SPSS syntax for naming individual analyses in output file outline - syntax

I have created syntax in SPSS that gives me 90 separate iterations of general linear model, each with slightly different variations fixed factors and covariates. In the output file, they are all just named as "General Linear Model." I have to then manually rename each analysis in the output, and I want to find syntax that will add a more specific name to each result that will help me identify it out of the other 89 results (e.g. "General Linear Model - Males Only: Mean by Gender w/ Weight covariate").
This is an example of one analysis from the syntax:
USE ALL.
COMPUTE filter_$=(Muscle = "BICEPS" & Subj = "S1" & SMU = 1 ).
VARIABLE LABELS filter_$ 'Muscle = "BICEPS" & Subj = "S1" & SMU = 1 (FILTER)'.
VALUE LABELS filter_$ 0 'Not Selected' 1 'Selected'.
FORMATS filter_$ (f1.0). FILTER BY filter_$.
EXECUTE.
GLM Frequency_Wk6 Frequency_Wk9
Frequency_Wk12 Frequency_Wk16
Frequency_Wk20
/WSFACTOR=Time 5 Polynomial
/METHOD=SSTYPE(3)
/PLOT=PROFILE(Time)
/EMMEANS=TABLES(Time)
/CRITERIA=ALPHA(.05)
/WSDESIGN=Time.
I am looking for syntax to add to this that will name this analysis as: "S1, SMU1 BICEPS, GLM" Not to name the whole output file, but each analysis within the output so I don't have to do it one-by-one. I have over 200 iterations at times that come out in a single output file, and renaming them individually within the output file is taking too much time.

Making an assumption that you are exporting the models to Excel (please clarify otherwise).
There is an undocumented command (OUTPUT COMMENT TEXT) that you can utilize here, though there is also a custom extension TEXT also designed to achieve the same but that would need to be explicitly downloaded via:
Utilities-->Extension Bundles-->Download And Install Extension Bundles--->TEXT
You can use OUTPUT COMMENT TEXT to assign a title/descriptive text just before the output of the GLM model (in the example below I have used FREQUENCIES as an example).
get file="C:\Program Files\IBM\SPSS\Statistics\23\Samples\English\Employee data.sav".
oms /select all /if commands=['output comment' 'frequencies'] subtypes=['comment' 'frequencies']
/destination format=xlsx outfile='C:\Temp\ExportOutput.xlsx' /tag='ExportOutput'.
output comment text="##Model##: This is a long/descriptive title to help me identify the next model that is to be run - jobcat".
freq jobcat.
output comment text="##Model##: This is a long/descriptive title to help me identify the next model that is to be run - gender".
freq gender.
output comment text="##Model##: This is a long/descriptive title to help me identify the next model that is to be run - minority".
freq minority.
omsend tag=['ExportOutput'].
You could use TITLE command here also but it is limited to only 60 characters.
You would have to change the OMS tags appropriately if using TITLE or TEXT.
Edit:
Given the OP wants to actually add a title to the left hand pane in the output viewer, a solution for this is as follows (credit to Albert-Jan Roskam for the Python code):
First save the python file "editTitles.py" to a valid Python search path (for example (for me anyway): "C:\ProgramData\IBM\SPSS\Statistics\23\extensions")
#editTitles.py
import tempfile, os, sys
import SpssClient
def _titleToPane():
"""See titleToPane(). This function does the actual job"""
outputDoc = SpssClient.GetDesignatedOutputDoc()
outputItemList = outputDoc.GetOutputItems()
textFormat = SpssClient.DocExportFormat.SpssFormatText
filename = tempfile.mktemp() + ".txt"
for index in range(outputItemList.Size()):
outputItem = outputItemList.GetItemAt(index)
if outputItem.GetDescription() == u"Page Title":
outputItem.ExportToDocument(filename, textFormat)
with open(filename) as f:
outputItem.SetDescription(f.read().rstrip())
os.remove(filename)
return outputDoc
def titleToPane(spv=None):
"""Copy the contents of the TITLE command of the designated output document
to the left output viewer pane"""
try:
outputDoc = None
SpssClient.StartClient()
if spv:
SpssClient.OpenOutputDoc(spv)
outputDoc = _titleToPane()
if spv and outputDoc:
outputDoc.SaveAs(spv)
except:
print "Error filling TITLE in Output Viewer [%s]" % sys.exc_info()[1]
finally:
SpssClient.StopClient()
Re-start SPSS Statistics and run below as a test:
get file="C:\Program Files\IBM\SPSS\Statistics\23\Samples\English\Employee data.sav".
title="##Model##: jobcat".
freq jobcat.
title="##Model##: gender".
freq gender.
title="##Model##: minority".
freq minority.
begin program.
import editTitles
editTitles.titleToPane()
end program.
The TITLE command will initially add a title to main output viewer (right hand side) but then the python code will transfer that text to the left hand pane output tree structure. As mentioned already, note TITLE is capped to 60 characters only, a warning will be triggered to highlight this also.
This editTitles.py approach is the closest you are going to get to include a descriptive title to identify each model. To replace the actual title "General Linear Model." with a custom title would require scripting knowledge and would involve a lot more code. This is a simpler alternative approach. Python integration required for this to work.

