joseblanca / vcf2fasta Goto Github PK

Reading VCF file [Osjap10g14600.1.gff] ... done
Reading VCF file [japonica.combine.vcf.gz] ... done
Reading VCF file [all.chrs.con.fa] ... done
Ploidy is: 2
No phased genotypes found on first variant. Treating as "unphased"
Concatenating all [ CDS ]
Setting output directory to: vcf2fasta_CDS
vcf2fasta_CDS exists. Do you want to proceed? [y|n]: y
Total number of genes found: 1
Traceback (most recent call last):
File "/home/zhouyanli/vcf2fasta/vcf2fasta.py", line 481, in
main()
File "/home/zhouyanli/vcf2fasta/vcf2fasta.py", line 119, in main
sequences = getSequences(gff, gene, args.feat, args.blend, ref, vcf, ploidy, phased, samples)
File "/home/zhouyanli/vcf2fasta/vcf2fasta.py", line 216, in getSequences
alleles,max_len = getAlleles(rec, ploidy)
File "/home/zhouyanli/vcf2fasta/vcf2fasta.py", line 264, in getAlleles
max_len = max([ len(i) for i in segregating if i is not None ])
ValueError: max() arg is an empty sequence

The vcf file is too big,

Hello @JoseBlanca !
I get an issue with: ImportError: cannot import name TemporaryDirectory
coming from from the definition of tempfile import NamedTemporaryFile, TemporaryDirectory
I am using python 2.7.9.

Or perhaps my syntax is incorrect I use:
python vcf2fasta.py refgenome.fasta markers.vcf region_sample.bed

Any suggestion?