FileNotFoundError: [Errno 2] No such file or directory

[emmannaemeka]

I also encountered this problem

Processing CBS11016_chr1A Traceback (most recent call last): File "./GFF2MSS.py", line 146, in with open(gff_filename, "rt") as gh: FileNotFoundError: [Errno 2] No such file or directory: '/CBS11016.genome.functional_blast.sorted_gff3sort.gff'

[maedat]

The error message indicates that the location of your GFF file is not correctly specified.

Did you get the demo script working? If it's working, but you may be able to solve it by replacing the files in the example directory with your own files and running it.

[emmannaemeka]

I did and got this error Processing CBS11016_chr1A Traceback (most recent call last): File "GFF2MSS.py", line 161, in product_name = DF_Extract(anno_in, mRNA_ID) File "GFF2MSS.py", line 31, in DF_Extract out_DATA= tmp_DF.iat[0,1] File "/Users/emmannadi/opt/anaconda3/lib/python3.7/site-packages/pandas/core/indexing.py", line 2200, in getitem return self.obj._get_value(*key, takeable=self._takeable) File "/Users/emmannadi/opt/anaconda3/lib/python3.7/site-packages/pandas/core/frame.py", line 2826, in _get_value return com.maybe_box_datetimelike(series._values[index]) IndexError: index 0 is out of bounds for axis 0 with size 0

[emmannaemeka]

Meanwhile is there a script you can share to help me convert this GFF3 to anno.txt?

[maedat]

Sure. If you are Mac user. Please use following commands on your terminal.

[Open your terminal] git clone https://github.com/maedat/GFF2MSS.git cd GFF2MSS/ python3 GFF2MSS.py -f example/Lj3.0_Chloroplastl.fna -g example/Lj3.0_cp_gene_models.gff3 -a example/Lj3.0_anno.txt -l "PRETEST" -n "Lotus japonicus" -s "MG-20" -o mss.out.txt

[maedat]

You need not only gff3 but also fasta file about the genomic sequence (e.g, example/Lj3.0_Chloroplastl.fna) and gene name file (example/Lj3.0_anno.tx) to make anno.txt

[emmannaemeka]

If you have a script that can make anno.txt from gff3 and fasta I would appreciate if you can share or I can share with you my gff3 and fasta

On Tue, 2 Jun 2020 at 6:37 AM, Taro Maeda notifications@github.com wrote:

You need not only gff3 but also fasta file about the genomic sequence (e.g, example/Lj3.0_Chloroplastl.fna) and gene name file (example/Lj3.0_anno.tx) to make anno.txt

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/maedat/GFF2MSS/issues/10#issuecomment-637289255, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHVLNZ7WVRRFLMQ4H3HEZADRUSF2JANCNFSM4NQLID2Q .

-- Nnadi Nnaemeka Emmanuel,Ph.D Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. +2348068124819 Publications: https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

[maedat]

If you send me your fasta, gff3, and gene name files, we will try to call GFF2MSS here. However, please be aware that we are not able to follow up with you if there are problems with the file contents or the sequence itself.

[emmannaemeka]

Can I get an email to share the files with you?

On Tue, 2 Jun 2020 at 6:59 AM, Taro Maeda notifications@github.com wrote:

If you send me your fasta, gff3, and gene name files, we will try to call GFF2MSS here. However, please be aware that we are not able to follow up with you if there are problems with the file contents or the sequence itself.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/maedat/GFF2MSS/issues/10#issuecomment-637297081, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHVLNZ6OONXNKZG4NOJ767LRUSINHANCNFSM4NQLID2Q .

-- Nnadi Nnaemeka Emmanuel,Ph.D Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. +2348068124819 Publications: https://www.researchgate.net/profile/Emmanuel_Nnadi/publications