NameError: name 'genBlast' is not defined

[yjx1217]

Hello,

I got the following error when invoking Easyfig from the command line on Linux. The Easyfig version that I am using is "Version 2.2.2 10.08.2015". Could you help me to figure out what might cause this error?

python /home/yjx/Programs/Easyfig/Easyfig.py -o test -blastn chrI.embl 1 40850 R chrI.embl 179930 219929
Traceback (most recent call last):
File "/home/yjx/Programs/Easyfig/Easyfig.py", line 10988, in
inlist = genBlast(templist, cutlist)
NameError: name 'genBlast' is not defined

Thanks!

Best,
Jia-Xing

[yjx1217]

hmm, I found out the current version at GitHub (not the released one) does not have this issue. But the "-i" option (for set min_identity cutoff for BLAST) seems not working properly. I set "-i 90" in my command line but the output still shows hits with identity < 90.

[mjsull]

Hi Jia-Xing,

Yes, someone emailed me about that bug last week, but thanks for letting me
know anyway. I have fixed it on github (as you noticed) but haven't had
time to create the new executables and update the website. I will make sure
I do it tomorrow.

When you say the output still shows hits with identity < 90 do you mean the
image or the BLAST output? The filtering is done by Easyfig after the BLAST
file has been created so that parameters can be adjusted without having to
generate a new BLAST file, so all hits will be in the BLAST output
(regardless of what settings were provided). If they aren't being filtered
in the image please let me know.

Best,

Mitchell

On 20 December 2015 at 16:20, Jia-Xing Yue notifications@github.com wrote:

hmm, I found out the current version at GitHub (not the released one) does
not have this issue. But the "-i" option (for set min_identity cutoff for
BLAST) seems not working properly. I set "-i 90" in my command line but the
output still shows hits with identity < 90.

—
Reply to this email directly or view it on GitHub
#2 (comment).

[yjx1217]

Dear Mitchell,

Thank you very much for the reply. About the BLAST, yes, I think the
filtering doesn't work in the image. I set min_identity cutoff as 90 but
the BLAST identity scale bar in the image still starts from 62 in my case.
So I think there might be something wrong. Also, is it possible to let
Easyfig keep the raw BLAST table result rather than delete it after the
image was generated? If not, could you add this feature in the near future?
I think this will be very helpful in some cases. Thanks again!

Best,
Jia-Xing

On Mon, Dec 21, 2015 at 10:55 PM, mjsull notifications@github.com wrote:

Hi Jia-Xing,

Yes, someone emailed me about that bug last week, but thanks for letting me
know anyway. I have fixed it on github (as you noticed) but haven't had
time to create the new executables and update the website. I will make sure
I do it tomorrow.

When you say the output still shows hits with identity < 90 do you mean the
image or the BLAST output? The filtering is done by Easyfig after the BLAST
file has been created so that parameters can be adjusted without having to
generate a new BLAST file, so all hits will be in the BLAST output
(regardless of what settings were provided). If they aren't being filtered
in the image please let me know.

Best,

Mitchell

On 20 December 2015 at 16:20, Jia-Xing Yue notifications@github.com
wrote:

hmm, I found out the current version at GitHub (not the released one)
does
not have this issue. But the "-i" option (for set min_identity cutoff for
BLAST) seems not working properly. I set "-i 90" in my command line but
the
output still shows hits with identity < 90.

—
Reply to this email directly or view it on GitHub
#2 (comment).

—
Reply to this email directly or view it on GitHub
#2 (comment).

Jia-Xing Yue

Population Genomics and Complex Traits Group
Tour Pasteur 8eme etage
Faculté de Médecine
Institute for Research on Cancer and Aging, Nice (IRCAN)
CNRS UMR 7284 - INSERM U 1081
Université de Nice Sophia Antipolis
28 Avenue de Valombrose
06107 NICE Cedex 2
France

Lab website: http://ircan.org/index.php?Itemid=98
Personal website: http://www.iamphioxus.org/

[yjx1217]

Dear Mitchell,

I've just tried the newest version code on github and found this error
still remains. I attached the test data for your check. As you can see that
I've already specified "-i 90" in my command (run_easyfig.sh) but the
resulting plot still shows hits with identity as low as 70% (based on the
scale bar). Could you have more check about this? Thanks in advance!

