Re^5: bioperl newbie's question: simple GFF3 peocessing

thank you, but I think it might be wasteful given that this is a standard file format supported by bioperl.

I'll bet you a pound to a penny that it will take you longer to write; be far harder to maintain; and run more slowly; than this:

c:\test>perl -F"\t" -ane"$F[8]=~/Gap=/ and print" chromosome_1.gff
DDB0232428      .       EST_match       15809   17104   .       +     
+  .       ID=DDB0014588;Target=DDB0014588 1 561;Gap=M405 I786 M104
DDB0232428      .       EST_match       66374   66803   .       +     
+  .       ID=DDB0014789;Target=DDB0014789 1 339;Gap=M96 I111 M222
DDB0232428      .       EST_match       117098  117584  .       -     
+  .       ID=DDB0017340;Target=DDB0017340 1 492;Gap=M486
DDB0232428      .       EST_match       122479  123082  .       +     
+  .       ID=DDB0041612;Target=DDB0041612 1 619;Gap=M603
DDB0232428      .       EST_match       162661  163197  .       -     
+  .       ID=DDB0017341;Target=DDB0017341 1 558;Gap=M536
DDB0232428      .       EST_match       162661  162971  .       -     
+  .       ID=DDB0161652;Target=DDB0161652 1 319;Gap=M310
DDB0232428      .       EST_match       162670  163422  .       +     
+  .       ID=DDB0127927;Target=DDB0127927 1 752;Gap=M752
DDB0232428      .       EST_match       162670  163375  .       +     
+  .       ID=DDB0112861;Target=DDB0112861 1 705;Gap=M705
DDB0232428      .       EST_match       162670  163335  .       +     
+  .       ID=DDB0031935;Target=DDB0031935 1 652;Gap=M26 I18 M621
DDB0232428      .       EST_match       162670  163285  .       +     
+  .       ID=DDB0061852;Target=DDB0061852 1 615;Gap=M615
DDB0232428      .       EST_match       162670  163398  .       +     
+  .       ID=DDB0117238;Target=DDB0117238 1 729;Gap=M728
DDB0232428      .       EST_match       162670  163308  .       +     
+  .       ID=DDB0061789;Target=DDB0061789 1 639;Gap=M638
DDB0232428      .       EST_match       162670  163378  .       +     
+  .       ID=DDB0067313;Target=DDB0067313 1 707;Gap=M708
DDB0232428      .       EST_match       162670  163402  .       +     
+  .       ID=DDB0064238;Target=DDB0064238 1 732;Gap=M732
DDB0232428      .       EST_match       162670  163430  .       +     
+  .       ID=DDB0063928;Target=DDB0063928 1 760;Gap=M760
DDB0232428      .       EST_match       162671  163372  .       +     
+  .       ID=DDB0126764;Target=DDB0126764 1 700;Gap=M701
DDB0232428      .       EST_match       162675  163332  .       +     
+  .       ID=DDB0028393;Target=DDB0028393 1 663;Gap=M657
DDB0232428      .       EST_match       162687  163332  .       +     
+  .       ID=DDB0065179;Target=DDB0065179 1 661;Gap=M645
DDB0232428      .       EST_match       162699  163215  .       -     
+  .       ID=DDB0018629;Target=DDB0018629 1 524;Gap=M516
[download]

That's a real GGF file downloaded from the web. It didn't have "locus_tag" tags, so I used "Gap", but it took longer to find the file than parse it.

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.

"Science is about questioning the status quo. Questioning authority".

In the absence of evidence, opinion is indistinguishable from prejudice.

RIP an inspiration; A true Folk's Guy

Comment on Re^5: bioperl newbie's question: simple GFF3 peocessing Download Code

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Re^6: bioperl newbie's question: simple GFF3 peocessing by daverave (Scribe) on Jul 31, 2010 at 09:48 UTC
You're probably right, but this will once again make me skip learning a bit if bioperl. I think I already mentioned this in the past, but learning new stuff is something I enjoy, although in the short run it might sometimes take longer than using techniques I already know. Thanks for the help though, I do appreciate it.	[reply]
Re^7: bioperl newbie's question: simple GFF3 peocessing by BrowserUk (Patriarch) on Jul 31, 2010 at 10:12 UTC
Hm. Long ago in my Mech.Eng. days, I spent 4 hours setting up a radial grinder to radius the egde of a push-fit spigot. The instructor watched from the other side of the shop until I got everything perfect and was putting my safety glasses on before coming over. Without saying a word he took the spigot out of the chuck, thereby complete screwing all the set-up work I'd done. I nearly had apoplexy. He then walked over to a bench, mounted it in a standard vice, picked up a fine file and radiused the edge with about six gentle strokes of the file. Job done. The lesson was that it was the taper on the spigot that required +0-0.0004" accuracy. The radius on the end is simply to stop it from binding in the hole. Expend your time wisely, and choose tools that are fit for purpose. Filtering a subset of line records from a text file is a bread&butter, simple Perl problem, regardless of whether it contains last week football scores or top-secret NBC Bio data. Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error. "Science is about questioning the status quo. Questioning authority". In the absence of evidence, opinion is indistinguishable from prejudice. RIP an inspiration; A true Folk's Guy	[reply]