How to write a python code Filtering gff file by gen list as input.

Question

[RunCoderRun]

I have a list of Genes (Ensemble ids). I want to filter the gff file based on the genes I give as input. My first idea was to use the 9th column "attributes" because the gene_id=ENSG0...... information is there.but I couldn't quite figure out how to handle it according to column 9.

Here is the first few lines of a GTF file.

##gff-version 3
1   havana  pseudogene  11869   14409   .   +   .   ID=gene:ENSG00000223972;Name=DDX11L1;biotype=transcribed_unprocessed_pseudogene;description=DEAD/H-box helicase 11 like 1 (pseudogene) [Source:HGNC Symbol%3BAcc:HGNC:37102];gene_id=ENSG00000223972;logic_name=havana_homo_sapiens;version=5
1   havana  lnc_RNA 11869   14409   .   +   .   ID=transcript:ENST00000456328;Parent=gene:ENSG00000223972;Name=DDX11L1-202;biotype=processed_transcript;tag=basic;transcript_id=ENST00000456328;transcript_support_level=1;version=2
1   havana  exon    11869   12227   .   +   .   Parent=transcript:ENST00000456328;Name=ENSE00002234944;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00002234944;rank=1;version=1
1   havana  exon    12613   12721   .   +   .   Parent=transcript:ENST00000456328;Name=ENSE00003582793;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00003582793;rank=2;version=1
1   havana  exon    13221   14409   .   +   .   Parent=transcript:ENST00000456328;Name=ENSE00002312635;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00002312635;rank=3;version=1
1   havana  pseudogenic_transcript  12010   13670   .   +   .   ID=transcript:ENST00000450305;Parent=gene:ENSG00000223972;Name=DDX11L1-201;biotype=transcribed_unprocessed_pseudogene;tag=basic;transcript_id=ENST00000450305;transcript_support_level=NA;version=2 
1   ensembl_havana  gene    215567304   215621807   .   +   .   ID=gene:ENSG00000136636;Name=KCTD3;biotype=protein_coding;description=potassium channel tetramerization domain containing 3 [Source:HGNC Symbol%3BAcc:HGNC:21305];gene_id=ENSG00000136636;logic_name=ensembl_havana_gene_homo_sapiens;version=13
1   ensembl_havana  mRNA    215567304   215621807   .   +   .   ID=transcript:ENST00000259154;Parent=gene:ENSG00000136636;Name=KCTD3-201;biotype=protein_coding;ccdsid=CCDS1515.1;tag=basic;transcript_id=ENST00000259154;transcript_support_level=1 (assigned to previous version 8);version=9

I got the GFF file from here Ensembl FTP site (for the homo sapiens)

Answer 1

[Juke34]

It sounds like an homework. You can use gffutils or BCBio to manipulate GFF ni Python. Otherwise there are tools ready to use like agat_sp_filter_feature_from_keep_list.pl from AGAT (in Perl).

[RunCoderRun]

My files are large and my code is doing different operations simultaneously with this operation. The 9th column filtering method was a bit rudimentary or I was wondering how I could make this process more practical. To use ram and processor more efficiently. Thank you for your kind response