Almost...
Hi Simon.
First of all, thank you very much!!!
Second:
Apparently, it worked. It was an ; extra in a pair of lines so it continues reading everything just until it arrives to the #fasta part:
htseq-count -s no -i ID s_1_sequence_clipped_tophat.bam TbruceiTreu927_TriTrypDB-3.3.3.gff
Error occured in line 46748 of file TbruceiTreu927_TriTrypDB-3.3.3.gff.
Error: need more than 1 value to unpack
[Exception type: ValueError, raised in __init__.py:214]
And when I look at this line this is what I can see:
tryp_XI-1036e06.p1k.snoRNA.0004;Dbxref=ApiDB:tryp_XI-1036e06.p1k.snoRNA.0004,taxon:185431
apidb|tryp_XI-1036e06.p1k ApiDB exon 22123 22200 . + . ID=apidb|exon_tryp_XI-1036e06.p1k.snoRNA.0004-1;Name=exon;description=exon;size=78;Parent=apidb|rna_tryp_XI-1036e06.p1k.snoRNA.0004-1
(This is line 46748)##FASTA
>apidb|TB927.5.300b
ATGGCTCACGGCTCGATTCCAGTTATTGATGTCGGCCCTCTGTTCTGTGATGGAGAAAAG
GGGATGATGGATGTTGCGAAACAGATTGATCATGCCTGTAGGACGTGGGGTGTTTTTCTT
GTTGTGGGTCATCCCATTCCCCGTGAGCGAACGGAAAAGTTGATGGAAATGGCCAAGGCT
TTTTTTTCGCTTCCATTGGAAGAGAAACTTAAGGTTGATATTCGAAAGAGCAAACATCAT
CGCGGTTACGGATGCCTCGATGCGGAGAATGTTGACCCAACGAAACCATTTGATTGTAAA
GAAACATTTAATATGGGCTGTCATCTCCCTGAGGATCACCCCGATGTTGCAGCTGGAAAG
CCATTGCGTGGACCGAACAATCACCCCACGCAAGTGAAAGGTTGGGTAGAGTTGATGAAC
AGACATTATCGCGAAATGCAGGAATTTGCCCTCGTTATTCTTCGTGCCCTCGCACTCGCT
ATTGGTTTAAAGAAAGACTTTTTCGATACCAAATTTGATGAACCTTTGAGTGTGTTCCGT
ATGCTACATTATCCTCCACAAAAGCAAGGGACCCGTTATCCCATCGTGTGTGGTGAGCAT
ACGGATTATGGTATTATTACATTACTCTACCAAGATTCGGTGGGAGGACTGCAGGTGCGC
AATCTGTCAGATGAGTGGGTGGATGTGGAACCCCTTGAAGGAAGTTTTGTTGTGAATATT
GGGGACATGATGAATATGTGGAGTAATGGCCGTTACCGCTCAACACCGCATCGCGTTCGC
TTAACCACAACTGATCGCTACTCCATGCCATTTTTCTGTCAGCCTAATCCTTATACTGTT
ATTAAATGCCTTGATCATTGCCATTCGCCAAGCAATCCCCCCAAATATCCACCAGTCCGT
GCTGTGGATTGGTTGCTGAAGCGTTTCGCGGAAACATATGCCCATCGCAAAACAAAGATG
TGA
>apidb|cds_TB927.5.300b-1
MAHGSIPVIDVGPLFCDGEKGMMDVAKQIDHACRTWGVFLVVGHPIPRERTEKLMEMAKA
FFSLPLEEKLKVDIRKSKHHRGYGCLDAENVDPTKPFDCKETFNMGCHLPEDHPDVAAGK
PLRGPNNHPTQVKGWVELMNRHYREMQEFALVILRALALAIGLKKDFFDTKFDEPLSVFR
MLHYPPQKQGTRYPIVCGEHTDYGIITLLYQDSVGGLQVRNLSDEWVDVEPLEGSFVVNI
GDMMNMWSNGRYRSTPHRVRLTTTDRYSMPFFCQPNPYTVIKCLDHCHSPSNPPKYPPVR
AVDWLLKRFAETYAHRKTKM
Why does htseq-count gives now an error?
Again, thanks for all!