Best,
Jia-Xing

On Mon, Dec 21, 2015 at 11:04 PM, Jia-Xing Yue yuejiaxing@gmail.com wrote:

Dear Mitchell,

Thank you very much for the reply. About the BLAST, yes, I think the
filtering doesn't work in the image. I set min_identity cutoff as 90 but
the BLAST identity scale bar in the image still starts from 62 in my case.
So I think there might be something wrong. Also, is it possible to let
Easyfig keep the raw BLAST table result rather than delete it after the
image was generated? If not, could you add this feature in the near future?
I think this will be very helpful in some cases. Thanks again!

Best,
Jia-Xing

On Mon, Dec 21, 2015 at 10:55 PM, mjsull notifications@github.com wrote:

Hi Jia-Xing,

Yes, someone emailed me about that bug last week, but thanks for letting
me
know anyway. I have fixed it on github (as you noticed) but haven't had
time to create the new executables and update the website. I will make
sure
I do it tomorrow.

When you say the output still shows hits with identity < 90 do you mean
the
image or the BLAST output? The filtering is done by Easyfig after the
BLAST
file has been created so that parameters can be adjusted without having to
generate a new BLAST file, so all hits will be in the BLAST output
(regardless of what settings were provided). If they aren't being filtered
in the image please let me know.

Best,

Mitchell

On 20 December 2015 at 16:20, Jia-Xing Yue notifications@github.com
wrote:

hmm, I found out the current version at GitHub (not the released one)
does
not have this issue. But the "-i" option (for set min_identity cutoff
for
BLAST) seems not working properly. I set "-i 90" in my command line but
the
output still shows hits with identity < 90.

—
Reply to this email directly or view it on GitHub
#2 (comment).

—
Reply to this email directly or view it on GitHub
#2 (comment).

Jia-Xing Yue

Population Genomics and Complex Traits Group
Tour Pasteur 8eme etage
Faculté de Médecine
Institute for Research on Cancer and Aging, Nice (IRCAN)
CNRS UMR 7284 - INSERM U 1081
Université de Nice Sophia Antipolis
28 Avenue de Valombrose
06107 NICE Cedex 2
France

Lab website: http://ircan.org/index.php?Itemid=98
Personal website: http://www.iamphioxus.org/

Jia-Xing Yue

Population Genomics and Complex Traits Group
Tour Pasteur 8eme etage
Faculté de Médecine
Institute for Research on Cancer and Aging, Nice (IRCAN)
CNRS UMR 7284 - INSERM U 1081
Université de Nice Sophia Antipolis
28 Avenue de Valombrose
06107 NICE Cedex 2
France

Lab website: http://ircan.org/index.php?Itemid=98
Personal website: http://www.iamphioxus.org/

[mjsull]

Hi Jia-Xing,

Should be all fixed now :)

Also if you add the "-keep" flag before your genbank files Easyfig will now keep the temp_easyfig folder with all the blast output in it.

Best,

Mitchell

[yjx1217]

Hi Mitchell,

Thank you very much for the fix and enhancement!

Best,
Jia-Xing

On Mon, Jan 25, 2016 at 4:52 PM, mjsull notifications@github.com wrote:

Hi Jia-Xing,

Should be all fixed now :)

Also if you add the "-keep" flag before your genbank files Easyfig will
now keep the temp_easyfig folder with all the blast output in it.

Best,

Mitchell

—
Reply to this email directly or view it on GitHub
#2 (comment).

Jia-Xing Yue

Population Genomics and Complex Traits Group
Tour Pasteur 8eme etage
Faculté de Médecine
Institute for Research on Cancer and Aging, Nice (IRCAN)
CNRS UMR 7284 - INSERM U 1081
Université de Nice Sophia Antipolis
28 Avenue de Valombrose
06107 NICE Cedex 2
France

Lab website: http://ircan.org/index.php?Itemid=98
Personal website: http://www.iamphioxus.org/