Also consider using:
SPLIT FILE SEPARATE BY <list of filter variables>.
This will automatically produce filter labels in the left hand pane.
This is easy to use for mutually exclusive filters but even if you have overlapping filters you can re-run multiple times (and have filters applied to get as close to your desired set of results).
For example:
get file="C:\Program Files\IBM\SPSS\Statistics\23\Samples\English\Employee data.sav".
sort cases by jobcat minority.
split file separate by jobcat minority.
freq educ.
split file off.

Related

What is wrong with this PDF file?

I have to work with a PDF form created by a person unknown to me. Why did the program with which the form was created (Word + PDF export?) split the term "Stunde" into "S", "t" and "unde" in line 6909 of the decoded PDF? There is no visual break between the three parts.
/TT1 1 Tf
11.04 0 0 11.04 59.16 476.1203 Tm
(Datum)Tj
/C2_1 1 Tf
<0003>Tj
/TT1 1 Tf
(der)Tj
0.424 -1.315 Td
(Tätigkeit)Tj
-0.0022 Tc 0 11.04 -11.04 0 261.24 437.7203 Tm
[(Ve)-4.6<7267fc74>-4.2(ungssat)-4.2(z)]TJ
/C2_1 1 Tf
0 Tc <0003>Tj
/TT1 1 Tf
-0.0021 Tc 0.935 -1.315 Td
[<2880>-6.1(/)-7.2(S)0.8(t)-4.1(unde)-4.5(\))]TJ % <<< the important line
0 Tc 11.04 0 0 11.04 340.92 468.8003 Tm
(Anlass/Art)Tj
/C2_1 1 Tf
resulting in
[]
To get the source code above, I decoded the PDF file as described here. I have no know-how concerning the PDF file format.
Background: I had to replace the word "Stunde", it drove me crazy to find the place where "Stunde" was written (in parts) within the source code, since no free PDF editor seems to be able to work with horizontal text without problems.
Academic Bonus questions: Is it possible to set the sum over a column as default value for a form field? (Modifiable; changed every time the column is changed.) Why was I able to replace "Stunde" with "Einsatz" without making the PDF file corrupt due to now irregular offsets?
Why did the program with which the form was created (Word + PDF export?) split the term "Stunde" into "S", "t" and "unde" in line 6909 of the decoded PDF?
As #gettalong mentioned in his answer, in your case this most likely has been done to apply kerning.
If you start looking into the outputs of some other PDF producers, you'll see that this export from Word actually is very unobtrusive in regard to splitting words:
there are PDF producers that draw each character individually after explicitly setting the text matrix for it, and
there also are PDF producers that have the width information for the characters of the used fonts set to zero and use the numbers in TJ instructions to forward the current text matrix between characters accordingly.
And this doesn't cover all the variants to be found, not by far...
Thus,
I had to replace the word "Stunde", it drove me crazy to find the place where "Stunde" was written (in parts) within the source code
in your case replacing actually was a fairly trivial task...
Is it possible to set the sum over a column as default value for a form field? (Modifiable; changed every time the column is changed.)
If all the column values in question are stored in form fields, you can use JavaScript to recalculate sums after form changes. To have it serve as "default" only, you can use some other (hidden) field for a flag whether the field has already been touched. Beware, though: JavaScript is not supported by all PDF viewers. Furthermore, the JavaScript object model for PDF is not specified in an independent (like ISO) specification but in an Adobe one which can make interpretation of the specification biased.
Why was I able to replace "Stunde" with "Einsatz" without making the PDF file corrupt due to now irregular offsets?
As we don't know how exactly you applied the changes, this obviously is hard to tell.
Most likely, though, you did corrupt the PDF and the PDF viewers you opened it in merely repair the corruption under the hood. There is a strong tendency in PDF viewers to do such under-the-hood repairs without informing the user; the result is that a large part of the PDFs in the wild actually being broken.
You don't see a visual break but the standard distance between "S", "t" and "unde" has been changed nonetheless. This is done by PDF writers that support e.g. kerning so that the word appear nicer. This is the reason why it is split that way.

