Closed sojichld closed 7 months ago
found error
It would be helpful if you document what was your problem and how you've fixed it.
It was missing the gene_name field. In the example posted to the isoseq.how, while it begins similarly to my file, there is indeed a gene_name field in column 9, just a few entries farther down. The gtf that I was using did not have this field, and I overlooked that this is mentioned as one of the three required fields.
I used the following awk script to add a gene_name field, identical to what is listed in the transcript id field (subfield of $9) to each line of my file, and I was able to proceed after that:
awk 'BEGIN{FS=OFS="\t"} {if (split($9, arr, "transcript_id \"") > 1) {split(arr[2], id, "\""); $9 = $9 " gene_name \"" id[1] "\"";} print;}' input.gtf > output.gtf
Operating system MAC (but I am using through an HPC so redhat linux)
Package name pigeon 1.2.0
Conda environment
Describe the bug I am trying to use pigeon classify, and though my file looks like it is formatted given examples on isoseq.how, it is telling me there is some formatting error.
When I look at my file to see if there is a missing tab or something of the sort, it looks like the tabs are correctly situated.![image](https://github.com/PacificBiosciences/pbbioconda/assets/31484193/5222c313-02c1-4b4d-afa7-49e86f2c3d56)
Above is a vim forward slash on the tab character.
Error message
This implies to me that it expects to see "gene_name"? However this format seems to me the same as the compatible file in isoseq.how
So I wouldn't expect this to fail, or run into this issue. To Reproduce I ran classify module on such a file, let me know files to provide for reproduction.
Expected behavior Provides output from the classify script