03-02-2009
thanks for all your suggestion,
vgersh99 and ShawnMilo, I forgot to mention that the rest of the line is different for every line in my file.
cfajohnson, your suggestion is good, but i am loosing the tab delimitations for those lines that have been modified, and i need them for the rest of my process?...
applying your script:
My file looks like this originally:
>HWI-EAS422_12:4:1:69:89 GGTTTAAATATTGCACAAAAGGTATAGAGCGT U0 1 0 0 ref_chr8.fa 6527777 F DD
>HWI-EAS422_12:4:1:1296:114 GAGATTGATCTTAAGCCTTTGGCACAGTTAAC U0 1 0 0 ref_chr12.fa 4777762 R DD
>HWI-EAS422_12:4:1:223:1514 GAATGATGTTGTTTGCTTAGACATGATTTTGT NM 0 0 0
>HWI-EAS422_12:4:1:1150:122 GAGCTTACATTGGACTATGAAAGAGGACAATT U0 1 0 0 ref_chr16.fa 30593383 F DD
>HWI-EAS422_12:4:1:190:83 GGTTTATCAAATACTCTGAAAATAAAATGGGC R0 19 2 0
>HWI-EAS422_12:4:1:151:1463 GATCTGGGACCCTTAATTTTTGGGAATCTGTT U1 0 1 0 ref_chr17.fa 52460364 R DD 16T
>HWI-EAS422_12:4:1:567:228 GATTTAACCGAAGATGATTTCGATTTTCTGAC NM 0 0 0
>HWI-EAS422_12:4:1:954:124 GATATGTATACCAGTGGAAGACAATGGAGAAT U0 1 0 0 ref_chr10.fa 57535899 F DD
>HWI-EAS422_12:4:1:193:486 GCACAGAGAGAGACAAAGGTGCCAACCTTGCT U0 1 0 0 ref_chr22.fa 32814752 R DD
>HWI-EAS422_12:4:1:621:157 GTCGAGCTTCTGGCCATCGGCATCGGCCATGA NM 0 0 0
and it becomes
>HWI-EAS422_12:4:1:69:89 GGTTTAAATATTGCACAAAAGGTATAGAGCGT U0 1 0 0 chr8 6527777 F DD
>HWI-EAS422_12:4:1:1296:114 GAGATTGATCTTAAGCCTTTGGCACAGTTAAC U0 1 0 0 chr12 4777762 R DD
>HWI-EAS422_12:4:1:223:1514 GAATGATGTTGTTTGCTTAGACATGATTTTGT NM 0 0 0
>HWI-EAS422_12:4:1:1150:122 GAGCTTACATTGGACTATGAAAGAGGACAATT U0 1 0 0 chr16 30593383 F DD
>HWI-EAS422_12:4:1:190:83 GGTTTATCAAATACTCTGAAAATAAAATGGGC R0 19 2 0
>HWI-EAS422_12:4:1:151:1463 GATCTGGGACCCTTAATTTTTGGGAATCTGTT U1 0 1 0 chr17 52460364 R DD 16T
>HWI-EAS422_12:4:1:567:228 GATTTAACCGAAGATGATTTCGATTTTCTGAC NM 0 0 0
>HWI-EAS422_12:4:1:954:124 GATATGTATACCAGTGGAAGACAATGGAGAAT U0 1 0 0 chr10 57535899 F DD
>HWI-EAS422_12:4:1:193:486 GCACAGAGAGAGACAAAGGTGCCAACCTTGCT U0 1 0 0 chr22 32814752 R DD
>HWI-EAS422_12:4:1:621:157 GTCGAGCTTCTGGCCATCGGCATCGGCCATGA NM 0 0 0
how can i resolve this issue?
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ASCII(7) Linux Programmer's Manual ASCII(7)
NAME
ascii - the ASCII character set encoded in octal, decimal, and hexadecimal
DESCRIPTION
ASCII is the American Standard Code for Information Interchange. It is a 7-bit code. Many 8-bit codes (such as ISO 8859-1, the Linux
default character set) contain ASCII as their lower half. The international counterpart of ASCII is known as ISO 646.
The following table contains the 128 ASCII characters.
C program 'X' escapes are noted.
Oct Dec Hex Char Oct Dec Hex Char
------------------------------------------------------------
000 0 00 NUL '