in reply to Re^2: bioperl newbie's question: simple GFF3 peocessing
in thread bioperl newbie's question: simple GFF3 peocessing

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.

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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]
      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.
[reply]
[d/l]
        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]

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