quwubin/mfeprimer-2.0

MFEprimer-2.0: A fast thermodynamics-based program for checking PCR primer specificity

mfeprimer-2.0's Issues

Some missing prerequisites to install MFEprimer server?

I don't know why, but when I intall a local mirror of MFEprimer-2.0 webserver in a new machine, after I follow https://github.com/quwubin/MFEprimer#create-a-local-mirror-of-mfeprimer-20 and installed Python (>= 2.7), psutil and Flask, it still encounter error:

$ ./MFEprimerWeb.py
Traceback (most recent call last):
  File "./MFEprimerWeb.py", line 25, in <module>
    from chilli import ve
  File "/var/www/cgi-bin/MFEprimerWeb-master/chilli/ve.py", line 12, in <module>
    import cairo
ImportError: No module named cairo

First I try to install pip install pycairo, however it has been removed from the pypi, then I have to pip install cairocffi, and then edit MFEprimerWeb-master/chilli/ve.py: change import cairo to import cairocffi as cairo

After that, it still encounter error:

$ ./MFEprimerWeb.py
Traceback (most recent call last):
  File "./MFEprimerWeb.py", line 35, in <module>
    from cron import get_blog_news
  File "/var/www/cgi-bin/MFEprimerWeb-master/cron/get_blog_news.py", line 6, in <module>
    import pytumblr
ImportError: No module named pytumblr

What should I do is: pip install pytumblr

Then it is OK

Some strang JS errors in MFEPrimerWeb

I don't know how these errors come out. Several months later all are OK. However recently there are some JS errors.

(1) click " Example" in "Enter the primer sequences" leads to a JS error:

TypeError: who is null   function.js:417:9

(2) select the background database leads to a JS error:

ReferenceError: db_selected_changed is not defined

The online server http://www.mfeprimer.com/ is not available

I remember http://www.mfeprimer.com/ is only available long long ago. It can't be accessed in these several months.

Incompatibility with actual version of psutil

It seems that the syntax of psutil has changed.
When running IndexDb.sh I got following the error

Begin indexing ...
Step 1/3: UniFasta done.
Step 2/3: faToTwoBit done.
Step 3/3: Index begin ...
0
Traceback (most recent call last):
  File "/home/maxime/1_MFEprimer/MFEprimer/chilli/mfe_index_db.py", line 227, in <module>
    main()
  File "/home/maxime/1_MFEprimer/MFEprimer/chilli/mfe_index_db.py", line 224, in main
    index(options.filename, options.k)
  File "/home/maxime/1_MFEprimer/MFEprimer/chilli/mfe_index_db.py", line 196, in index
    memory_percent = get_memory_percent()
  File "/home/maxime/1_MFEprimer/MFEprimer/chilli/mfe_index_db.py", line 54, in get_memory_percent
    return p.get_memory_percent()
AttributeError: 'Process' object has no attribute 'get_memory_percent'
Step 3/3: Index done

Changing return p.get_memory_percent() by return p.memory_percent()at line 54 of mfe_index_db.py is fixing it.

See : This link

"No space left on device" bug

When the user doesn't have root access, all the functions using "/temp" directory will cause "No space left on device" error. I think it's better to change the default "parent_dir" in "chilli.session" function as the user output directory.

What's the meaning of negative PPC values

Sometimes I found negative PPC values. They always appear on Seq1xSeq1 or Seq2xSeq2 combinations (that is, FF or RR instead of normal FR combination). But I don't know why this could lead to negative PPC values.

missing possible amplicons

Suppose a pair of PCR primer:

F: ACCAAACCCCAGAGTCAATTAA
R: TCTATCTATTGCACTGCCTGTTG

And the database is:

