I have a binary file, generated in Windows XP (not 64), and copied it (via script, no modifications done) to a linux machine. Here I try to read in the file via this programm, which I found on the net:
my ($orf_file) = @_;
my $record_length = 230;
open ORF_DATA, "<$orf_file" or die "Can't open $orf_file: $!\n";
binmode ORF_DATA; # Tell Perl this isn't a text file
my $buffer;
while (read ORF_DATA, $buffer, $record_length) {
my ($orf_name, $orf_left, $orf_right, $orf_direction, $orf_descr
+)
= unpack("x5x4A11x4x4x1a8x1a8x4A1x4x14x4x5x1x8x4A50", $buffer
+);
foreach my $coordinate ($orf_left, $orf_right) {
$coordinate = unpack("d", reverse($coordinate));
}
print "$orf_name, $orf_left, $orf_right, $orf_direction, $orf_de
+scr\n";
}
read ORF_DATA, $buffer, 5;
close ORF_DATA;
But it gives me that output:
, -8.57210024934386e+303, 5.05923221341436e-321, , ^@��&
+#65533;�������ᦙ
+3;��������
+5533;��������
+��������ʏ
+33;��������&#
+65533;���
��������ᦙ
+3;��, -nan, -nan, �, ���
+5533;��������
+��������ʏ
+33;��������&#
+65533;��������
+;��������A
+533;���
��������ᦙ
+3;��, -nan, -nan, �, ���
+5533;��������
+��������ʏ
+33;��������&#
+65533;��������
+;��������A
+533;���
��������ᦙ
+3;��, -nan, -nan, �, ���
+5533;��������
+��������ʏ
+33;��������&#
+65533;��������
+;��������A
+533;���
��������ᦙ
+3;��, -nan, -nan, �, ���
+5533;��������
+�R^@o^@o^@t^@ ^@E^@n^@t^@r^@y
, 0, 0, ,
, 0, 0, , ^@^@^@^@^@������&#
+65533;�����
, 4.17271145058687e-317, 4.26518227762202e-135, , ^@^@^@^@^@^@^@^@^@^@
+^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^X^@^A^@���
+5533;�����^@^@^@Zp�3�
+;"�
^@^@^@^@^@^@^@*^@^A^A, 3.10794187231649e-312, -1.4360283086302e+92, ,
+^@a^@ ^@P^@r^@o^@c^@e^@s^@s^@i^@n^@g^@-^@2
^@ ^@^@^@^R^@^@^@�, 1.94693962667949e-308, 1.2882298355029
+3e-231, ^S, ^@^@^@^^^@^@^@^_^@^@^@ ^@^@^@!^@^@^@"^@^@^@#^@^@^@$^@^@^@
+%^@^@^@&^@^@^@'^@^@^@(^@^@^@)
^@^@^@C^@^@^@����, 2.14321574923559e-312,
+4.01990882735322e-310, , ^@W^@^@^@X^@^@^@Y^@^@^@Z^@^@^@[^@^@^@\^@^@^@
+]^@^@^@^^@^@^@_^@^@^@`^@^@^@a^@^@^@b^@^@^@c
^@|^@^@^@}^@^@^@~, 2.55894867708661e-307, 1.80715861907036e+159, o, ^@
+^@^@*^@^A^A^C^@^@^@^S^@^@^@�^@^@^@�v��
+5533;5�^Q��^@�O���^@
+^@^@^@���I�^A���
��ҁ$�^Q�^O^@^D, -9.68134237028327e+1
+48, -1.56966257731664e+146, , ^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^
+@^@^@^@^@^@^@^@^@^@^\^@^A^A�����&#
+65533;��������
+;�ҁ
^@^@^@^@^@^@^@^@^@^\, 7.29112201821461e-304, -3.79584680120728e-303, ,
+ ^@a^@t^@u^@s^@ ^@I^@n^@f^@o^@r^@m^@a^@t^@i^@o^@n
^@n, 0, 4.30034738140221e-320, , I�^A^@^@^@^@^@^@^@^@^@^@^@^@H^
+@S^@4^@0^@ ^@P^@a^@r^@a^@m^@e^@t^@e^@r^@s
^@S^@-^@X^@ ^@P, 1.7801962549761e-306, 0, , Y�^Q�v^@^D&#
+65533;Q��^@^@^@^@���I�^A
+5533;��I�^A^@^@^@^@^@^@^@^@^@^@^@^@A^@O^@C
^H�^A���I�^A, 1.5066387057954e-312,
+ 7.94196901705514e+115, r, ^@^@^@^@^@6^@^A^A���&
+#65533;����_^@^@^@���
+;^Qrg�^Q�;^@^D�Q�i^@^@^@^@��
+;�I�^A�
^@a�ΧR8�^Q�^K, 3.00306280016903e-306, -1.758
