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

[Unaiza Batool]

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!