gff file containing "fasta" section raises an error

[adirot]

• pandasgff version:
• Python version: 3.7
• Operating System: ubuntu

Description

I have a gff file containing a section starting with "##FASTA". gffpd.read_gff3 raises an error on it.
When I delete the section after "##FASTA" the function gffpd.read_gff3 works, so it looks like an easy to fix issue.
Thank you for this code!

The file that works:
##gff-version 3 ##source-version geneious 2020.2.2 ##sequence-region pZA21RVapCmCherry 1 4048 pZA21RVapCmCherry Geneious region 1 4048 . + 0 Is_circular=true pZA21RVapCmCherry Geneious exon 2327 3046 . - . Name=tetR pZA21RVapCmCherry Geneious exon 3043 3837 . - . Name=KanR pZA21RVapCmCherry Geneious exon 109 510 . + . Name=vapC pZA21RVapCmCherry Geneious exon 494 1237 . + . Name=mCherry

the file that does not work:

`##gff-version 3
##source-version geneious 2020.2.2
##sequence-region pZA21RVapCmCherry 1 4048
pZA21RVapCmCherry Geneious region 1 4048 . + 0 Is_circular=true
pZA21RVapCmCherry Geneious exon 2327 3046 . - . Name=tetR
pZA21RVapCmCherry Geneious exon 3043 3837 . - . Name=KanR
pZA21RVapCmCherry Geneious exon 109 510 . + . Name=vapC
pZA21RVapCmCherry Geneious exon 494 1237 . + . Name=mCherry
##FASTA

