Re^2: bioperl newbie's question: simple GFF3 peocessing

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Re^3: bioperl newbie's question: simple GFF3 peocessing by BrowserUk (Patriarch) on Jul 31, 2010 at 09:18 UTC
Well first your read a line of the file; then parse it into the nine fields; and the test the 9th column for a 'locus_tag=', using index or a regex. If it contains one, store the record in an array or to another file.	[reply]
Re^4: bioperl newbie's question: simple GFF3 peocessing by daverave (Scribe) on Jul 31, 2010 at 09:22 UTC
thank you, but I think it might be wasteful given that this is a standard file format supported by bioperl. I got some help from this: http://doc.bioperl.org/releases/bioperl-1.0.1/Bio/SeqFeatureI.html, I hope I will get it right.	[reply]
Re^5: bioperl newbie's question: simple GFF3 peocessing by BrowserUk (Patriarch) on Jul 31, 2010 at 09:40 UTC
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	[reply] [d/l]
Re^6: bioperl newbie's question: simple GFF3 peocessing by daverave (Scribe) on Jul 31, 2010 at 09:48 UTC
Re^7: bioperl newbie's question: simple GFF3 peocessing by BrowserUk (Patriarch) on Jul 31, 2010 at 10:12 UTC