vcffirstheader python 2 dependency in Snippy 4.x

[amilesj]

vcffirstheader seems to use python 2. When I ran Snippy 4.0.5 in my normal environment with python 3.6.2, I got the following error in the log after the freebayes-parallel line:

File "/home/amiles/miniconda3/bin/vcffirstheader", line 9 print line.strip() ^ SyntaxError: invalid syntax

I changed my script to activate my environment with python 2.7 before running Snippy, and it worked fine.

Best,
Arianna

[luckystar008]

I had the same problem，When I run Snippy 4.0.5, vcffirstheader reports an error：
`### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60
--min-coverage 10 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf

File "/disk1/cau/cvmjxx/miniconda3/bin/vcffirstheader", line 9
print line.strip()
^
SyntaxError: invalid syntax
And the version of python：Python 3.6.2 |Continuum Analytics, Inc.| (default, Jul 20 2017, 13:51:32)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.`

[tseemann]

Yes, it seems freebayes or vcflib have a hidden dependency on python 2 for that script.

I will have to think about how best to tackle this.

[tseemann]

@luckystar008 @amilesj
Can you tell me what these command say?

head -n 1 $(which vcffirstheader)
head -n 1 $(which fasta_generate_regions.py)
head -n 1 $(which freebayes-parallel)

[amilesj]

#!/usr/bin/env python
#!/home/amiles/miniconda3/bin/python
#!/bin/bash

[tseemann]

@amilesj thank you! and what does /home/amiles/miniconda3/bin/python --version say?

Under python PEP rules it should be 2.x .... but my guess is 3.x due to Conda madness.

[amilesj]

Yes its 3.6.2

[luckystar008]

1.#!/usr/bin/env python
2.#!/disk1/cau/cvmjxx/miniconda3/bin/python
3.#!/bin/bash
Python 3.6.2 |Continuum Analytics, Inc.| (default, Jul 20 2017, 13:51:32)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux
Hope to solve this problem.All the best！

[tseemann]

I think I will need to write my own wrappers for these python tools, as the conda 2 vs 3 problem will keep cropping up.

Until then, you can change /usr/bin/env python to /usr/bin/python or whereever your system has python 2.x installed. they use no modules so should just work.

[luckystar008]

@tseemann Do I just change the version of pyhon used by vcffirstheader or change the pyhon version of entire snippy and dependency package?

[tseemann]

Snippy is written in Perl. not python.

Snippy uses other packages (freebayes, vcflib) which include some python 2.x scripts in them. They are the issue, not snippy itself. You just need to edit the first line of all the failing scripts to point to a python 2 executable.

I am unable to fix the other packages.

[rtfcoimbra]

One can also change all instances of print line.strip() to print(line.strip()) in the vcffirstheader script. That should fix the syntax compatibility with python 3.

[jdeligt]

Please also see #309 for another python 2 dependecy fix

[tseemann]

I have joined the vcflib project and made a 1.0.0-rc3 release which is py3 now.
Will be in Conda soon: bioconda/bioconda-recipes#17050

[tseemann]

Fixed now