Trying to run a program within a python script on multiple output files creating by the same script

Unaiza Batool ubatool at ufl.edu
Mon Apr 24 16:53:56 EDT 2017


On Monday, April 24, 2017 at 3:52:09 PM UTC-4, Peter Otten wrote:
> Unaiza Batool wrote:
> 
> > i'm confused here as the script gives an error saying simple_to_fasta and
> > fasta_to_mafft are not defined. 
> 
> You have to write this functions yourself (I gave one example) and make sure 
> that they are defined before the 'for barcode' loop.
> 
> > How do I combine the part of infile,
> > outfile with the conversion. You said it should go in the for barcode
> > loop? Or just it just go after infname has it's correct value or just
> > before each command when the new output file is needed?
> 
> A sketch of the final script (pseudo code, not runnable Python):
> 
> for barcode in barcodes
>     write simple file
>     convert simple file to fasta
>     convert fasta file to mafft
>     etc
> 
> To illustrate the idea here's a runnable example that reads words from a 
> file into individual files, then converts them to upper case, then 
> intersperses them with "-":
> 
> $ ls
> demo.py  words.txt
> $ cat words.txt
> the
> quick
> brown
> fox
> $ cat demo.py
> def convert_to_upper(infile, outfile):
>     with open(infile) as instream:
>         with open(outfile, "w") as outstream:
>             outstream.write(instream.read().upper())
> 
> def convert_to_interspersed(infile, outfile):
>     with open(infile) as instream:
>         with open(outfile, "w") as outstream:
>             outstream.write("-".join(instream.read()))
> 
> with open("words.txt") as words:
>     for word in words:
>         word = word.strip()
>         filename = word
>         with open(filename, "w") as f:
>             f.write(word)
>         convert_to_upper(filename, filename + ".upper")
>         convert_to_interspersed(
>             filename + ".upper",
>             filename + ".interspersed"
>         )
> $ python demo.py
> $ ls
> brown               fox               quick.interspersed  the.upper
> brown.interspersed  fox.interspersed  quick.upper         words.txt
> brown.upper         fox.upper         the
> demo.py             quick             the.interspersed
> $ cat quick.interspersed 
> Q-U-I-C-K$



Oh my god, thank you so much. You have no idea how much you literally saved my life. Pretty much all I changed was increasing indentation on everything to make sure it's within the for barcode in barcodefile loop and now my script is running for all output files! 


More information about the Python-list mailing list