Sandra
Hi Simon.
First of all, thank you very much!!!
Second:
Apparently, it worked. It was an ; extra in a pair of lines so it continues reading everything just until it arrives to the #fasta part:
htseq-count -s no -i ID s_1_sequence_clipped_tophat.bam TbruceiTreu927_TriTrypDB-3.3.3.gff
Error occured in line 46748 of file TbruceiTreu927_TriTrypDB-3.3.3.gff.
Error: need more than 1 value to unpack
[Exception type: ValueError, raised in __init__.py:214]
And when I look at this line this is what I can see:
tryp_XI-1036e06.p1k.snoRNA.0004;Dbxref=ApiDB:tryp_XI-1036e06.p1k.snoRNA.0004,taxon:185431
apidb|tryp_XI-1036e06.p1k ApiDB exon 22123 22200 . + . ID=apidb|exon_tryp_XI-1036e06.p1k.snoRNA.0004-1;Name=exon;description=exon;size=78;Parent=apidb|rna_tryp_XI-1036e06.p1k.snoRNA.0004-1
(This is line 46748)##FASTA
>apidb|TB927.5.300b
ATGGCTCACGGCTCGATTCCAGTTATTGATGTCGGCCCTCTGTTCTGTGATGGAGAAAAG
GGGATGATGGATGTTGCGAAACAGATTGATCATGCCTGTAGGACGTGGGGTGTTTTTCTT
GTTGTGGGTCATCCCATTCCCCGTGAGCGAACGGAAAAGTTGATGGAAATGGCCAAGGCT
TTTTTTTCGCTTCCATTGGAAGAGAAACTTAAGGTTGATATTCGAAAGAGCAAACATCAT
CGCGGTTACGGATGCCTCGATGCGGAGAATGTTGACCCAACGAAACCATTTGATTGTAAA
GAAACATTTAATATGGGCTGTCATCTCCCTGAGGATCACCCCGATGTTGCAGCTGGAAAG
CCATTGCGTGGACCGAACAATCACCCCACGCAAGTGAAAGGTTGGGTAGAGTTGATGAAC
AGACATTATCGCGAAATGCAGGAATTTGCCCTCGTTATTCTTCGTGCCCTCGCACTCGCT
ATTGGTTTAAAGAAAGACTTTTTCGATACCAAATTTGATGAACCTTTGAGTGTGTTCCGT
ATGCTACATTATCCTCCACAAAAGCAAGGGACCCGTTATCCCATCGTGTGTGGTGAGCAT
ACGGATTATGGTATTATTACATTACTCTACCAAGATTCGGTGGGAGGACTGCAGGTGCGC
AATCTGTCAGATGAGTGGGTGGATGTGGAACCCCTTGAAGGAAGTTTTGTTGTGAATATT
GGGGACATGATGAATATGTGGAGTAATGGCCGTTACCGCTCAACACCGCATCGCGTTCGC
TTAACCACAACTGATCGCTACTCCATGCCATTTTTCTGTCAGCCTAATCCTTATACTGTT
ATTAAATGCCTTGATCATTGCCATTCGCCAAGCAATCCCCCCAAATATCCACCAGTCCGT
GCTGTGGATTGGTTGCTGAAGCGTTTCGCGGAAACATATGCCCATCGCAAAACAAAGATG
TGA
>apidb|cds_TB927.5.300b-1
MAHGSIPVIDVGPLFCDGEKGMMDVAKQIDHACRTWGVFLVVGHPIPRERTEKLMEMAKA
FFSLPLEEKLKVDIRKSKHHRGYGCLDAENVDPTKPFDCKETFNMGCHLPEDHPDVAAGK
PLRGPNNHPTQVKGWVELMNRHYREMQEFALVILRALALAIGLKKDFFDTKFDEPLSVFR
MLHYPPQKQGTRYPIVCGEHTDYGIITLLYQDSVGGLQVRNLSDEWVDVEPLEGSFVVNI
GDMMNMWSNGRYRSTPHRVRLTTTDRYSMPFFCQPNPYTVIKCLDHCHSPSNPPKYPPVR
AVDWLLKRFAETYAHRKTKM
Why does htseq-count gives now an error?
Again, thanks for all!
Sandra
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