merge pdf files with extra blank page at the end of odd-paged documents - qpdf

i'm hoping to use qpdf for this.
I'm printing lots of small files and need to print them double sided, so I merge, say, 20 documents and wind up with a single 200 page pdf. I then can let the printer print, even pages reversed, then flip the stack over and put it back into the printer and print the odd ones, so we're using both sides of the paper.
my question is how i can detect and add a single blank page to the end of any document that has an odd number of pages; that way, when i do double sided printing, each document is completely separate from the others, rather than just printing on the back of a finished document.
If you have an odd number of pages, just call
cpdf -pad-multiple
with the even number one larger than the odd number. For example, for 19 pages, run
cpdf -pad-multiple 20 in.pdf -o out.pdf
You can get the number of pages with cpdf -pages.
Currently using FOSS qpdf 10.6.3 this is possible in windows by something like (note %% is for use in a batch.cmd)
for /f %%N in ('qpdf --show-npages in.pdf') do set VAR=%%N& set /a num=2*(%%N/2)+1& if .%num%.==.%var%. qpdf in.pdf --pages . blankA4P.pdf -- out.pdf
Note the integer maths is rounding odds down so 31 = 30+1 is a match but 32 = 32+1 will not match.
Without checking the dimensions of in.pdf is not easy to know if blankA4P.pdf is required so best to either get last page dimensions for a matching prepared page or batch apply each shape in groups.
using cpdf (as mentioned in previous answer) we could build a blank on demand along the lines of cpdf -create-pdf -create-pdf-pages 1 -o blank.pdf and use a page size, However cpdf has the even better option for OP case so simplest is cpdf -pad-multiple 2 in.pdf -o out.pdf as 1st hinted by johnwhittington
So now we have a perfect short one line solution. however cpdf is not FOSS
I have queried with qpdf if there may be a simpler way with just qpdf so watch this space https://github.com/qpdf/qpdf/issues/753
I will continue looking for a way to streamline this further because I would love a simpler workflow, but here is what I use to ensure I do not have two articles sharing one sheet of paper.
pacman::p_load(tidyverse, pdftools, qpdf)
# some prep
directory <- "Some/FileFolder/Path"
filelist <- (paste(directory, "/",
list.files(directory,
pattern = "*.pdf"), sep = ""))
# bust apart all pdf to inspect
my_pages <- as.list(lapply(filelist, pdf_split))
page_summ <- cbind.data.frame(filelist,
lengths(my_pages)) %>%
rename(filename = 1,
pages = 2) %>%
mutate(is_odd = pages %%2==1)
# separate into odd and even sets
odd_docs <- page_summ %>%
filter(is_odd == TRUE)
even_docs <- page_summ %>%
filter(is_odd == FALSE)
# I could not find an R process for adding a page to PDFs.
# For now, I will add a buffer page to docs via a PDF program.
# Once you are satisfied with your even_docs subset, pdf_combine
tocombine <- as.data.frame(even_docs$filename)
lapply(tocombine, pdf_combine)
This auto-generates the combo file into the previously defined directory. The new file name is not able to be set using "output = " within lapply(). Look for new file name = "firstnameintocombine_combined.pdf".

