I want to convert a binary file to a text file for the first time (ex> sff files from GS FLX sequencer). Although I heard that Perl is slow in terms of binary handling, I found I forgot many things about C.

So a Perl script is adapted from a certain website although its running times are long.

    $filename0=$ARGV[1];
    open($RF1, "<", $filename0);
    binmode $RF1;  
    $filename1=$filename0; 
    $filename1.="test.txt"; 
    open($WF1, ">", $filename1); 
    for(;($n=read $RF1, $data, 65536) !=0;$buf.=$data)
    {
    }
    @buffer=unpack('(C1)*', $buf);
    foreach(@buffer)
    {
        print $WF1 "$_\n";
    }
    close $RF1;
    close $WF1;

[download]

I expected a text file that I can understand. But I got only numbers like


46 115 102 102 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 111 100 3 136 0 17 
+3 82 1 84 65 67 71 84 65 67 71 84 67 84 71 65 71 67 65 84 67 71 65 84
+ 67 71 65 84 71 84 65 67 65 71 67 84 65 67 71 84 65 67 71 84 67 84 71
+ 65 71 67 65 84 67 71 65 84 67 71 65 84 71 84 65 67 65 71 67 84 65 67
+ 71 84 65 67 71 84 67 84 71 65 71 67 65 84 67 71 65 84 67 71 65 84 71
+ 84 65 67 65 71 67 84 65 67 71 84 65 67 71 84 67 84 71 65 71 67 65 84
+ 67 71 65 84 67 71 65 84 71 84 65 67 65 71 67 84 65 67 71 84 65 67 71
+ 84 67 84 71 65 71 67 65 84 67 71 65 84 67 71 65 84 71 84 65 67 65 71
+ 67 84 65 67 71 84 65 67 71 84 67 84 71 65 71 67 65 84 67 71 65 84 67
+ 71 65 84 71 84 65 67 65 71 67 84 65 67 71 84 65 67 71 84 67 84 71 65
+ 71 67 65 84 67 71 65 84 67 71 65 84 71 84 65 67 65 71 67 84 65 67 71
+ 84 65 67 71 84 67 84 71 65 71 67 65 84 67 71 65 84 67 71 65 84 71 84
+ 65 67 65 71 67 84 65 67 71 84 65 67 71 84 67 84 71 65 71 67 65 84 67
+ 71 65 84 67 71 65 84 71 84 65 67 65 71 67 84 65 67 71 84 65 67 71 84
+ 67 84 71 65 71 67 65 84 67 71 65 84 67 71 65 84 71 84 65 67 65 71 67
+ 84 65 67 71 84 65 67 71 84 67 84 71 65 71 67 65 84 67 71 65 84 67 71
+ 65 84 71 84 65 67 65 71 67 84 65 67 71 84 65 67 71 84 67 84 71 65 71
+ 67 65 84 67 71 65 84 67 71 65 84 71 84 65 67 65 71 67 84 65 67 71 84
+ 65 67 71 84 67 84 71 65 71 67 65 84 67 71 65 84 67 71 65 84 71 84 65
+ 67 65 71 67 84 65 67 71 84 65 67 71 84 67 84 71 65 71 67 65 84 67 71
+ 65 84 67 71 65 84 71 84 65 67 65 71 67 84 65 67 71 84 65 67 71 84 67
+ 84 71 65 71 67 65 84 67 71 65 84 67 71 65 84 71 84 65 67 65 71 67 84
+ 65 67 71 84 65 67 71 84 67 84 71 65 71 67 65 84 67 71 65 84 67 71 65