+31693470781e-304, , ^@g^@ ^@O^@r^@i^@g^@i^@n^@a^@l^@^@^@^@^@^@^@^@^@^
+@^@8^@^A^A^M^@^@^@^Q^@^@^@E^@^@^@a��
^@-^@1, -nan, -7.08341916115841e-227, �, ^@a^@t^@a^@ ^@P^@r^@o^
+@c^@e^@s^@s^@i^@n^@g^@ ^@O^@r^@i^@g^@i^@n^@a^@l^@-^@2
^@s^@i^@n^@g, 1.3351101829727e-306, 4.86173068582902e-63, �, &#
+65533;�I�^A^@^@^@^@^@^@^@^@^@^@^@^@C^@h^@r^@o^@m^@a^@t^
+@o^@g^@r^@a^@m^@ ^@P^@a^@r
^@C^@ ^@B^@a^@t, 8.0109992628362e-307, 0, , sA(�^Q�ʏ
+33;^@^D�Q��^@^@^@^@���IA
+533;^A���I�^A^@^@^@^@^@^@^@^@^@^@^@^@G^@C
I�^A���I, 2.65513496623009e-317, 3.1891827
+709762e+231, o, ^@^@^@^@^@^@^@^\^@^A^@����
+;����^\^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@
+^@^@^@^@^@^@���I�
���, 0, 0, , ^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@
+^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^Z^@^B^A^A^@^@^@^W^@^@^@��
+;��
, -nan, 0, , ^@e^@d^@d^@i^@n^@g^@ ^@3^@3
, 0, 0, ^A, ^A���I�^A^@^@^@^@^@^@^@^@^@^@^
+@^@����^B^@^@^@^C^@^@^@^D^@^@^@^E^@^@^@^F
+^@^@^@^G^@^@^@^H
^@!^@^@^@"^@^@^@#, 6.11895311342037e-308, 5.07588444990605e-116, +, ^@
+^@^@��������8
+^@^@^@9^@^@^@:^@^@^@;^@^@^@<^@^@^@=^@^@^@���A
+533;����@^@^@^@A
^@^@^@[^@^@^@\, 2.03711595980591e-312, 5.32366304162584e-310, , ᦙ
+3;��������
+5533;�������s^@^@^@t
+^@^@^@u^@^@^@����w^@^@^@x^@^@^@y^@^@^@
+5533;���{
SU6^@^@^@^@^@Ad, 0, 0, >, ��I�^A^B^@^@^@2.30.00
+SU6^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^Q
, 4.1995579896506e-322, 1.39783876650346e+54, , ^@^@^@^@^@^@^@^@^@^@^@
+�?^@^@�?^@^@�?^@^@�?^@^@�?^@^@A
+533;?^@^@�?^@^@�?^@^@�?^@^@�?
@^A, 0, 1.63096010348654e-319, �, etra_UNK-0018_16.03.2012_1.gc
+d
, 0, 0, , ion\Data\Project1\gcm\GC1_Hydrogen Method_100m_sp2
, 0, 0, ,
, 0, 0, , ^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@
+^@^@^@^@^@^@^@^@^@^@^@^@C:\GCsol
, 0, 0, ,
, 0, 0, ,
, 0, 0, ,
gcm\GC1_Hyd, 1.14579591627385e+195, 1.13242004846932e+248, r,
\GCsolution, 3.35295120276734e+204, 1.02942023076379e-71, ,
, 0, 0, ,
, 0, 0, ,
etc.
If I convert the bin file in a windows programm i get output like this:
[Header]
Data File Name C:\Dokumente und Einstellungen\fsc\Desktop\20110919\
+LaborHoppe_P1_UNK-0010_09.09.2011_1.gcd
Output Date 20.09.2011
Output Time 10:45:33
[File Information]
Type Data File
Generated 09.09.2011 19:22:14
Generated by Admin
Modified 20.09.2011 10:42:10
Modified by Admin
[Sample Information]
Operator Name Admin
Acquisition Date 09.09.2011 19:24:27
Type Unknown
Level 1
Sample Name LaborHoppe_P1
Sample ID UNK-0010
ISTD Amount1 1
ISTD Amount2 1
ISTD Amount3 1
ISTD Amount4 1
ISTD Amount5 1
ISTD Amount6 1
ISTD Amount7 1
ISTD Amount8 1
ISTD Amount9 1
ISTD Amount10 1
ISTD Amount11 1
ISTD Amount12 1
ISTD Amount13 1
ISTD Amount14 1
ISTD Amount15 1
ISTD Amount16 1
Sample Amount 1
Dilution Factor 1
Vial# 10
Injection Volume 2
Injection Count 1
Bar Code
[Original Files]
Data File C:\GCsolution\Data\Project1\LaborHoppe_P1_UNK-0010_09.09.
