also use them without a problem on Windows (no need to start playing with the registry), should you decide to run your code there as well. Configuration files are easy to document (and you just need to attach them in the aforementioned email to the new-comer), and can be created/updated on the fly, even just before the main program is called. If you feel that many parameters are pretty standard, take advantage of the __DATA__ section strategically located at the end of your Perl code. This way, you keep default values and code together, eliminating the need for "code.pl" and "code.config". In sum, always use default values, don't worry if you only have too many on/off command line options, and consider (if you have more than a dozen parameters) reading defaults from a configuration file. |> column and then check whether the data in that column is present in |> another text file. So, my approach is to either read the second text | |BioPerl has some flat database file drivers. DBD::CSV, DBD::Sprite or |DBD::File might provide some DBI drivers to handle flat files and simplify |your work. I personally like CSV: it's text, portable and you can import it to almost anything (from spreadsheets to DBs, even to plotting applications). Of course, CSVs are extremely easy to handle in Perl (with or without CPAN modules) |> Nothing else comes to my mind at this moment so i am dealing with a |> bunch of scattared scripts. I would consider putting the balk of the code in a module. It will simplify usage (the scripts will contain a few module function calls), centralize the code, and you may even consider uploading it to CPAN :) |Where are these text files coming from that they are in different formats? | |> * What kind of format should i use for writing log file. Flat text file |> or xml format. | |I'd avoid XML like the plague, unless you need to pass the logs to a program |which requires it in XML. I'd prefer plain text, possibly CSV. However, XML is not the plague :) and it's not a bad idea if you move the logs around from one application to another. Besides, XML can render the logs self-documenting. If you decide to use it, avoid manual XML generation. Use a standard CPAN module for reading and writing. |Do you really need sophisticated markup for a log file? Not really, at least for the garden variety log file. Just my $0.02. Best regards, Kostas