Adjusting the MAFFT command line algorithm to better account for gaps

I've been attempting to use the MAFFT command line tool as a means to identify coding regions within a genome. My general process is to align the amino acid consensus sequence of a gene to a translated reading frame of a target sequence. My method has been largely successful. However, I've noticed some peculiar alignments which will unfortunately impede my annotation method. The following is one such example (Note - I've also included a pairwise alignment from the Pairwise2 Biopython module to demonstrate my desired output. Unfortunately, the computation time for Pairwise2 is nearly 20 times slower than MAFFT command line):
from time import *
from Bio.SubsMat import MatrixInfo as matlist
from Bio import pairwise2
from Bio.pairwise2 import format_alignment
from Bio.Align.Applications import MafftCommandline
startTime = time()
sample_tList = [['>Frame 1', 'RIGVGSIPRHLYCQELPLAQPKTCCAETPFRDSPLQGRLGVCPHLASGVALLYGLSTPLTMSGILDRCTCTPNARVFMAEGQVYCTRCLSARSLLPLNLQVPELGVLGLFYRPEEPLRWTLPRAFPTVECSPAGACWLSAIFPIARMTSGNLNFQQRMVRVAAEIYRAGQLTPAVLKVLQVYERGCRWYPIVGPVPGVGVYANSLHVSDKPFPGATHVLTNLPLPQRPKPEDFCPFECAMADVYDIGHGAVMFVAGGKVSWAPRGGDEVRFETVPEELKLIANRLHISFPPHHLVDMSKFAFIVPGSGVSLRVEHQHGCLPADIVPKGNCWWCLFDLLPPGVQNREIRYANQFGYQTKHGVSGKYLQRRLQINGLRAVTDTHGPIVVQYFSVKESWIRHFRLAGEPSLPGFEDLLRIRVESNTSPLADKDEKIFRFGSHKWYGAGKRARKARSGATTTVAHRASSARETRQAKKHEGVDANNAAHLEHYSPPAEGNCGWHCISAIVNRMVNSNFETTLPERVRPSDDWATDEDFVNTIQILRLPAALDRNGACKSAKYVLKLEGEHWTVSVAPGMSPSLLPLECVQGCCEHKGGLGSPDAVEVSGFDPTCLDRLAEVMHLPSSVIPAALAEMSNNSDRPASLVNTAWTVSQFYARHTGGNHRDQVRLGKIISLCQVIEECCCHQNKTNRATPEEVAAKIDQYLRGATSLEECLIKLERVSPPSAADTSFDWNVVLPGVEAAGPTTEQPHANQCCAPVPVVTQEPLDKDSVPLTAFSLSNCYYPAQGDEVRHRERLNSVLSKLEEVVLEEYGLMPTGLGPRPVLPSGLDELKDQMEEDLLKLANAQATSEMMALAAEQVDLKAWVKSYPRWIPPPPPPKVQPRRMKPVKSLPENKPVPAPRRKVRSDPGKSILAVGGPLNFSTPSELVTPLGEPVLMPASQHVSRPVTPLSEPAPVPAPRRIVSRPMTPLSEPTFVFAPWRKSQQVEEANPAAATLTCQDEPLDLSASSQTEYEAYPLAPLENIGVLEAGGQEAEEVLSGISDILDNTNPAPVSSSSSLSSVKITRPKYSAQAIIDSGGPCSGHLQKEKEACLRIMREACDAARLGDPATQEWLSHMWDRVDVLTWRNTSVYQAFRTLDGRFGFLPKMILETPPPYPCGFVMLPHTPTPSVSAESDLTIGSVATEDVPRILGKTENTGNVLNQKPLALFEEEPVCDQPAKDSRTLSRESGDSTTAPPVGTGGAGLPTDLPPLDGVDADGGGLLRTAKGKAERFFDQLSRQVFNIVSHLPVFFSHLFKSDSGYSPGDWGFAAFTLFCLFLCYSYPFFGFAPLLGVFSGSSRRVRMGVFGCWLAFAVGLFKPVSDPVGAACEFDSPECRNILHSFELLKPWDPVRSLVVGPVGLGLAILGRLLGGARYIWHFLLRLGIVADCILAGAYVLSQGRCKKCWGSCIRTAPNEIAFNVFPFTRATRSSLIDLCDRFCAPKGMDPIFLATGWRGCWTGQSPIEQPSEKPIAFAQLDEKRITARTVVSQPYDPNQAVKCLRVLQAGGAMVAEAVPKVVKVSAIPFRAPFFPTGVKVDPECRIVVDPDTFTTALRSGYSTTNLVLGVGDFAQLNGLKIRQISKPSGGGPHLIAALHVACSMVLHMLAGVYVTAVGSCGTGTSDPWCANPFAVPGYGPGSLCTSRLCISQHGLTLPLTALVAGFGLQEIALVVLIFVSIGGMAHRLSCKADMLCILLAIASYVWVPLTWLLCVFPCWLRWFSLHPLTILWLVFFLISVNMPSGILAVVLLVSLWLLGRYTNIAGLVTPYDIHHYTSGPRGVAALATAPDGTYLAAVRRAALTGRTMLFTPSQLGSLLEGAFRTRKPSLNTVNVVGSSMGSGGVFTIDGRIKCVTAAHVLTGNSARVSGVGFNQMLDFDVKGDFAIADCPNWQGVAPKTQFCGDGWTGRAYWLTSSGVEPGVIGDGFAFCFTACGDSGSPVITEAGELVGVHTGSNKQGGGIVTRPSGQFCNVTPIKLSELSEFFAGPKVPLGDVKVGSHIIKDTSEVPSDLCALLAAKPELEGGLSTVQLLCVFFLLWRMMGHAWTPLVAVGFFILNEVLPAVLVRSVFSFGMFALSWLTPWSAQVLMIRLLTAALNRNRVSLIFYSLGAVTGFVADLATTQGHPLQAVMNLSTYAFLPRMMVVTSPVPAIACGVVHLLAIILYLFKYRCLHHVLVGDGAFSAAFFLRYFAEGKLREGVSQSCGMSHESLTGALAIKLSDEDLDFLTKWTDFKCFVSASNMRNAAGQFIEAAYAKALRIELAQLVQVDKVRGTLAKLEAFADTVAPQLSPGDIVVALGHTPVGSIFDLKVGSTKHTLQAIETRVLAGSKMTVARVVDPTPAPPPAPVPIPLPPKVLENGPNAWGGEDRLNKRKRRRMEAVGIFVMDGKKYQKFWDKNSGDVFYEEVHNSTDEWECLRAGDPADFDPETGIQCGHVTIEDKVYNVFTSPSGRRFLVPANPENRRIQWEAARLSVEQALGMMNVDGELTAKELEKLKRIIDKLQGLTKEQCLNCPPVAPAVVAAAWLLLRQRKNFTTGPSPDLTKWPVRLSRTRSSTTNIRLPNRLMVVLCSCAPLFLRLMSSPALMHLLSYLPATGRETLGLMARFGILRPRPPKRKSHLVRKYRLVTLGAVTHLKLVSLISCTLLGATLSGKEFYRIQGLETYLTEPPVTLEAQCMRLPASRPMLLRLMGVPSWPQPCPPVLSCMYRPFQRPSLIILILGLTALNSQSTVVRMLLGTSPNTICPPKALFCLEFFALCGSTCLPMWVSARPFIGLPLTLPRILWLEMGTDFQPRIFRASLKSTFCAHRLCEKTGKLLLLVPSRSSIVGRRRLGQYLALITLRWPTGQRVVLPRASKRHSTRPSPSEKTNLRNYILQFAGALKLILHPAIDPHLQLSAGSLPIFFMNSPVLKSIYRRTCLTAVTTYWLRSPARLREAACRLATRLPPCQTPFTAYMHSTWCSVTLKVVTLMAFCFCKTSSLRTCSRFNPSSIQTTSCCMPSLPPCQITTGGLNITLCVSKRTQRRQPQTRHHFVAGMGVSSLTVTGFLRPSPTIRQAMSLNTTPRRLQYLWTAVLVSMILSGLKSSWLVRSAPARTVTASQARRSSCPCGKNSGPIMKGRSPECAGTAEPRLRTPLPVASTSVLTTPISTSIVLSSGVATRRVLALVVSVNLPWEKAQVLWMRCNKSRISLRGLSCMWSRVSPLLTQVDTKLAADSPLGVASGETKLTCQTVIMPVPPCSPLVKRSTWSLSPPTCCAAGSSSVPPALGKHTGSSNRSRMVMSFTRQLTRPCLTLGLWGCAGSTSQRVRRCNSLPPLVPARGFASWPAVGVLVRIPFWTKQRIAITLMSGFLAKPPLPAEISNNSTRWVLTLIAMFLTSCLRPNRPSGDSDRISVMPSNQITGTNLCPWSTQPVPRWTNLSGMGKSSPPTTGTERTAPSLSTPVKVPHLMWLHCICPLKIHSTGNEPLLLSPGQDMQSSCMTHTGNCRACLIFLRKAHPSTSQCSVTSSSYIEITKNARLLRLAMEINSGLQTSALILSAPFVQIWKGRAPRSPKLHITWGSISHLIHSLLNSQQNSHPTGPWQPRTMKSGLIGWLPAFAPSINIAARALVQAIWWAPRCFAPQGLCHTTSQNLLGARLKCFLRQSSAPAELRIAGSTSMIGSEKLLSPSHMPSLATSKALPVGDVITSPPDTFRASFLRNQLRSGFLAPEKLQRQFAHQMCTSQILKRTSTQRPSPSAGKCWILEKSDWSGKTRRPIFNLKAAISPGINLQATPHTSEFLLILQCIWTPAWALPFATGGLLGPPIGELTSRSPLMITVPKSFCLVHTMVKCLQGTKFWRARSSRLTTQGTNTLGDLNRIQRICTSLLGMVRTGRIIMKRFGRARKGKFIRLLPPASFIFPRALSLNQLATEMKWGLCRASLTKLVNFLWMLSRNFWCPLLISSYFWPFCLASPSPAGWWSFASDWFAPRYSVRALPFTLSNYRRSYEAFLSQCQVDIPTWGVKHPLGILWHHKVSTLIDEMVSRRMYRIMEKAGQAAWKQVVSEATLSRISNLDVVAHFQHLAAIEAETYKYLASRLPMLHNLRMTGSNVTIVYNSTLNQVFAIFPTSGSRPRLHDSQQWLIAVHSSIFSSVVASCTLFVVLWLRIPMLRSVFGFRWLGAIFLLNSRITRCVRLASPGRPLLRSMNPVGLFGAGGMTDAVRTTMTNGSWFRLASAKATPVFTPGWRSCHSATRPSSIPRYLGGTVKFMLTSRTNSFAPSTTGRTPPCLAMTTFQPYFRPTTNIRSTAVIGFTNGCAPSFPLGWFMFRGFSGVRLQAMFQFKSFRHQDQHYRSIRLCCPPGHQLPVWRLAPSDGSQELSVPHGDRDTRVHHHHSQCHRELFTFFSPHAFLLPFLCFDEKGIQSGIWQCVRHRGCVCLYQLRPTCQGVHPTLLGSRSCATASFHDTDHEVGNRFSLSFCHPTGNLNVQVCWGNAPRAVTRNCFLCGVSCRSVLLCSSTPAATAALIFSFITRYVSMAQIGWQKDLTGQWRLLSFFLCLTLFPMEHSPPAIFLTRLVSLCPPPGSITGGMSVVSMRSVLWLRFASSLGLRRTACPGATLVLDTPTSFWTLRADSIVGGRPLLRKGVRLKSRVTSTSKELCLMVPWQPLPEFQRNNGVVSRRLLPHGSTKGAFGVFHYLYASDDICSKGKSRPTARASAPFDLPELCFYLRVHDIRALSEHKGRAHYGGSSCTSLGGVLSHRNLEIHHLQMPFVLARPQVHSGPCPPRRKCRGLSSDCGKPRICRPASRLHYGRHIGARVEKPRVGWQKSCTGSGKPCQICQITTASSKRERRGTASQSISCARCWVRSSPNKTSPEARDRGRKIIREARRSPIFLRLKKMSGTTSPLVSGNCVCRRSRLPLTRAPGHVPCQIQGGVTLWSLVCRRIILCASASQHHPQHDELAFFGHLGVMIGRMCGEWHLTLCLVTYSIRATVWGSLIGENHAAAIKKKKKKKK'], ['>ORF2_GP2', 'MKWGLCKASLTKLANFLWMLSRSFWCPLLISSYFWPFCLASQSPVGWWSFASDWFAPRYSVRALPFTLSNYRRSYEAFLSQCQVDIPTWGVKHPLGVLWHHKVSTLIDEMVSRRMYRIMEKAGQAAWKQVVSEATLSRISGLDVVAHFQHLAAIEAETCKYLASRLPMLHNLRLTGSNVTIVYNSTLDQVFAIFPTPGSRPKLHDFQQWLIAVHSSIFSSVAASCTLFVVLWLRIPMLRSVFGFRWLGATFLLNSW']]
ex_file = open("newTempFile112233.fasta", "w")
for items in sample_tList:
ex_file.write(items[0] + "\n")
ex_file.write(items[1] + "\n")
ex_file.close()
in_file = '.../msa_example.fasta'
mafft_exe = '/usr/local/bin/mafft'
mafft_cline = MafftCommandline(mafft_exe, input=in_file) #have to change file path
#mafft_cline = MafftCommandline(mafft_exe, input=in_file, localpair=True, lexp=-1.5, lop=0.5)
stdout, stderr = mafft_cline()
print(stdout)
test_align = AlignIO.read(io.StringIO(stdout), "fasta")
#print(test_align)
os.remove("newTempFile112233.fasta")
