Globplot/Globpipe in python3
Has anyone tried to modify the Globpipe (http://globplot.embl.de/) code in python3? I found out that the current version imports some modules that are obscure in py3.
python
globplot
• 1,978 views
•
link
written
by
User 6777 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Where can I find GMAP? All links appear dead. Was the project abandoned?
written by mcsimenc •I want to use GMAP for my project, because Exonerate doesn't seem to be able to do multiprocessing/threading. I see the repo: https://github.com/juliangehring/GMAP-GSNAP has not …
-
From the concatenated fasta file, how to find individual range of locations in each protein sequence
written by User 6777 •Hi all, I have a protein fasta file (protein.txt) like: >a mnspq >b rstuvw >c mnqa Note that the length of a, b and c …
-
Selecting non-redundant Gene Ontology terms
written by saketn •Hi, I am trying to assign Gene Ontology (GO) Biological Process terms to proteins so that I can decompose a protein interaction network into GO-derived …
-
How To Create Pam Or Blossum Matrix (Substitution Matrix)
written by loicatraile •<p>Hi guys! I´m looking for a hint or if someone has a recipe on how to compute a PAM or BLOSSUM matrix. I found this …
-
Can I Use The Gatk Snp Calling On Sam Files With Missing Quality Values
written by Varun Gupta<p>Hello Everyone</p> <p>I have a set of <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> files obtained by using bowtie1 as aligner. I want to use GATK's current version for carrying …
-
Orthomcl Output File Processing
written by User 6777 •<p>Hi all, </p> <p>Anyone has any idea about the processing of output file that has been generated by orthomcl (groups.txt)?? I generate a bit matrix …
-
Orthomcl Blast Error: No Hits Are Being Saved
written by User 6777 •<p>when i try to run blast in orthomcl using the command below:</p> <pre><code>blastp -query goodProteins.fasta -db goodProteins.fasta -evalue 1e-5 -out goodProteins.blast -outfmt 6 -seg yes …
-
Multithreading Clustalw On Amazon Ec2
written by User 7351 •<p>I just got acquainted with Amazon EC2 and need to conduct some rather large alignments. Unfortunately, each alignment uses only one out of 8 cores …
-
Fasta Module In Python/Biopython
written by openly •<p>I am trying to run a python script <a href="http://globplot.embl.de/html/GlobPipe-2.3.tgz">http://globplot.embl.de/html/GlobPipe-2.3.tgz</a> for predicing globular regions in proteins. Unfortunalte, there is a Python error which is probably …
-
Appending Seqrecords In Biopython
written by User 5433 •<p>I'm trying to generate a test dataset of randomly sampled 150bp sequences from a complete genome. I found what appeared to be the perfect Biopython …
It looks like Globpipe was written before python3 existed...
Yes. It was written in Python2. But it should be converted to py3 to remain practical. I asked Michael Kuhn (author) also, but he is saying he can't help. The problem is with the obscure modules that are imported in python2. I don''t know how to change those modules in code. Code is here: https://github.com/mkuhn/globplot.
fpformat can be replaced by standard python. For example,
fpformat.fix(something, 10)isfloat("{:15.10f}".format(something)).popen3can be replaced byPopenfrom the subprocess module.As an aside, I wouldn't be surprised if the majority of python programs are still python2 only. While there are some benefits to python3, there's no real killer feature (UTF8 everywhere and a 64bit integer type aren't really killer features).