shutil.copy may be better than os.link in line 111 in ls_bsr.py

[cvn001]

Dear Devs

When I try to use LS-BSR, an error occur:

Traceback (most recent call last): File "ls_bsr.py", line 492, in <module> options.filter_scaffolds,options.prefix,options.temp_dir,options.debug) File "ls_bsr.py", line 111, in main os.link("%s" % infile, "%s/%s.new" % (fastadir,name)) OSError: [Errno 18] Invalid cross-device link

I try myself to use shutil.copy to replace os.link in main script. No such error occur again.

Best,

Xiangchen Li

[jasonsahl]

Thanks Xiangchen. I will look into that.

In the meantime, I now have an option (“-y”) to specify a temporary directory to write to. This also seems to have fixed the problem.

regards, Jason

On May 13, 2016, at 7:23 AM, Li Xiangchen notifications@github.com wrote:

Dear Devs

When I try to use LS-BSR, an error occur:

Traceback (most recent call last): File "ls_bsr.py", line 492, in options.filter_scaffolds,options.prefix,options.temp_dir,options.debug) File "ls_bsr.py", line 111, in main os.link("%s" % infile, "%s/%s.new" % (fastadir,name)) OSError: [Errno 18] Invalid cross-device link

I try myself to use shutil.copy to replace os.link in main script. No such error occur again.

Best,

Xiangchen Li

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[cvn001]

Hi Jason

I am glad to tell you that LS-BSR have been successfully completed with 100 bacteria genomes in my computer. It is really faster than ITEP and Get_Homologues I used before and very attractive to me.

Unfortunately, when I look at these output files, I cannot extract each gene or CDS families(clusters) of 100 genomes that I can build each gene tree to compare with the species phylogeny. I know ITEP can get a fasta format alignment of each cluster, but this tool are too slow to handle my large data.

Are there any ways to get these results?

Best,

Xiangchen

[jasonsahl]

Xiangchen,

Look to this script that's included in the distribution (tools directory): "extract_core_genome.py"

If you run the script and choose to keep temporary files "-k T", the directory labeled "work_xxx", will have sequences and alignments (*aln.seqs) for each of your targets. The main caveat is that I'm only keeping core genes here (those present in all genomes). If you want alignments for those genes in your accessory genome, let me know and I provide you with a different script.

[vaofford]

Hi Jason,

When running ls-bsr.py on the test data we are also getting a similar error:

Error: Traceback (most recent call last): File "/software/pathogen/external/apps/usr/bin/ls_bsr.py", line 488, in options.filter_scaffolds,options.prefix,options.temp_dir,options.debug) File "/software/pathogen/external/apps/usr/bin/ls_bsr.py", line 111, in main os.link("%s" % infile, "%s/%s.new" % (fastadir,name)) OSError: [Errno 18] Invalid cross-device link

Supplying a temporary directory seems to fix the issue.

Many thanks,

Victoria