print('Total time = ' + str(time() - startTime))
startTime = time()
matrix = matlist.blosum62
pWise_align = pairwise2.align.localds(sample_tList[0][1], sample_tList[1][1], matrix, -6, -1)
print(format_alignment(*pWise_align[0]))
print('Total time = ' + str(time() - startTime))
I've attempted to change the MAFFT command line alignment algorithm by referencing the help document (http://mafft.cbrc.jp/alignment/software/manual/manual.html). I don't get any error messages, but the alignment output does not change. I'm unsure what adjustments need to be made. I believe that by increasing the gap extension penalty (which is zero by default), the alignment will be improved. I haven't been able to find many documentation examples where custom variables are used when using MAFFT command line on this forum or through Google search. Help is much appreciated. For reference, documentation on the Pairwise2 alignment parameters can be found here: http://biopython.org/DIST/docs/api/Bio.pairwise2-module.html
Managed to figure out a possible solution. The alignment of the example sequences provided results in a long terminal/end gap which should not be present. Changing the MAFFT alignment algorithm using localpair, lexp, and lop had no effect (causing me a good deal of confusion). However, I have noticed differences in the alignment output when each input sequence is reversed. Oddly, the only way I was able to remove the terminal/end gap was to set the lop (gap opening penalty) to a lesser amount relative to lexp (gap extension penalty). I suspect my solution is niche and may not be applicable to other similar occurrences of terminal gaps. Changing the alignment settings also likely reduces the optimal alignment.
Going forward, I plan to use an automated process to run alignments of consensus sequences to raw sequences. In the event I detect irregularities with the alignment output (specifically terminal gaps), I'll attempt to reverse the input sequences and apply custom alignment settings. I suppose if that isn't a consistent solution, I'll figure out a way to refine the alignment output directly.
For anyone curious, I used a lexp value of -1.5 and lop value of 0.5 (now included in a hashed out line in my example code).

