Re: [DIYbio] modifying the FASTQ>FASTA script

I tried to add some kind of indicator but, they always make my the
conversion script 10x slow. So I just put simple print warnings, cause
that's the best I could do. One thing I have been told is to use
os.path because it is an acutal basename function. Also added a prompt
for user to check there is enough room on HDD, cause it seems they
don't delete or move files to archive. I compared the outputs of the
original with my modified script and I didn't find any differences.

Can someone check my modified script to make sure I didn't miss
something? Anything I can do better? This is the best I can do with my
abilities. Its for use with python 2.7 (thru Anaconda on windows).
Right now, I tested it on my linux machine; hopefully it works on
windows when I get back to work next week.

=======================CODE============================
#!/usr/bin/env python

#Takes a single FASTQ file and splits to .fasta + .qual files
import sys
import os.path
from Bio import SeqIO

#Disk space Checking
print "Warning! Please check that there is at least 50GB of Free Disk
Space per file conversion."
DiskCheck = raw_input('Is there enough space? (yes or no) ')
if DiskCheck == 'yes':

if len(sys.argv) == 1:
print "Please specify a single .fastq file to convert."
sys.exit()

filetoload = sys.argv[1]
basename = filetoload

#BETTER WAY: Chop the extension to get names for output files
basename, extension = os.path.splitext(os.path.basename(filetoload))

print "\nWorking on", basename
print "Don't close this window."

SeqIO.convert(filetoload, "fastq", basename + ".fasta", "fasta")

#QUAL file creation disabled
#SeqIO.convert(filetoload, "fastq", basename + ".qual", "qual")

print "\nDone converting", basename, "to FASTA format."

elif DiskCheck == 'no':
print "\nMake room on disk, then run script again"
sys.exit()
=======================CODE============================

On Thu, Mar 26, 2015 at 1:37 PM, Gavin Scott <gavin@learn.bio> wrote:
> 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
>>
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>
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--
In necessariis unitas, in dubiis libertas, in omnibus caritas.
-Marco Antonio Dominis

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