Re: [DIYbio] modifying the FASTQ>FASTA script

Not to distract from your Python explorations, but at some point you
might find it interesting to explore what you can do with the free
Galaxy bioinformatics workflow service:

http://galaxyproject.org/

Going through their tutorial is worthwhile and enlightening.

G.

On Thu, Mar 26, 2015 at 11:46 AM, Jeswin <phillyj101@gmail.com> wrote:
> Hi all,
> Once again, thanks for helping me with my python issue. Let me just
> point out that my programming skills are very low (script kiddie at
> best) and I don't have much time nowadays to sit down and really learn
> python. I know the basics.
>
> Anyway, my boss wanted to convert FASTQ to FASTA. The only way is thru
> a script and I settled with python. I found the script online that
> works:
> ================================================
> #!/usr/bin/env python
>
> #Takes a single FASTQ file and splits to .fasta + .qual files
> import sys
> from Bio import SeqIO
>
> if len(sys.argv) == 1:
> print "Please specify a single .fastq file to convert."
> sys.exit()
>
> filetoload = sys.argv[1]
> basename = filetoload
>
> #Chop the extension to get names for output files
> if basename.find(".") != -1:
> basename = '.'.join(basename.split(".")[:-1])
>
> SeqIO.convert(filetoload, "fastq", basename + ".fasta", "fasta")
> SeqIO.convert(filetoload, "fastq", basename + ".qual", "qual")
> ================================================
>
> I'm thinking about adding 2 features to it for the convenience for my
> colleagues. I know you all don't like leading people step by step, so
> I'm fine if you all can point me in the right direction (simplest and
> fastest solutions).
>
> [1] I would like to add something that shows progress {bar, text,
> etc.} of the conversion so that people on the computer know it's
> working and not frozen. Maybe read the size of the output file every
> 30 seconds (first the FASTA file, then a QUAL file)?
>
> [2] I am not sure if the script can process more than one file
> (sequentially) in the argument. I just ran "fastq_to_fasta.py
> file1.fastq". I am wondering if I can do: "fastq_to_fasta.py
> file1.fastq file2.fastq"? Basically, I am not sure if python can do
> that?
>
> BTW, I got the script from:
> http://nebc.nerc.ac.uk/nebc_website_frozen/nebc.nerc.ac.uk//tools/code-corner/scripts/sequence-formatting-and-other-text-manipulation
>
> Thanks
>
> --
> In necessariis unitas, in dubiis libertas, in omnibus caritas.
> -Marco Antonio Dominis
>
> --
> -- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
> Learn more at www.diybio.org
> ---
> You received this message because you are subscribed to the Google Groups "DIYbio" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to diybio+unsubscribe@googlegroups.com.
> To post to this group, send email to diybio@googlegroups.com.
> Visit this group at http://groups.google.com/group/diybio.
> To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/CAAhF0RKiRhWGYQ%2B%2Bu06xZ3mqTf9eF4UD0Oh2w2aOd0cOXQAWDw%40mail.gmail.com.
> For more options, visit https://groups.google.com/d/optout.

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at http://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/CA%2BcsFZiNfGqANizvXbzBcAbjx13H8FoM01KP1uQVV0WLO%2Bp9sA%40mail.gmail.com.
For more options, visit https://groups.google.com/d/optout.