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  • #31
    Might help us if you demonstrated that the file is indeed not empty. How about a 'ls -l' on the file. Or an 'od -c yourfile.sff | head --lines 4' or the actual command you sent to SeqIO.convert so that we can be sure that you did send your file to it.

    Comment


    • #32
      Hi,
      I was actually able to get it to run today.. Not sure what the problem was yesterday. But i got some funny results anyhow. Some of the nt's are uppercase and some are lowercase. This caused problems for some of the Galaxy fastx tools that summarize quality data.

      Any thoughts?

      @HH42GP401CAJLD
      gactagactcgacgtGTACTCAGGCTCGCACCGTGGCATGTCGCACTGTACTCAAGGCTCGCACCGTGGCATGTCGCACTGTACTTAAGGCTCACACCGTGGCATGTCGCACTGTACTCAAGGCACACAGGGGntaggnn
      +
      IIIIIIIIIIIIIIIIIIIGD666IIIIIIIIGDDDIIIIIIIIIIIIIIIGB;;;;IIIGGGGGCC>>>CIHID@@@C==:99==GGIIIIHIIIIIIIGGGCCCHIDDDC@777@C>1111AA@>;84445!;:44!!
      @HH42GP401B4BC5
      gactagactcgacgtGCAGTAGCTGCAATGGCGCAGAAGGCGTGCTTCtctctcncacgcacacacgagagagagngnnn
      +
      FFFFFFFFFFFFFFFIIIIIIIIIFFFFDDAAAB?<4444<>>9422323663/!//5///59=///2222////!2!!!

      The code that I ran is here, (117,221 is the right number of reads for this file)
      >>> SeqIO.convert("454Reads.JA11255_155_RL13.sff", "sff", "untrimmed.fastq", "fastq")
      117221

      Comment


      • #33
        Originally posted by lplough81 View Post
        Hi,
        I was actually able to get it to run today.. Not sure what the problem was yesterday. But i got some funny results anyhow. Some of the nt's are uppercase and some are lowercase.
        You'll see the same from Roche's own tools. The lower case are the bits which would be trimmed off as adapters or low quality bases.

        Originally posted by lplough81 View Post
        This caused problems for some of the Galaxy fastx tools that summarize quality data.

        Any thoughts?
        That could be an oversight in fastx - ask them about it.

        Or, what you probably want to do is ask for the trimmed sequences (which will be all upper case):

        Code:
        SeqIO.convert("454Reads.JA11255_155_RL13.sff", "sff-trim", "trimmed.fastq", "fastq")

        Comment


        • #34
          OK!

          Got it. Fairly new work for me, so I appreciate the patient replies. Can I specify the quality cutoff for trimming? Or what is the default that the biopython fastq trimmer uses?

          Thanks again.

          LP

          Comment


          • #35
            Originally posted by lplough81 View Post
            Got it. Fairly new work for me, so I appreciate the patient replies. Can I specify the quality cutoff for trimming? Or what is the default that the biopython fastq trimmer uses?
            There are two things to consider - getting rid of the adapter sequences and quality trimming. Roche does a good job of this as part of the base calling and production of the SFF file. When reading SFF files, Biopython (and other tools like sff_extract and Roche's own tools) will just apply the trimming information recorded in the SFF file. Using the Roche trimming is usually fine.

            You may need to further trim off PCR primers or other library specific adapters if the Roche software wasn't told about them.

            You may decide to further apply some quality cutoff trimming as well. This may be a good idea for some downstream analysis, not for others.

            It is possible to do this kind of trimming in Biopython, but not in one line. There are some examples in the tutorial. I've written some SFF trimming tools using Biopython available within the Galaxy Tool Shed (if your institute runs its own Galaxy instance that may be interesting).

            There are also other tools which will do it for you - especially if you want to work with the FASTQ file (or FASTA+QUAL) instead of the SFF file.

            Comment


            • #36
              how to trim FASTA name

              Hi,
              Is there a simple way to reduce the fasta name (e.g /
              "> HH42GP401CAJLD length=118 xy=0823_0287 region=1 run=R_2012_01_27_13_59_03_ "

              to ">HH42GP401CAJLD"?

              Similar to trimming an SFF file to FASTA with biopython SeqIOconvert(), but taking a fasta file as the input and then outputting another fasta file?

              Thanks,

              Louis

              Comment


              • #37
                Try something like this, untested:
                Code:
                from Bio import SeqIO
                
                in_file = "example.fasta"
                out_file = "new.fasta"
                file_format = "fasta"
                
                def remove_descr(record):
                    record.description=""
                    return record
                
                #This is a generator expression - not all in memory at once!
                wanted = (remove_descr(r) for r in SeqIO.parse(in_file, file_format))
                count = SeqIO.write(wanted, out_file, file_format)
                print "Saved %i records" % count

                Comment


                • #38
                  Originally posted by lplough81 View Post
                  Hi,
                  Is there a simple way to reduce the fasta name (e.g /
                  "> HH42GP401CAJLD length=118 xy=0823_0287 region=1 run=R_2012_01_27_13_59_03_ "

                  to ">HH42GP401CAJLD"?
                  I don't think you need a script for that. If your file is "454reads.fas" then just do:
                  Code:
                  sed 's/\s.*//' 454reads.fas > 454reads_trimmedheader.fas

                  Comment


                  • #39
                    Originally posted by kmcarr View Post
                    Nice catch drio, thanks. One of those really subtle things you don't catch until you work with a different set of files.

                    Eugeni, sorry I didn't get back to you on this; got really crushed at work. I have uploaded a modified version of the script incorporating drio's fix.
                    @kmcarr: I found your script very useful and I am currently as a MSc Bioinformatics students working on an assignment which involves developing a web interface to a little mapping pipeline. This is purely for educational purposes. Would I be allowed to use your script to prepare the fastq file for the pipeline?
                    I really would appreciated it.

                    Comment


                    • #40
                      I am a beginner for using Perl command. Wen I am trying FastaQual2fastq.pl script for making my fastq file but they like this error - readline() on closed filehandle.
                      So please help me to give a right solution for putting fasta seq.

                      Comment

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