Extract longest mRNA from .GFF when I have multiple rows of same seqID

Question

[todd.ugine]

Hello,

I have a GFF file that has multiple rows for each seqID.

Using python:

I want to extract the longest mRNA sequence for each seqID and return in a new tab-delimited file

<seqID> <start> <end>

The original GFF is formatted as follows

<seqid><SOURCE><FEATURE><START><END><SCORE><STRAND><FRAME><ATTRIBUTES><COMMENTS>

I'm very new to this and could use a hand for what is likely easy for someone with more experience.

Thanks for any help you can provide, and I'm not likely able to successfully modify someone else script appropriately

[Ram]

1. This post is a Question type post, not a Forum type post. I've made the necessary change but please be more careful in the future. Reading posts under the how-to tag will help.

2. Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.
   

3. Please avoid the use of emojis and such in a professional/scientific setting.

Answer 1

[GouthamAtla]

There are some GTF parsers in python. For example pyGTF by which you can get the length of seqIDs or try to get a bed file of seqIDs and use groupBy to get the first/last coordinates and then get length. If you provide head of your file, we could help a bit further.

Answer 2

[todd.ugine]

Thanks for your help. This was my first-ever post. I'll be sure to put things in the appropriate place moving forward. Should the head portion of this post be considered code?

##gff-version 3
BHEC01006359.1  .   contig  1   807 .   .   .   ID=BHEC01006359.1;Name=BHEC01006359.1
###
BHEC01012377.1  .   contig  1   805 .   .   .   ID=BHEC01012377.1;Name=BHEC01012377.1
###
BHEC01004863.1  .   contig  1   8509    .   .   .   ID=BHEC01004863.1;Name=BHEC01004863.1
BHEC01004863.1  snap_masked match   4053    8297    29.048  +   .   ID=BHEC01004863.1:hit:1841:4.5.0.0;Name=snap_masked-BHEC01004863.1-abinit-gene-0.1-mRNA-1
BHEC01004863.1  snap_masked match_part  4053    4314    12.637  +   .   ID=BHEC01004863.1:hsp:6435:4.5.0.0;Parent=BHEC01004863.1:hit:1841:4.5.0.0;Target=snap_masked-BHEC01004863.1-abinit-gene-0.1-mRNA-1 1 262 +;Gap=M262
BHEC01004863.1  snap_masked match_part  8263    8297    16.411  +   .   ID=BHEC01004863.1:hsp:6436:4.5.0.0;Parent=BHEC01004863.1:hit:1841:4.5.0.0;Target=snap_masked-BHEC01004863.1-abinit-gene-0.1-mRNA-1 263 297 +;Gap=M35
BHEC01004863.1  augustus_masked match   4055    4327    0.83    +   .   ID=BHEC01004863.1:hit:1842:4.5.0.0;Name=augustus_masked-BHEC01004863.1-abinit-gene-0.0-mRNA-1
BHEC01004863.1  augustus_masked match_part  4055    4327    0.83    +   .   ID=BHEC01004863.1:hsp:6437:4.5.0.0;Parent=BHEC01004863.1:hit:1842:4.5.0.0;Target=augustus_masked-BHEC01004863.1-abinit-gene-0.0-mRNA-1 1 273 +;Gap=M273
###
BHEC01004863.1  est_gff:est2genome  expressed_sequence_match    8071    8351    805 -   .   ID=BHEC01004863.1:hit:1840:3.12.0.0;Name=Csept_BB_C55352;score=805
BHEC01004863.1  est_gff:est2genome  match_part  8071    8351    805 -   .   ID=BHEC01004863.1:hsp:6434:3.12.0.0;Parent=BHEC01004863.1:hit:1840:3.12.0.0;Target=Csept_BB_C55352 7 284 +;Gap=M281
BHEC01053345.1  .   contig  1   2142    .   .   .   ID=BHEC01053345.1;Name=BHEC01053345.1
###
BHEC01052641.1  .   contig  1   803 .   .   .   ID=BHEC01052641.1;Name=BHEC01052641.1
###
BHEC01000922.1  .   contig  1   1466    .   .   .   ID=BHEC01000922.1;Name=BHEC01000922.1
###
BHEC01008444.1  .   contig  1   9527    .   .   .   ID=BHEC01008444.1;Name=BHEC01008444.1
BHEC01008444.1  snap_masked match   3239    9054    54.086  +   .   ID=BHEC01008444.1:hit:1739:4.5.0.0;Name=snap_masked-BHEC01008444.1-abinit-gene-0.1-mRNA-1
BHEC01008444.1  snap_masked match_part  3239    3312    11.140  +   .   ID=BHEC01008444.1:hsp:6367:4.5.0.0;Parent=BHEC01008444.1:hit:1739:4.5.0.0;Target=snap_masked-BHEC01008444.1-abinit-gene-0.1-mRNA-1 1 74 +;Gap=M74
BHEC01008444.1  snap_masked match_part  5275    5320    11.772  +   .   ID=BHEC01008444.1:hsp:6368:4.5.0.0;Parent=BHEC01008444.1:hit:1739:4.5.0.0;Target=snap_masked-BHEC01008444.1-abinit-gene-0.1-mRNA-1 75 120 +;Gap=M46
BHEC01008444.1  snap_masked match_part  5469    5541    6.534   +   .   ID=BHEC01008444.1:hsp:6369:4.5.0.0;Parent=BHEC01008444.1:hit:1739:4.5.0.0;Target=snap_masked-BHEC01008444.1-abinit-gene-0.1-mRNA-1 121 193 +;Gap=M73
BHEC01008444.1  snap_masked match_part  8183    8261    10.882  +   .   ID=BHEC01008444.1:hsp:6370:4.5.0.0;Parent=BHEC01008444.1:hit:1739:4.5.0.0;Target=snap_masked-BHEC01008444.1-abinit-gene-0.1-mRNA-1 194 272 +;Gap=M79
BHEC01008444.1  snap_masked match_part  9024    9054    13.758  +   .   ID=BHEC01008444.1:hsp:6371:4.5.0.0;Parent=BHEC01008444.1:hit:1739:4.5.0.0;Target=snap_masked-BHEC01008444.1-abinit-gene-0.1-mRNA-1 273 303 +;Gap=M31
BHEC01008444.1  snap_masked match   7114    7425    -11.831 -   .   ID=BHEC01008444.1:hit:1740:4.5.0.0;Name=snap_masked-BHEC01008444.1-abinit-gene-0.2-mRNA-1
BHEC01008444.1  snap_masked match_part  7114    7425    -11.831 -   .   ID=BHEC01008444.1:hsp:6372:4.5.0.0;Parent=BHEC01008444.1:hit:1740:4.5.0.0;Target=snap_masked-BHEC01008444.1-abinit-gene-0.2-mRNA-1 1 312 +;Gap=M312
BHEC01008444.1  augustus_masked match   7114    7425    0.52    -   .   ID=BHEC01008444.1:hit:1741:4.5.0.0;Name=augustus_masked-BHEC01008444.1-abinit-gene-0.0-mRNA-1
BHEC01008444.1  augustus_masked match_part  7114    7425    0.52    -   .   ID=BHEC01008444.1:hsp:6373:4.5.0.0;Parent=BHEC01008444.1:hit:1741:4.5.0.0;Target=augustus_masked-BHEC01008444.1-abinit-gene-0.0-mRNA-1 1 312 +;Gap=M312