+ 84 71 84 65 67 65 71 67 84 65 67 71 84 65 67 71 84 67 84 71 65 71 67
+ 65 84 67 71 65 84 67 71 65 84 71 84 65 67 65 71 67 84 65 67 71 84 65
+ 67 71 84 67 84 71 65 71 67 65 84 67 71 65 84 67 71 65 84 71 84 65 67
+ 65 71 67 84 65 67 71 84 65 67 71 84 67 84 71 65 71 67 65 84 67 71 65
+ 84 67 71 65 84 71 84 65 67 65 71 67 84 65 67 71 84 65 67 71 84 67 84
+ 71 65 71 67 65 84 67 71 65 84 67 71 65 84 71 84 65 67 65 71 67 84 65
+ 67 71 84 65 67 71 84 67 84 71 65 71 67 65 84 67 71 65 84 67 71 65 84
+ 71 84 65 67 65 71 67 84 65 67 71 84 65 67 71 84 67 84 71 65 71 67 65
+ 84 67 71 65 84 67 71 65 84 71 84 65 67 65 71 67 84 65 67 71 84 65 67
+ 71 84 67 84 71 65 71 67 65 84 67 71 65 84 67 71 65 84 71 84 65 67 65
+ 71 67 84 65 67 71 84 65 67 71 84 67 84 71 65 71 67 65 84 67 71 65 84
+ 67 71 65 84 71 84 65 67 65 71 67 84 65 67 71 84 65 67 71 84 67 84 71
+ 65 71 67 65 84 67 71 65 84 67 71 65 84 71 84 65 67 65 71 67 84 65 67
+ 71 84 65 67 71 84 67 84 71 65 71 67 65 84 67 71 65 84 67 71 65 84 71
+ 84 65 67 65 71 67 84 65 67 71 84 65 67 71 84 67 84 71 65 71 67 65 84
+ 67 84 67 65 71 67 84 65 65 71 71 84 65 65 67 71 65 84 0 0 0 0 0 0 0 
+40 0 17 0 0 0 102 0 18 0 0 0 0 0 0 53 55 75 50 72 58 48 48 48 50 54 5
+8 48 48 48 51 54 0 0 0 0 0 0 0 0 82 0 0 0 77 0 0 0 0 0 86 0 0 0 85 0 
+0 0 89 0 91 0 0 0 190 0 186 0 0 0 0 0 102 0 0 0 0 0 195 0 5 0 100 0 9
+ 0 2 0 110 0 114 0 5 0 16 0 117 0 4 0 123 0 13 0 17 0 125 0 9 0 14 0 
+124 0 15 0 214 0 128 0 7 0 7 0 0 0 0 0 213 0 188 0 196 0 1 0 1 0 1 0 
+79 0 98 0 1 0 91 0 1 0 2 0 87 0 2 0 2 0 2 0 106 0 1 0 98 0 1 0 3 0 77
+ 1 4 0 68 0 1 0 1 0 181 0 1 0 84 0 1 0 1 0 75 0 84 0 1 0 1 0 0 0 88 0
+ 178 0 4 0 0 0 190 0 107 0 0 0 100 0 10 0 0 0 1 0 0 0 95 0 2 0 88 0 9
+2 0 4 1 138 0 0 0 86 0 9 0 0 1 42 0 0 0 0 0 1 0 1 0 1 0 105 0 177 0 1
+ 0 103 0 6 0 91 0 3 0 89 0 8 0 190 0 2 0 117 0 88 0 2 0 2 0 2 0 177 0
+ 3 0 3 0 3 0 96 0 3 0 3 0 80 0 92 0 3 0 107 0 76 0 3 0 94 0 92 0 178 
+0 14 0 2 0 172 0 2 0 23 0 8 0 104 0 11 0 17 0 102 0 5 0 1 0 113 0 100
+ 0 6 0 193 0 25 0 11 0 111 0 197 0 48 0 40 0 30 0 229 0 33 0 124 0 54
+ 0 44 0 100 0 210 0 31 0 127 0 51 0 7 0 16 0 0 0 96 0 10 0 182 0 82 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 3 2 2 1 
+2 0 1 0 3 3 0 2 1 1 1 1 3 2 3 3 2 0 1 5 0 1 0 1 0 4 1 2 3 4 2 3 1 0 0
+ 1 3 0 2 3 1 4 1 0 3 0 1 2 5 2 1 2 0 0 0 2 3 0 0 6 1 0 2 2 2 2 0 2 1 
+4 0 4 3 1 2 1 2 1 1 0 3 0 4 3 3 1 2 0 3 1 0 2 2 0 0 2 84 67 65 71 67 
