Handling for the scenario where blastn -query returns no results

[allaway]

Hi there,

Yesterday I ran into a situation where prep_genome_lib/ctat-vif-lib-integration.py errored on line 79:
df = pd.read_csv(blastn_outfile, sep="\t", header=None, usecols=[1,2,8,9]) when the previous blastn step outputs a file with no contents.

This checks for the number of lines in the blastn output file and bypasses the processing instead creating a dummy file just with column headers for use downstream.

I am a bit of a python novice so please let me know I've done something silly!

[brianjohnhaas]

oh, interesting. Thanks for pointing this out. Leave the PR in, but I might handle it differently when I put out a future release.

…

On Fri, Aug 19, 2022 at 9:57 AM Robert Allaway ***@***.***> wrote: Hi there, Yesterday I ran into a situation where prep_genome_lib/ctat-vif-lib-integration.py errored on line 79: df = pd.read_csv(blastn_outfile, sep="\t", header=None, usecols=[1,2,8,9]) when the previous blastn step outputs a file with no contents. This checks for the number of lines in the blastn output file and bypasses the processing instead creating a dummy file just with column headers for use downstream. I am a bit of a python novice so please let me know I've done something silly! ------------------------------ You can view, comment on, or merge this pull request online at: #45 Commit Summary - 19b2734 <19b2734> Update ctat-vif-lib-integration.py File Changes (1 file <https://github.com/broadinstitute/CTAT-VirusIntegrationFinder/pull/45/files> ) - *M* prep_genome_lib/ctat-vif-lib-integration.py <https://github.com/broadinstitute/CTAT-VirusIntegrationFinder/pull/45/files#diff-022fe316496fd04c2235f6074c3d786f20c15b39f6ff3cd8e331cf695a2f0c6d> (24) Patch Links: - https://github.com/broadinstitute/CTAT-VirusIntegrationFinder/pull/45.patch - https://github.com/broadinstitute/CTAT-VirusIntegrationFinder/pull/45.diff — Reply to this email directly, view it on GitHub <#45>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX4A5UPKYTZEKYZZEKTVZ6HDRANCNFSM57A2VINQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[brianjohnhaas]

Also, just in case, please be aware that we provide a virus database collection to use with ctat-vif, but go ahead and use it on your own set too if that's of interest. On Fri, Aug 19, 2022 at 10:32 AM Brian Haas ***@***.***> wrote:

…

oh, interesting. Thanks for pointing this out. Leave the PR in, but I might handle it differently when I put out a future release. On Fri, Aug 19, 2022 at 9:57 AM Robert Allaway ***@***.***> wrote: > Hi there, > > Yesterday I ran into a situation where > prep_genome_lib/ctat-vif-lib-integration.py errored on line 79: > df = pd.read_csv(blastn_outfile, sep="\t", header=None, usecols=[1,2,8,9]) > when the previous blastn step outputs a file with no contents. > > This checks for the number of lines in the blastn output file and > bypasses the processing instead creating a dummy file just with column > headers for use downstream. > > I am a bit of a python novice so please let me know I've done something > silly! > ------------------------------ > You can view, comment on, or merge this pull request online at: > > #45 > Commit Summary > > - 19b2734 > <19b2734> > Update ctat-vif-lib-integration.py > > File Changes > > (1 file > <https://github.com/broadinstitute/CTAT-VirusIntegrationFinder/pull/45/files> > ) > > - *M* prep_genome_lib/ctat-vif-lib-integration.py > <https://github.com/broadinstitute/CTAT-VirusIntegrationFinder/pull/45/files#diff-022fe316496fd04c2235f6074c3d786f20c15b39f6ff3cd8e331cf695a2f0c6d> > (24) > > Patch Links: > > - > https://github.com/broadinstitute/CTAT-VirusIntegrationFinder/pull/45.patch > - > https://github.com/broadinstitute/CTAT-VirusIntegrationFinder/pull/45.diff > > — > Reply to this email directly, view it on GitHub > <#45>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/ABZRKX4A5UPKYTZEKYZZEKTVZ6HDRANCNFSM57A2VINQ> > . > You are receiving this because you are subscribed to this thread.Message > ID: ***@***.***> > -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[allaway]

oh, interesting. Thanks for pointing this out. Leave the PR in, but I
might handle it differently when I put out a future release.
Sounds good, I figure there is probably a better way to handle this. :)

Also, just in case, please be aware that we provide a virus database
collection to use with ctat-vif, but go ahead and use it on your own set
too if that's of interest.

Thanks! I did see that.

I am revisiting a 2021 summer intern's project- IIRC (and I certainly might be wrong about this) - the collection of viruses provided was only HPV at that time or maybe HPV plus some other viruses?

I believe she retrieved all of the available human viral sequences from NCBI and used that - so I am trying to use that for consistencies sake, but I'll check out the virus fasta you have provided as well.