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What the option "-a accesion" parameter should to be set(means:What type?) #65

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chemy-cm opened this issue Jul 13, 2021 · 3 comments

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@chemy-cm
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chemy-cm commented Jul 13, 2021

Nearly I used the RATT-with-GFF(from github)
but the scrpit showed a error:

EMBLmyGFF3: error: unrecognized arguments: CM000429.1

The CM000429.1 is the name of contigs
the script‘s code about EMBLmyGFF3 as follow:

#calls EMBLmyGFF3.py to convert the contig gff to an embl file
#called by main
def gffsToEmbls(contigNames):
    for contig in contigNames:
        print "\n<RATTwithGFF.py> converting "+contig+".gff to "+contig+".embl...."
        subprocess.call(["EMBLmyGFF3",\
                            "contig_gff/"+contig+".gff",\
                            "contig_fasta/"+contig+".fa",\
                            "-o", "contig_embl/"+contig+"_tmp1.embl",\
                            "-i", "tag",\
                            "-p", contig,\
                            "-s", "unknown",\
                            "-t", "linear",\
                            "-d", "STD",\
                            "-m", "genomic DNA",\
                            "-x", "UNC",\
                            "--rg","none",\
                            "-r","1",\
                            "-a",contig,\
                            "--keep_duplicates",\
                            "-q",\
                            "--shame"])
        cleanEmbl(contig)

What is the type of this parameter "-a accesion"?
It seems not useful when I just set a normal String like "123456" or "ABCD"
Could U tell me how to do?
Thanks a lot!

@Juke34
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Juke34 commented Jul 13, 2021

Please see the README:
https://github.com/NBISweden/EMBLmyGFF3#parameters
or the code:

parser.add_argument("-a", "--accession", default=None, action="store_true", help="Bolean. Accession number(s) for the entry. Default value: XXX. The proper value is automatically filled up by ENA during the submission by a unique accession number they will assign. The accession number is used to set up the AC line and the first token of the ID line as well. Please visit [this page](https://www.ebi.ac.uk/ena/submit/accession-number-formats) and [this one](https://www.ebi.ac.uk/ena/submit/sequence-submission) to learn more about it. Activating the option will set the Accession number with the fasta sequence identifier.")

It is a boolean, False by default putting -a will become true. No need to give any value

@Juke34
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Juke34 commented Jul 13, 2021

Thank you for the feedback.
I have PR a fix to RATT-with-GFF. Let see if the owner is stll active on this project.

@Juke34 Juke34 closed this as completed Jul 13, 2021
@CEPHAS-01
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Please see the README: https://github.com/NBISweden/EMBLmyGFF3#parameters or the code:

parser.add_argument("-a", "--accession", default=None, action="store_true", help="Bolean. Accession number(s) for the entry. Default value: XXX. The proper value is automatically filled up by ENA during the submission by a unique accession number they will assign. The accession number is used to set up the AC line and the first token of the ID line as well. Please visit [this page](https://www.ebi.ac.uk/ena/submit/accession-number-formats) and [this one](https://www.ebi.ac.uk/ena/submit/sequence-submission) to learn more about it. Activating the option will set the Accession number with the fasta sequence identifier.")

It is a boolean, False by default putting -a will become true. No need to give any value

I think it is confusing in the documentation to state that the data type is Boolean when indeed there is no value to be supplied. Anyone with experience with other documentation files will naturally supply a boolean argument to that parameter. I wasted so much time on this aspect. I think it would be better understood if it stated explicitly that no value is to be supplied, rather setting the parameter or otherwise is sufficient

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