Hide Labels with No Data in SPSS

I just started using SPSS, there is a option of Select cases that I was trying in SPSS, and later on finding frequency based on that filter.
For Eg:
Suppose Q1 has 12 parts, Q1_1 Q1_2 Q1_3 Q1_4 Q1_5 Q1_6 Q1_7 Q1_8 Q1_9 Q1_10 Q1_11 Q1_12
I want to see data in these variables based on a condition that I used in select cases. Now when I try to see frequencies of these variables based on the filter, only 4 out of 12 satisfy has data.
Now my question is can I hide rest 8 and show only 4 with data on my output window.
It's not entirely clear what you are trying to describe however reading between the lines, I'm guessing you are trying to delete tables generated from FREQUENCIES which may happen to be empty (likely due to a filter applied but perhaps not necessarily either)
You could do this with SPSS Scripting but avoiding that, you may want to explore using CTABLES, which though may not be in the exact same format as FREQUENCY table output it will still none the less retrieve the same information.
Solution below. Assumes Python Integration with SPSS SELECT VARIABLES installed and of course the CTABLE add-on module.
/****** Simulate example data ******/.
input program.
loop #j = 1 to 100.
compute ID=#j.
vector Q(12).
loop #i = 1 to 12.
do if #j<51 and #i<9.
compute Q(#i) = $sysmis.
else.
compute Q(#i) = trunc(rv.uniform(1,5)).
end if.
end loop.
end case.
end loop.
end file.
end input program.
execute.
/************************************/.
/* frequencies without filtering applied */.
freq q1 to q12.
/* frequencies WITH filtering applied */.
/* Empty table here shoult be removed */.
temp.
select if (ID<51).
freq q1 to q12.
spssinc select variables macroname="!Qp" /properties pattern = "^Q\d+$"/options separator="+" order=file.
spssinc select variables macroname="!Qs" /properties pattern = "^Q\d+$"/options separator=" " order=file.
temp.
select if (ID<51).
ctables /table (!Qp)[c][count colpct]
/categories variables=!Qs empty=exclude.
Note if you had assess empty variables at a total level then there is a function in spssaux2 (spssaux2.FindEmptyVars) which could help you find the empty variables and then you could build the syntax to exclude these and so contain the variables with only valid responses and then run FREQUENCIES. But I don't think spssaux2.FindEmptyVars will honor any filtering.

Update existing excel file template formulas using ruby

I had been using spreadsheet to read in a template excel file, modify it and output a new file for the end-user.
As far as I can identify from the documentation spreadsheet provides no way to input or edit formulas in the produced document.
However, the purpose of my script is to read an undefined number of items from a site and enter them into the spreadsheet, then calculate totals and subtotals.
The end user (using excel or libreoffice etc) is then able to make slight modifications to the quantity of items whilst the totals update (due to formulas) as they are accustomed.
I have looked into the writeexcel gem which claims to be able to input formulas, but I can't see how to take an existing template file and modify it to produce my output. I can only create fresh workbooks.
Any tips please? I do not want to use Win32OLE.
This is surprisingly difficult; apparently all Gems for handling Excel files are missing some crucial functionality.
I can think of two approaches for this problem:
use a combination of spreadsheet (to read the Excel file) and use writeexcel (to write the output file)
use an input file that already contains the required formulas on a separate "formula" sheet and copies the formulas to the "real" sheet
Here's a simplistic version of the second approach:
require 'rubygems'
require 'spreadsheet'
Dir.chdir(File.dirname(__FILE__))
# input file, contains this data
# Sheet0: headers + data (for this simple demo, we will generate the data on-the-fly)
# Sheet1: Formula '=SUM(Worksheet1.A2:A255) in cell A1
book = Spreadsheet.open 'in.xls'
sheet = book.worksheet 0
formulasheet = book.worksheet 1
# insert some input data (in a real application,
# this data would already be present in the input sheet)
rows = rand(20) + 1
(1..rows).each do |i|
sheet[i,0] = i
end
# add total at bottom of column C
sheet[rows+1,2] = formulasheet[0,0]
# write output file
book.write 'out.xls'
However, this will fail if
you're using the same column for your input data and your totals (since then, the total will try to include itself in the calculation)

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