Collapse.py file

Question

Collapse.py file

Closed this issue 2 years ago · 6 comments

@agraubert @joshua-gould @francois-a @dmcgoldrick
Hi, can you please guide how to convert the full length annotation gtf to the input gtf for rnaseqc. I have been using schmidtea_mediterranea.PRJNA379262.WBPS14.canonical_geneset.rnaseqc.gtf downloaded from here.

ftp://ftp.ebi.ac.uk/pub/databases/wormbase/parasite/releases/WBPS14/species/schmidtea_mediterranea/PRJNA379262/schmidtea_mediterranea.PRJNA379262.WBPS14.canonical_geneset.gtf.gz

I used collapse.py which produced this error:

python collapse_annotation.py schmidtea_mediterranea.PRJNA379262.WBPS14.canonical_geneset.rnaseqc_type.gtf new.gtf File "collapse_annotation.py", line 100
print('Parsing GTF: {0:d} genes processed\r'.format(len(self.genes)), end='\r')
^
SyntaxError: invalid syntax

And while running rnaseqc command, I'm facing issue of duplicate exon ids.

Failed to parse the GTF: Detected non-unique Exon ID: SMEST026639001.e4

Answer 1 · 2020-11-29T20:02:50.000Z

Hi @jjyotikataria, so sorry for the delayed response. At first glance, it seems like you're using python 2. Could you try running the collapse_annotation.py script using python3.5 or greater?

Answer 2 · 2021-03-16T07:16:10.000Z

Hi,
Related to this issue, I ran collapse_annotation.py using python 3.6.2 and got the below error. Any help would be appreciated. My end goal is to make rnaseqc work which core-dumps with my existing gtf file (that was downloaded from NCBI)

python3 collapse_annotation.py GCF_003668045.3_CriGri-PICRH-1.0_genomic.gtf GCF_003668045.3_CriGri-PICRH-1.0_genomic_collapsed.gtf

Traceback (most recent call last):
File "collapse_annotation.py", line 279, in
annotation = Annotation(args.transcript_gtf)
File "collapse_annotation.py", line 67, in init
attributes[kv[0]] = kv[1]
IndexError: list index out of range

Answer 3 · 2021-03-16T09:39:34.000Z

Hi if you are okay we can look into it together on google meet or Skype?

…

On Tue, Mar 16, 2021, 12:46 PM Anto007 ***@***.***> wrote: Hi, Related to this issue, I ran collapse_annotation.py using python 3.6.2 and got the below error. Any help would be appreciated. My end goal is to make rnaseqc work which core-dumps with my existing gtf file (that was downloaded from NCBI) python3 collapse_annotation.py GCF_003668045.3_CriGri-PICRH-1.0_genomic.gtf GCF_003668045.3_CriGri-PICRH-1.0_genomic_collapsed.gtf Traceback (most recent call last): File "collapse_annotation.py", line 279, in annotation = Annotation(args.transcript_gtf) File "collapse_annotation.py", line 67, in *init* attributes[kv[0]] = kv[1] IndexError: list index out of range — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#47 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOAMGNF3MWFHOSF7VRJWJ4LTD4AUXANCNFSM4S232GHQ> .

Answer 4 · 2021-03-16T09:42:33.000Z

It worked for me. On Tue, Mar 16, 2021, 3:09 PM Jyoti Kataria ***@***.***> wrote:

…

Hi if you are okay we can look into it together on google meet or Skype? On Tue, Mar 16, 2021, 12:46 PM Anto007 ***@***.***> wrote: > Hi, > Related to this issue, I ran collapse_annotation.py using python 3.6.2 > and got the below error. Any help would be appreciated. My end goal is to > make rnaseqc work which core-dumps with my existing gtf file (that was > downloaded from NCBI) > > python3 collapse_annotation.py > GCF_003668045.3_CriGri-PICRH-1.0_genomic.gtf > GCF_003668045.3_CriGri-PICRH-1.0_genomic_collapsed.gtf > > Traceback (most recent call last): > File "collapse_annotation.py", line 279, in > annotation = Annotation(args.transcript_gtf) > File "collapse_annotation.py", line 67, in *init* > attributes[kv[0]] = kv[1] > IndexError: list index out of range > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#47 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AOAMGNF3MWFHOSF7VRJWJ4LTD4AUXANCNFSM4S232GHQ> > . >

Answer 5 · 2021-03-16T10:31:48.000Z

Thank you for your quick response Jyoti- much appreciated! When you say it worked for you, do you mean to say you tried running "collapse_annotation.py" on the gtf file downloaded from here: https://www.ncbi.nlm.nih.gov/assembly/GCF_003668045.3/ ??
This is the exact gtf file that I'm interested in collapsing. Thanks again!

Answer 6 · 2021-03-16T10:46:24.000Z

I'll check the link by night. I am away from laptop at the moment. But before collapsing the gtf, we need to meet one more criteria as far as I remember. I'll share you that link as well.

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On Tue, Mar 16, 2021, 4:02 PM Anto007 ***@***.***> wrote: Thank you for your quick response Jyoti- much appreciated! When you say it worked for you, do you mean to say you tried running "collapse_annotation.py" on the gtf file downloaded from here: https://www.ncbi.nlm.nih.gov/assembly/GCF_003668045.3/ ?? This is the exact gtf file that I'm interested in collapsing. Thanks again! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#47 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOAMGNGCHKFWLZVOEJ67WN3TD4XSPANCNFSM4S232GHQ> .