Inconsistent Ordering of exon_number attribute in introns
mbiokyle29 opened this issue · comments
Not sure this is technically a bug, but something that could cause issues. I noticed an inconsistency with the ordering of values in the exon_number attribute in introns (generated from create_introns). For most introns, the exon_number field will contain a list like ["1", "2"]. The idea being that this intron occurs after exon 1 and before exon 2, and is therefore "intron 1". This holds for all introns until the intron spanning exon 9 -> exon 10. The sorting is done using strings (at least based on how its formatted in an NCBI gtf). "10" will sort before "9", and thus the result will be ["10", "9"].
Example:
# all BCRA2 exons from GCF_000001405.39_GRCh38.p13_genomic.gtf
NC_000013.11 BestRefSeq exon 32315508 32315667 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "1";
NC_000013.11 BestRefSeq exon 32316422 32316527 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "2";
NC_000013.11 BestRefSeq exon 32319077 32319325 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "3";
NC_000013.11 BestRefSeq exon 32325076 32325184 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "4";
NC_000013.11 BestRefSeq exon 32326101 32326150 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "5";
NC_000013.11 BestRefSeq exon 32326242 32326282 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "6";
NC_000013.11 BestRefSeq exon 32326499 32326613 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "7";
NC_000013.11 BestRefSeq exon 32329443 32329492 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "8";
NC_000013.11 BestRefSeq exon 32330919 32331030 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "9";
NC_000013.11 BestRefSeq exon 32332272 32333387 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "10";
NC_000013.11 BestRefSeq exon 32336265 32341196 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "11";
NC_000013.11 BestRefSeq exon 32344558 32344653 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "12";
NC_000013.11 BestRefSeq exon 32346827 32346896 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "13";
NC_000013.11 BestRefSeq exon 32354861 32355288 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "14";
NC_000013.11 BestRefSeq exon 32356428 32356609 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "15";
NC_000013.11 BestRefSeq exon 32357742 32357929 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "16";
NC_000013.11 BestRefSeq exon 32362523 32362693 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "17";
NC_000013.11 BestRefSeq exon 32363179 32363533 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "18";
NC_000013.11 BestRefSeq exon 32370402 32370557 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "19";
NC_000013.11 BestRefSeq exon 32370956 32371100 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "20";
NC_000013.11 BestRefSeq exon 32376670 32376791 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "21";
NC_000013.11 BestRefSeq exon 32379317 32379515 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "22";
NC_000013.11 BestRefSeq exon 32379750 32379913 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "23";
NC_000013.11 BestRefSeq exon 32380007 32380145 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "24";
NC_000013.11 BestRefSeq exon 32394689 32394933 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "25";
NC_000013.11 BestRefSeq exon 32396898 32397044 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "26";
NC_000013.11 BestRefSeq exon 32398162 32400268 . + . gene_id "BRCA2"; transcript_id "NM_000059.4"; db_xref "Ensembl:ENST00000380152.8"; db_xref "GeneID:675"; gene "BRCA2"; product "BRCA2 DNA repair associated"; tag "MANE Select"; transcript_biotype "mRNA"; exon_number "27";
Code:
import gffutils
db_filename = 'brca2_bug.db'
feature_db = gffutils.create_db(
'brca2.gtf',
db_filename,
merge_strategy='warning',
)
introns = [f for f in feature_db.create_introns()]
[i.attributes['exon_number'] for i in introns]
Out[12]:
[['1', '2'],
['2', '3'],
['3', '4'],
['4', '5'],
['5', '6'],
['6', '7'],
['7', '8'],
['8', '9'],
['10', '9'], # <---- this is the issue
['10', '11'],
['11', '12'],
['12', '13'],
['13', '14'],
['14', '15'],
['15', '16'],
['16', '17'],
['17', '18'],
['18', '19'],
['19', '20'],
['20', '21'],
['21', '22'],
['22', '23'],
['23', '24'],
['24', '25'],
['25', '26'],
['26', '27']]I think the issue is here:
Line 333 in 4b5b28e
Might be tricky to get this to work in all cases, but seems like you could check str.isdigit on each item in v. If all are true, cast to int for the sorting, then cast back to string. Perhaps enable this via a flag.
Now addressed in v0.11.