pZA21RVapCmCherry
CTCGAGTCCCTATCAGTGATAGAGATTGACATCCCTATCA
GTGATAGAGATACTGAGCACATCAGCAGGACGCACTGACC
GAATTCGACATATCCACATAAGGAGGCACTGATGCTGAAG
TTTATGCTCGATACCAACATCTGCATTTTTACGATAAAGA
ACAAACCCGCCAGTGTCAGGGAACGTTTTAACCTGAACCA
GGGGAGAATGTGCATCAGTTCGGTCACTCTGATGGAGGTG
ATATATGGTGCAGAAAAAAGCCAGATGCCTGAACGTAATC
TCGCTGTGATCGAGGGATTTGTTTCCCGCATTGACGTTCT
GGATTACGACGCTGCTGCTGCCACACACACCGGCCAGATA
AGAGCAGAACTTGCCCTTCAGGGACGCCCTGTCGGGCCAT
TTGATCAAATGATCGCAGGTCATGCCCGCAGTCGGGGACT
GATTATTGTGACTAATAACACCCGGGAATTTGAACGTGTG
GGCGGCCTGAGAATTGAAGACTGGAGTTGACCTGTTAGGA
GGTACCATGGTGAGCAAGGGCGAGGAGGATAACATGGCCA
TCATCAAGGAGTTCATGCGCTTCAAGGTGCACATGGAGGG
CTCCGTGAACGGCCACGAGTTCGAGATCGAGGGCGAGGGC
GAGGGCCGCCCCTACGAGGGCACCCAGACCGCCAAGCTGA
AGGTGACCAAGGGTGGCCCCCTGCCCTTCGCCTGGGACAT
CCTGTCCCCTCAGTTCATGTACGGCTCCAAGGCCTACGTG
AAGCACCCCGCCGACATCCCCGACTACTTGAAGCTGTCCT
TCCCCGAGGGCTTCAAGTGGGAGCGCGTGATGAACTTCGA
GGACGGCGGCGTGGTGACCGTGACCCAGGACTCCTCCCTG
CAGGACGGCGAGTTCATCTACAAGGTGAAGCTGCGCGGCA
CCAACTTCCCCTCCGACGGCCCCGTAATGCAGAAGAAGAC
CATGGGCTGGGAGGCCTCCTCCGAGCGGATGTACCCCGAG
GACGGCGCCCTGAAGGGCGAGATCAAGCAGAGGCTGAAGC
TGAAGGACGGCGGCCACTACGACGCTGAGGTCAAGACCAC
CTACAAGGCCAAGAAGCCCGTGCAGCTGCCCGGCGCCTAC
AACGTCAACATCAAGTTGGACATCACCTCCCACAACGAGG
ACTACACCATCGTGGAACAGTACGAACGCGCCGAGGGCCG
CCACTCCACCGGCGGCATGGACGAGCTGTACAAGTAAAAG
CTTAATTAGCTGAGTCTAGAGGCATCAAATAAAACGAAAG
GCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTT
TGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGCC
CTAGACCTAGGGGATATATTCCGCTTCCTCGCTCACTGAC
TCGCTACGCTCGGTCGTTCGACTGCGGCGAGCGGAAATGG
CTTACGAACGGGGCGGAGATTTCCTGGAAGATGCCAGGAA
GATACTTAACAGGGAAGTGAGAGGGCCGCGGCAAAGCCGT
TTTTCCATAGGCTCCGCCCCCCTGACAAGCATCACGAAAT
CTGACGCTCAAATCAGTGGTGGCGAAACCCGACAGGACTA
TAAAGATACCAGGCGTTTCCCCCTGGCGGCTCCCTCGTGC
GCTCTCCTGTTCCTGCCTTTCGGTTTACCGGTGTCATTCC
GCTGTTATGGCCGCGTTTGTCTCATTCCACGCCTGACACT
CAGTTCCGGGTAGGCAGTTCGCTCCAAGCTGGACTGTATG
CACGAACCCCCCGTTCAGTCCGACCGCTGCGCCTTATCCG
GTAACTATCGTCTTGAGTCCAACCCGGAAAGACATGCAAA
AGCACCACTGGCAGCAGCCACTGGTAATTGATTTAGAGGA
GTTAGTCTTGAAGTCATGCGCCGGTTAAGGCTAAACTGAA
AGGACAAGTTTTGGTGACTGCGCTCCTCCAAGCCAGTTAC
CTCGGTTCAAAGAGTTGGTAGCTCAGAGAACCTTCGAAAA
ACCGCCCTGCAAGGCGGTTTTTTCGTTTTCAGAGCAAGAG
ATTACGCGCAGACCAAAACGATCTCAAGAAGATCATCTTA
TTAATCAGATAAAATATTTCTAGATTTCAGTGCAATTTAT
CTCTTCAAATGTAGCACCTGAAGTCAGCCCCATACGATAT
AAGTTGTTACTAGTGCTTGGATTCTCACCAATAAAAAACG
CCCGGCGGCAACCGAGCGTTCTGAACAAATCCAGATGGAG
TTCTGAGGTCATTACTGGATCTATCAACAGGAGTCCAAGC
GAGCTCTAGCTCTAGGCTACTCAGCTATCTAGAAAGCTTA
AGATCCTTAAGACCCACTTTCACATTTAAGTTGTTTTTCT
AATCCGCATATGATCAATTCAAGGCCGAATAAGAAGGCTG
GCTCTGCACCTTGGTGATCAAATAATTCGATAGCTTGTCG
TAATAATGGCGGCATACTATCAGTAGTAGGTGTTTCCCTT
TCTTCTTTAGCGACTTGATGCTCTTGATCTTCCAATACGC
AACCTAAAGTAAAATGCCCCACAGCGCTGAGTGCATATAA
TGCATTCTCTAGTGAAAAACCTTGTTGGCATAAAAAGGCT
AATTGATTTTCGAGAGTTTCATACTGTTTTTCTGTAGGCC
GTGTACCTAAATGTACTTTTGCTCCATCGCGATGACTTAG
TAAAGCACATCTAAAACTTTTAGCCTTATTACGTAAAAAA
TCTTGCCAGCTTTCCCCTTCTAAAGGGCAAAAGTGAGTAT
GGTGCCTATCTAACATCTCAATGGCTAAGGCGTCGAGCAA
AGCCCGCTTATTTTTTACATGCCAATACAATGTAGGCTGC
TCTACACCTAGCTTCTGGGCGAGTTTACGGGTTGTTAAAC
CTTCGATTCCGACCTCATTAAGCAGCTCTAATGCGCTGTT
AATCACTTTACTTTTATCTAATCTAGACATATGAATTCGG
GGCGGGATTTCATGGATATGTTTCTTTCTGCGAGAACCAG
CCATATCAGTACCTCCTGAGCTCTCGAACCCCAGAGTCCC
GCTCAGAAGAACTCGTCAAGAAGGCGATAGAAGGCGATGC
GCTGCGAATCGGGAGCGGCGATACCGTAAAGCACGAGGAA
GCGGTCAGCCCATTCGCCGCCAAGCTCTTCAGCAATATCA
CGGGTAGCCAACGCTATGTCCTGATAGCGGTCCGCCACAC
CCAGCCGGCCACAGTCGATGAATCCAGAAAAGCGGCCATT
TTCCACCATGATATTCGGCAAGCAGGCATCGCCATGGGTC
ACGACGAGATCCTCGCCGTCGGGCATGCGCGCCTTGAGCC
TGGCGAACAGTTCGGCTGGCGCGAGCCCCTGATGCTCTTC
GTCCAGATCATCCTGATCGACAAGACCGGCTTCCATCCGA
GTACGTGCTCGCTCGATGCGATGTTTCGCTTGGTGGTCGA
ATGGGCAGGTAGCCGGATCAAGCGTATGCAGCCGCCGCAT
TGCATCAGCCATGATGGATACTTTCTCGGCAGGAGCAAGG
TGAGATGACAGGAGATCCTGCCCCGGCACTTCGCCCAATA
GCAGCCAGTCCCTTCCCGCTTCAGTGACAACGTCGAGCAC
AGCTGCGCAAGGAACGCCCGTCGTGGCCAGCCACGATAGC
CGCGCTGCCTCGTCCTGCAGTTCATTCAGGGCACCGGACA
GGTCGGTCTTGACAAAAAGAACCGGGCGCCCCTGCGCTGA
CAGCCGGAACACGGCGGCATCAGAGCAGCCGATTGTCTGT
TGTGCCCAGTCATAGCCGAATAGCCTCTCCACCCAAGCGG
CCGGAGAACCTGCGTGCAATCCATCTTGTTCAATCATGCG
AAACGATCCTCATCCTGTCTCTTGATCAGATCTTGATCCC
CTGCGCCATCAGATCCTTGGCGGCAAGAAAGCCATCCAGT
TTACTTTGCAGGGCTTCCCAACCTTACCAGAGGGCGCCCC
AGCTGGCAATTCCGACGTCTAAGAAACCATTATTATCATG
ACATTAACCTATAAAAATAGGCGTATCACGAGGCCCTTTC
GTCTTCAC
working.gff.txt
not_working.gff.txt
`

What I Did

Paste the command(s) you ran and the output.
If there was a crash, please include the traceback here.

[elhossary]

Thanks for pointing us to this issue, It is handled in the upcoming release