Comments (5)
gschroe
commented on August 28, 2024
Hi,
"chep -- help” gives you a usage message. The typical usage is:
chep --infile run_it025_data.star --header=40 --class_col=29 --helix_col=3 --cluster_num=4 --elbow_clusters=11
where run_it025_data.star is the output of a 2D classification. A window should appear showing the clustering and results from the elbow test. chep needs scikit-learn, matplotlib, scipy.
Note that this version does not write out new .star files for the individual clusters, yet. This will be done in the next version.
Gunnar
…On 07 Jun 2019, at 17:03, Bryan Hansen ***@***.***> wrote:
Hi - I'm trying to execute the chep.py command. When I do I see my cursor gets turned into a cross-hair like I should be selecting something, but nothing else pops up on screen. I looked at the chep.py command and made sure I had all the python elements it was trying to import and call. I even tried just giving the chep.py command with no arguments to try and get the usage message to show, but nothing seems to happen other than the grabbing of the mouse. Is there some config that I missed. The readme didn't specify anything for requirements or install
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_____________________________________________________________
Prof. Dr. Gunnar F. Schröder
Computational Structural Biology Group
Institute of Complex Systems (ICS-6)
Forschungszentrum Jülich
tel +49-2461-61-3259
http://www.schroderlab.org
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hansenbry
commented on August 28, 2024
Hi Gunnar,
When do you think the next version would be ready? I can see making the new .star file for the clusters will be really useful.
How do you go from the .log to making the new .star file for the clusters now?
Bryan
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gschroe
commented on August 28, 2024
Hi Bryan,
we try to have the new version ready by the end of this week.
I have a bash script to create the .star files for the individual clusters from cluster.log (see below, not very elegant), where you need to specify the cluster ID, input and output file names in the script.
All the best,
Gunnar
…-------
cluster_id="1"
output="run_it025_data_cluster1.star"
i=0
awk 'NF>5 {print}' run_it025_data.star > run_it025_data.body
awk 'NF<5 && NF>0 {print}' run_it025_data.star > ${output}
while read line
do
if [ ${i} -gt 0 ]
then
#echo ${line}
a[${i}]=${line}
fi
i=$((i+1))
done < cluster.log
fil=0
while read line
do
# 3 tubeid
# 9 micrograph
ll=( ${line} )
n=${ll[2]}
m=${ll[8]}
if [ "${n}" != "${n_old}" ]
then
fil=$((fil+1))
else
if [ "${m}" != "${m_old}" ]
then
fil=$((fil+1))
fi
fi
fil_index=$((fil-1))
if [ "${a[${fil_index}]}" == "${cluster_id}" ]
then
echo ${line} >> ${output}
fi
n_old=${n}
m_old=${m}
done < run_it025_data.body
--------------
On 11 Jun 2019, at 23:57, Bryan Hansen ***@***.***> wrote:
Hi Gunnar,
When do you think the next version would be ready? I can see making the new .star file for the clusters will be really useful.
How do you go from the .log to making the new .star file for the clusters now?
Bryan
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--
_____________________________________________________________
Prof. Dr. Gunnar F. Schröder
Computational Structural Biology Group
Institute of Complex Systems (ICS-6)
Forschungszentrum Jülich
tel +49-2461-61-3259
http://www.schroderlab.org
from chep.
hansenbry
commented on August 28, 2024
That's awesome Gunnar! I think we can wait for the end of the week or early next week for the new version. We are super excited for this tool! It's potentially going to be HUGE for us.
Bryan
from chep.
krpothula
commented on August 28, 2024
Hi Bryan,
Now we attached the code for writing clusters. Please try and let us know your comments.
Best,
Karunakar
from chep.
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