[miso-users] problems with exon_utils.py

[Pooja Singh]

Hi everyone,

I am trying to use MISO to assess the transcriptomes of cichlid fishes. I
have run into
some problems while doing this and would appreciate your help:

*1.*The  index_gff.py generates the indexed annotations but it adds a chr
in front of the
"LG" labels when it creates the indexes. So "LG1" is changes to "chrLG1"
and so on. Should
I fix the names of these folders or let them be? Since in my BAM files and
GFF files, the
label is "LG1".

*2. *Also, when i try to generate the gff with consecutive exons using the
following command:

/export/bio/python/Python-2.7.5/bin/python
/export/bio/python/Python-2.7.5/lib/python2.7/site-packages/misopy/exon_utils.py
--get-const-exons Oreochromis_niloticus.BROADON2.gff --min-exon-size 1000
--output-dir ./exons/

I get the following error:

Getting constitutive exons...

  - Input GFF:
/nas2/pooja/pharyngeal_jaw_transcriptomes/raw_demultiplexed_bam/paper1/map2Onil/all_bam/alternative_splicing/Oreochromis_niloticus.BROADON2.gff

  - Output dir:
/nas2/pooja/pharyngeal_jaw_transcriptomes/raw_demultiplexed_bam/paper1/map2Onil/all_bam/alternative_splicing/exons

  - Output format: gff

  - Including only exons greater than or equal to 1000-bp

Constitutive exon retrieval took 86.17 seconds (2782 exons).

Outputting exons to file:
/nas2/pooja/pharyngeal_jaw_transcriptomes/raw_demultiplexed_bam/paper1/map2Onil/all_bam/alternative_splicing/exons/Oreochromis_niloticus.BROADON2.min_1000.const_exons.gff

Traceback (most recent call last):

  File
"/export/bio/python/Python-2.7.5/lib/python2.7/site-packages/misopy/exon_utils.py",
line 369, in <module>

    main()

  File
"/export/bio/python/Python-2.7.5/lib/python2.7/site-packages/misopy/exon_utils.py",
line 363, in main

    min_size=options.min_exon_size)

  File
"/export/bio/python/Python-2.7.5/lib/python2.7/site-packages/misopy/exon_utils.py",
line 314, in get_const_exons_by_gene

    output_format=output_format)

  File
"/export/bio/python/Python-2.7.5/lib/python2.7/site-packages/misopy/exon_utils.py",
line 103, in output_exons_to_file

    gff_writer.write_recs(recs)

  File
"/export/bio/python/Python-2.7.5/lib/python2.7/site-packages/misopy/gff_utils.py",
line 888, in write_recs

    self.write(rec)

  File
"/export/bio/python/Python-2.7.5/lib/python2.7/site-packages/misopy/gff_utils.py",
line 883, in write

    self._record_writer(rec)

  File
"/export/bio/python/Python-2.7.5/lib/python2.7/site-packages/misopy/gff_utils.py",
line 918, in _write_rec_v3

    fields = [_seqid_pat.sub(url_quote, rec.seqid),

  File "/export/bio/python/Python-2.7.5/lib/python2.7/urllib.py", line
1280, in quote

    if not s.rstrip(safe):

AttributeError: '_sre.SRE_Match' object has no attribute 'rstrip'

I am not sure what I am doing wrong since my gff file looks good (some
lines pasted below).
I would appreciate if someone could tell me what I am doing wrong!


my GFF:

##gff3-version3

LG1 protein_coding gene 5964 9889 . + . ID=on.gene.LG1.1;Name=on.gene.LG1.1

LG1 protein_coding mRNA 5964 9889 . + .
ID=on.mrna.LG1.1.1;Name=on.gene.LG1.1;Parent=on.gene.LG1.1

LG1 protein_coding exon 5964 6017 . + .
ID=on.mrna.LG1.1.1.1;Name=on.gene.LG1.1;Parent=on.mrna.LG1.1.1

LG1 protein_coding exon 7911 8060 . + .
ID=on.mrna.LG1.1.1.2;Name=on.gene.LG1.1;Parent=on.mrna.LG1.1.1

LG1 protein_coding exon 8147 8269 . + .
ID=on.mrna.LG1.1.1.3;Name=on.gene.LG1.1;Parent=on.mrna.LG1.1.1

LG1 protein_coding exon 8386 8584 . + .
ID=on.mrna.LG1.1.1.4;Name=on.gene.LG1.1;Parent=on.mrna.LG1.1.1

LG1 protein_coding exon 8669 8784 . + .
ID=on.mrna.LG1.1.1.5;Name=on.gene.LG1.1;Parent=on.mrna.LG1.1.1

LG1 protein_coding exon 8980 9034 . + .
ID=on.mrna.LG1.1.1.6;Name=on.gene.LG1.1;Parent=on.mrna.LG1.1.1

LG1 protein_coding exon 9822 9889 . + .
ID=on.mrna.LG1.1.1.7;Name=on.gene.LG1.1;Parent=on.mrna.LG1.1.1

LG1 protein_coding mRNA 5964 8290 . + .
ID=on.mrna.LG1.1.2;Name=on.gene.LG1.1;Parent=on.gene.LG1.1

LG1 protein_coding exon 5964 6017 . + .
ID=on.mrna.LG1.1.2.1;Name=on.gene.LG1.1;Parent=on.mrna.LG1.1.2

LG1 protein_coding exon 7911 8060 . + .
ID=on.mrna.LG1.1.2.2;Name=on.gene.LG1.1;Parent=on.mrna.LG1.1.2

LG1 protein_coding exon 8147 8290 . + .
ID=on.mrna.LG1.1.2.3;Name=on.gene.LG1.1;Parent=on.mrna.LG1.1.2

LG1 protein_coding gene 13041 54863 . - .
ID=on.gene.LG1.2;Name=on.gene.LG1.2

LG1 protein_coding mRNA 16786 54863 . - .
ID=on.mrna.LG1.2.1;Name=on.gene.LG1.2;Parent=on.gene.LG1.2

LG1 protein_coding exon 16786 16986 . - .
ID=on.mrna.LG1.2.1.8;Name=on.gene.LG1.2;Parent=on.mrna.LG1.2.1

LG1 protein_coding exon 17288 17392 . - .
ID=on.mrna.LG1.2.1.7;Name=on.gene.LG1.2;Parent=on.mrna.LG1.2.1

LG1 protein_coding exon 17496 17612 . - .
ID=on.mrna.LG1.2.1.6;Name=on.gene.LG1.2;Parent=on.mrna.LG1.2.1

LG1 protein_coding exon 17785 17949 . - .
ID=on.mrna.LG1.2.1.5;Name=on.gene.LG1.2;Parent=on.mrna.LG1.2.1




Best regards,

Pooja Singh
-- 
*PhD student*
*Institute of Zoology*
*Universitätplatz 2*
*University of Graz*
*Graz 8010*

*Austria*
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