+2011_1.gcd
Method File C:\GCsolution\Data\Project1\gcm\GC1_Hydrogen Method_100
+m_sp2560_integration_UNKNOWN_782.gcm
Batch File C:\GCsolution\Data\Project1\g110909.gcb
Report Format File C:\GCsolution\System\DEFAULT.gcr
[File Comment]
[Configration]
Instrument Name Instrument1
Instrument # 1
Line # 1
[Peak Table (Ch1)]
# of Peaks 26
Peak# R.Time I.Time F.Time Area Height A/H Conc.
+ Mark ID# Name k' Plate # Plate Ht. Tailing Re
+solution Sep.Factor
1 5,332 5,292 5,399 1048 462 0,02 0,00000
+ 1 C14:0 0,000 131066,080 0,000 1,208 0,000 0,
+000
2 6,238 6,178 6,378 72242 26891 0,03 0,00000
+ 2 C16:0 0,170 144557,069 0,000 1,449 14,585
+ 0,000
3 6,498 6,479 6,595 419 93 0,04 0,00000
+ 3 C16:1n7t 0,219 0,000 0,000 0,000 0,000 1,288
4 6,734 6,689 6,769 2583 1039 0,02 0,00000
+ 4 C16:1n7 0,263 159918,329 0,000 0,000 0,000
+ 1,202
5 7,549 7,489 7,752 56859 16389 0,03 0,00000
+ 5 C18:0 0,416 141705,713 0,000 1,787 11,077
+ 1,582
6 7,953 7,905 8,062 971 258 0,04 0,00000
+ 6 C18:1t 0,492 88990,255 0,000 1,516 4,337 1,1
+82
7 8,135 8,072 8,319 42929 11611 0,04 0,00000
+ 7 C18:1n9 0,526 174140,874 0,000 1,965 1,976
+ 1,069
8 8,496 8,452 8,618 910 186 0,05 0,00000
+ 8 C18:2n6tt 0,593 38673,668 0,000 2,000 2,886
+1,129
9 8,661 8,618 8,692 16 9 0,02 0,00000 9
+ C18:2n6ct 0,624 464832,815 0,000 0,792 1,481 1,
+052
10 8,853 8,732 8,889 448 88 0,05 0,00000
+ 10 C18:2n6tc 0,660 302521,825 0,000 0,648 3,337
+ 1,058
11 8,987 8,918 9,135 20278 6647 0,03 0,00000
+ 11 C18:2n6 0,685 229386,429 0,000 1,475 1,935
+ 1,038
12 9,191 9,145 9,258 205 80 0,03 0,00000
+ 12 C20:0 0,724 316287,435 0,000 1,400 2,913 1,
+056
13 9,634 9,598 9,698 198 77 0,03 0,00000
+ 13 C18:3n6 0,807 283128,526 0,000 1,271 6,448
+1,115
14 9,784 9,739 9,838 472 175 0,03 0,00000
+ 14 C20:1n9 0,835 295677,357 0,000 1,210 2,077
+ 1,035
15 9,971 9,932 10,012 180 78 0,02 0,00000
+ 15 C18:3n3 0,870 419534,533 0,000 1,043 2,810
+ 1,042
16 10,639 10,589 10,712 587 203 0,03 0,00000
+ 16 C20:2n6 0,995 341241,962 0,000 1,285 9,964
+ 1,144
17 10,866 10,822 10,895 321 138 0,02 0,00000
+ 17 C22:0 1,038 502890,145 0,000 0,890 3,402
+ 1,043
18 11,257 11,198 11,352 4474 1522 0,03 0,00000
+ 18 C20:3n6 1,111 375323,728 0,000 1,451 5,8
+15 1,071
19 11,727 11,645 11,929 59239 19809 0,03 0,00000
+ 19 C20:4n6 1,199 430565,779 0,000 1,566 6
+,502 1,079
20 12,466 12,419 12,569 2208 618 0,04 0,00000
+ 20 C24:0 1,338 311187,077 0,000 1,614 9,211
+ 1,116
21 12,726 12,662 12,809 2990 1049 0,03 0,00000
+ 21 C20:5n3 1,387 486334,875 0,000 1,320 3,2
+00 1,036
22 13,023 12,969 13,179 3383 825 0,04 0,00000
+ 22 C24:1n9 1,442 302863,559 0,000 1,941 3,56
+3 1,040
23 13,466 13,399 13,585 7656 2247 0,03 0,00000
+ 23 C22:4n6 1,526 417011,386 0,000 1,530 4,9
+90 1,058
24 13,921 13,839 13,992 1577 458 0,03 0,00000