>seq1
ACTGAGAGTACAACCGCTTCTGCAATGCCAAGTCCAGCAGCAAGTGCTAAGGAAGGGAAG
AACTTTCTTGCCTTGATGCTCAAATTCACCATCTTAATTATACCAAACCCCAGAGTCAAT
TAAAAGTTCAACCAAACGATCATTTTCATGAAGTATTGCAGTTATTGTATAATCTTTTCA
CTGAAAATTACCATCCTTGCTTTTACTAATCAATGCTTGCTCTTCAGCAACAAAGGATGT
TGTGATATTAAGTAAAGGAACATTAAACAATCTCGACACCAGATTGAATATCGATACAGA
TACCCCAACTGCCGCCAATTCAACCGACCCTTCACCACAAAAAAACTAATATTTATCAGC
CAATAGTTACCTGTGTGATTAATAGATAAAGCTACAAAAGCAAGCTTGGTATGATAGTAT
TAATAATAAAAAAAGAAAAAACAAGTATCCAAATGGCCAACAAAGGCTGTATCAACAAGT
GAAGCAATGGGATCAGCAGCCAAAGCCAATGCAACAGGCAGTGCAATAGATAGATGCCAA
TTTTTAACGATAGTTACATGATTCAACTAATTTGATGAATCAAGTCTTAAACTTTCTAAA
ACCTGAAACTAATGCATGATTCAATTTCTAGAAATGTTGAATCTTCCATCATAGA
>seq2
CAGCAAGTGCTAAGGAAGGGAAGAACTTTCTTGCCTTGATGCTCAAATTCACCATCTTAA
TTATACCAAACCCCAGAGTCAATTAAAAGTTCAACCAAACGATCATTTTCATGAAGTATT
GCAGTTATTGTATAATCTTTTCACTGAAAATTACCATCCTTGCTTTTACTAATCAATGCT
TGCTCTTCAGCAACAAAGGATGTTGTGATATTAAGTAAAGGAACATTAAACAATCTCGAC
ACCAGATTGAATATCGATACAGATACCCCAACTGCCGCCAATTCAACCGACCCTTCACCA
CAAAAAAACTAATATTTATCAGCCAATAGTTACCTGTGTGATTAATAGATAAAGCTACAA
AAGCAAGCTTGGTATGATAGTATTAATAATAAAAAAAGAAAAACAAGTATCCAAATGGCC
AACAAAGGCTGTATCAACAAGTGAAGCAATGGGATCAGCAGCCAAAGCCAATGCAGCAGG
CAGTGCAATAGATAGATGCCAATTTTTAACGATAGTTACATGATTCAACTAATTTGATGA
ATCAAGTCTTAAACTTTCTAAAAC

Index the database with all default parameters, and search the query primer in the database would leads to a single hit on seq1, seems as if the primer is unique in the database:

                                                                  FP      RP      FP      RP      FP      RP 
                                                 Size    PPC      Tm      Tm      ΔG     ΔG    3'ΔG   3'ΔG
Primers producing potential PCR products:        (bp)    (%)      ℃      ℃      (kcal/mol)        (kcal/mol)  


1: seq1                                           433    96.9    58.1    59.1   -21.7   -23.0    -0.7    -2.6


>>>F
   1                    22
5' ACCAAACCCCAGAGTCAATTAA 3'
   ::::::::::::::::::::::                                                                 534
5' ACCAAACCCCAGAGTCAATTAAaagttcaaccaaacgatcat...atcagcagccaaagccaatgCAACAGGCAGTGCAATAGATAGA 3'
   102                                                              :::::::::::::::::::::::
                                                                 3' CAACAGGCAGTGCAATAGATAGA 5'
                                                                   23                     1
                                                                                          R<<<

However, in fact, this primer might also target on seq2, only one mismatch in the R primer (This graph is made manually, MFEPrimer can not report this hit):

>>>F
   1                    22
5' ACCAAACCCCAGAGTCAATTAA 3'
   ::::::::::::::::::::::                                                                 496
5' ACCAAACCCCAGAGTCAATTAAaagttcaaccaaacgatcat...atcagcagccaaagccaatgCAGCAGGCAGTGCAATAGATAGA 3'
    65                                                              :: ::::::::::::::::::::
                                                                 3' CAACAGGCAGTGCAATAGATAGA 5'
                                                                   23                     1
                                                                                          R<<<

In fact, this prodcut could still be produced in real PCR

We are developing MFEprimer-2.0

Some new features will be reported later.