+84 65 65 71 71 84 65 65 67 71 65 84 71 67 71 65 84 67 67 71 65 65 71 
+71 67 67 71 65 67 84 67 71 65 67 67 67 71 67 67 84 71 65 84 67 67 84 
+84 67 65 67 71 67 65 65 65 65 71 67 67 67 65 71 71 65 67 65 67 67 65 
+84 67 67 84 71 84 67 71 67 84 71 71 67 67 71 67 84 71 65 65 71 67 67 
+65 71 71 71 65 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 19 
+24 24 19 19 19 17 19 19 17 19 24 31 23 25 26 34 33 33 28 29 24 30 16 
+24 24 30 30 29 29 32 33 30 34 35 34 33 31 26 19 19 19 19 11 24 24 24 
+16 24 35 32 34 34 34 38 31 33 27 26 23 26 31 31 26 27 27 34 35 29 33 
+29 30 24 15 15 16 11 15 15 11 11 9 9 8 9 0 0 0 40 0 17 0 0 0 86 0 18 
+0 0 0 0 0 0 53 55 75 50 72 58 48 48 48 48 53 58 48 48 48 57 50 0 0 0 
+0 0 0 0 0 71 0 0 0 125 0 0 0 0 0 99 0 0 0 93 0 0 0 125 0 46 0 0 0 235
+ 0 192 0 0 0 0 0 85 0 0 0 0 0 219 0 0 0 121 0 0 0 0 0 78 0 96 0 0 0 0
+ 0 160 0 0 0 96 0 0 0 0 0 125 1 8 0 98 0 0 0 195 0 12 0 180 0 1 0 112
+ 0 1 0 185 0 129 0 1 0 129 0 1 0 57 0 123 0 98 0 113 0 2 1 17 0 110 0
+ 2 0 2 0 2 0 2 0 2 0 218 0 2 0 2 0 2 0 65 0 2 0 7 0 92 0 2 0 89 0 3 0
+ 3 0 53 0 178 0 157 0 3 0 3 0 3 0 125 0 68 0 3 0 112 0 82 0 3 0 3 0 1
+38 0 3 1 104 0 3 0 70 0 3 0 3 1 5 0 89 0 167 0 3 0 3 0 114 0 96 0 3 0
+ 3 0 91 0 203 0 3 0 3 0 3 0 3 0 3 0 115 0 3 0 3 0 3 0 44 0 217 0 3 0 
+3 0 55 0 28 0 67 0 2 0 42 0 2 0 2 0 2 0 142 0 2 0 83 0

[download]

Line breaks removed from data block by GrandFather to reduce code block size

They may be bytes in a binary file. Well. But I don't know how to convert this numbers to texts. Would you please help me?

Thank you for many replies. I should find a good program like sra-tools to convert sff files. But some of us may want to work on my sff files. OK. You can download SRR1653474.sff on NCBI website. But there is no direct link. Or you can download my file from http://me2.do/58g2qYMR up to 2016-04-26 and 100 persons. Click a red arrow to download the file. password 1234

Many thanks to you. Recently, I am busy and won't solve this problem anymore. But I thought about the solution.

1. Covert numbers into letters like chr(no.).

2. Check converted parts and unconverted numbers. Maybe DNA bases like ATGC will be converted, and flowgrams like 0.03 will not be converted.

3. Study about unconverted data and convert them into letters or whatever.

In reply to Convert numbers from a binary file to texts by bestfa

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.