+ 24 C22:5n6 1,611 416308,716 0,000 1,000 5,37
+2 1,056
25 14,579 14,509 14,739 9154 2520 0,04 0,00000
+ 25 C22:5n3 1,734 450041,035 0,000 1,679 7,6
+12 1,077
26 15,109 15,039 15,255 17589 4969 0,04 0,00000
+ 26 C22:6n3 1,834 475309,805 0,000 1,437 6,
+095 1,057
[Compound Results (Ch1)]
# of IDs 26
ID# Name R.Time Area Height Conc. Curve 3rd 2n
+d 1st Constant
1 C14:0 5,332 1048 462 0,00000 Default 0,0000000
+ 0,0000000 0,0000000 0,0000000
2 C16:0 6,238 72242 26891 0,00000 Default 0,00000
+00 0,0000000 0,0000000 0,0000000
3 C16:1n7t 6,498 419 93 0,00000 Default 0,0000000
+ 0,0000000 0,0000000 0,0000000
4 C16:1n7 6,734 2583 1039 0,00000 Default 0,00000
+00 0,0000000 0,0000000 0,0000000
5 C18:0 7,549 56859 16389 0,00000 Default 0,00000
+00 0,0000000 0,0000000 0,0000000
6 C18:1t 7,953 971 258 0,00000 Default 0,0000000
+ 0,0000000 0,0000000 0,0000000
7 C18:1n9 8,135 42929 11611 0,00000 Default 0,000
+0000 0,0000000 0,0000000 0,0000000
8 C18:2n6tt 8,496 910 186 0,00000 Default 0,00000
+00 0,0000000 0,0000000 0,0000000
9 C18:2n6ct 8,661 16 9 0,00000 Default 0,0000000
+ 0,0000000 0,0000000 0,0000000
10 C18:2n6tc 8,853 448 88 0,00000 Default 0,00000
+00 0,0000000 0,0000000 0,0000000
11 C18:2n6 8,987 20278 6647 0,00000 Default 0,000
+0000 0,0000000 0,0000000 0,0000000
12 C20:0 9,191 205 80 0,00000 Default 0,0000000
+ 0,0000000 0,0000000 0,0000000
13 C18:3n6 9,634 198 77 0,00000 Default 0,0000000
+ 0,0000000 0,0000000 0,0000000
14 C20:1n9 9,784 472 175 0,00000 Default 0,000000
+0 0,0000000 0,0000000 0,0000000
15 C18:3n3 9,971 180 78 0,00000 Default 0,0000000
+ 0,0000000 0,0000000 0,0000000
16 C20:2n6 10,639 587 203 0,00000 Default 0,00000
+00 0,0000000 0,0000000 0,0000000
17 C22:0 10,866 321 138 0,00000 Default 0,0000000
+ 0,0000000 0,0000000 0,0000000
18 C20:3n6 11,257 4474 1522 0,00000 Default 0,000
+0000 0,0000000 0,0000000 0,0000000
19 C20:4n6 11,727 59239 19809 0,00000 Default 0,0
+000000 0,0000000 0,0000000 0,0000000
20 C24:0 12,466 2208 618 0,00000 Default 0,000000
+0 0,0000000 0,0000000 0,0000000
21 C20:5n3 12,726 2990 1049 0,00000 Default 0,000
+0000 0,0000000 0,0000000 0,0000000
22 C24:1n9 13,023 3383 825 0,00000 Default 0,0000
+000 0,0000000 0,0000000 0,0000000
23 C22:4n6 13,466 7656 2247 0,00000 Default 0,000
+0000 0,0000000 0,0000000 0,0000000
24 C22:5n6 13,921 1577 458 0,00000 Default 0,0000
+000 0,0000000 0,0000000 0,0000000
25 C22:5n3 14,579 9154 2520 0,00000 Default 0,000
+0000 0,0000000 0,0000000 0,0000000
26 C22:6n3 15,109 17589 4969 0,00000 Default 0,00
+00000 0,0000000 0,0000000 0,0000000
[Group Results (Ch1)]
# of Groups 0
etc.
I have made the file available for download here, including the TXT file: www.spectramab.com/example.zip
Anyone knows how I can achive a similar thing in perl?
Thank you very much in advace!
Adrian
