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LuyiTian / FLAMES

Full-length transcriptome splicing and mutation analysis
GNU General Public License v3.0
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empty transcript_assembly.fa file using example SIRV data #25

Closed luiseze closed 2 years ago

luiseze commented 2 years ago

Hi, I tried running the example in the example folder of the python installation of FLAMES which gives an error: subprocess.CalledProcessError: Command '['samtools faidx FLAMES_output/transcript_assembly.fa']' returned non-zero exit status 1. I noticed that the transcript_assembly.fa file is empty. In the get_transcript_seq function in gff3_to_fa.py, it exits the first for loop right away as the following statement is false: if ch not in chr_to_gene:. However, it also does not enter the next for loop (for tr_seq in global_seq_dict:) because the dictionary is empty. I'd really appreciate your help.

ChangqingW commented 2 years ago

Seems like it's due to wrong mode used in gzip.open, should be fixed by 54be4e0ab4c7ef43795ea523afa5f3e805fb646c .