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  • peromhc
    replied
    Also, a BioPython solution. In this case filtering my length 200nt

    Code:
    #!/usr/bin/python
    from Bio import SeqIO
    import sys
    import os
    
    #usage: python long.seq.py in.fasta out.fasta 200
    
    input_seq_iterator = SeqIO.parse(open(sys.argv[1], "rU"), "fasta")
    short_seq_iterator = (record for record in input_seq_iterator \
                          if len(record.seq) > int(sys.argv[3]))
    
    output_handle = open(sys.argv[2], "w")
    SeqIO.write(short_seq_iterator, output_handle, "fasta")
    output_handle.close()

    Leave a comment:


  • hchang10
    replied
    Awesome!!!

    Dario, I appreciate it!!!!

    Thank you so much!!!!

    Leave a comment:


  • dariober
    replied
    Originally posted by hchang10 View Post
    Hi everyone,

    I'd like to filter a multi-fasta file by length, for example, keep length <300bp and filter out longer ones. I knew there is tool in Galaxy doing this, but it takes so long to upload the file. Can anyone share a script or tool to me?

    Thank you very much.
    Hi- This strategy should be quite fast (untested):

    Code:
    samtools faidx myfasta.fa
    awk '{if($2 < 300) print $1 "\t0\t" $2 "\t" $1}' myfasta.fa.fai > selectSeq.bed
    fastaFromBed -fi myfasta.fa -bed selectSeq.bed -name -fo  selectSeq.fa
    fastaFromBed is part of bedtools

    Dario

    Leave a comment:


  • GenoMax
    replied
    See this thread for script examples: http://seqanswers.com/forums/showthread.php?t=13966

    Leave a comment:


  • hchang10
    started a topic Filter multi-fasta by length

    Filter multi-fasta by length

    Hi everyone,

    I'd like to filter a multi-fasta file by length, for example, keep length <300bp and filter out longer ones. I knew there is tool in Galaxy doing this, but it takes so long to upload the file. Can anyone share a script or tool to me?

    Thank you very much.

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