01-05-2014
Gave awk a try, but this appears to print the filename in the first header only, not to change it in place, and also this does not affect the subsequent headers. Any alternative solutions?
Last edited by Mauve; 01-05-2014 at 02:18 PM..
10 More Discussions You Might Find Interesting
1. Shell Programming and Scripting
Hi ,
I have a typical situation. I have 4 files and with different headers (number of headers is varible ).
I need to make such a merged file which will have headers combined from all files (comman coluns should appear once only).
For example -
File 1
H1|H2|H3|H4
11|12|13|14
21|22|23|23... (1 Reply)
Discussion started by: marut_ashu
1 Replies
2. Shell Programming and Scripting
Hello,
A bioperl problem I thought could be done with awk: convert the fasta format (Note: the length of each row is not the same for each entry as they were combined from different files!) to tabular format.
input.fasta:
>YAL069W-1.334 Putative promoter sequence... (6 Replies)
Discussion started by: yifangt
6 Replies
3. UNIX for Dummies Questions & Answers
Hi
I have an alignment file (.fasta) with ~80 sequences. They look like this-
>JV101.contig00066(+):25302-42404|sequence_index=0|block_index=4|species=JV101|JV101_4_0
GAGGTTAATTATCGATAACGTTTAATTAAAGTGTTTAGGTGTCATAATTT
TAAATGACGATTTCTCATTACCATACACCTAAATTATCATCAATCTGAAT... (2 Replies)
Discussion started by: baika
2 Replies
4. Shell Programming and Scripting
Hi,
I want to match the sequence id (sub-string of line starting with '>' and extract the information upto next '>' line ). Please help .
input
> fefrwefrwef X900
AGAGGGAATTGG
AGGGGCCTGGAG
GGTTCTCTTC
> fefrwefrwef X932
AGAGGGAATTGG
AGGAGGTGGAG
GGTTCTCTTC
> fefrwefrwef X937... (2 Replies)
Discussion started by: ritakadm
2 Replies
5. Shell Programming and Scripting
I have two files. File1 is shown below.
>153L:B|PDBID|CHAIN|SEQUENCE
RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL
KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM
DIGTTHDDYANDVVARAQYYKQHGY
>16VP:A|PDBID|CHAIN|SEQUENCE... (7 Replies)
Discussion started by: nelsonfrans
7 Replies
6. UNIX for Advanced & Expert Users
Hi. Unix rookie here. Been looking for a few days for reference documents on how BSD UNIX lays the logical file format onto a disk. Goal is to view/edit with hex editor for data repair. Lots of docs are available for how to use Unix commands (like xxd), but I want to learn the map of how Unix... (4 Replies)
Discussion started by: Chris_top_he_r
4 Replies
7. UNIX for Dummies Questions & Answers
I have the following script:
awk 'FNR==NR{s+=$3;next;} { print $1 , $2, 100*$3/s }'
and the following file:
>P39PT-1224 Freq 900
cccctacgacggcattggtaatggctcagctgctccggatcccgcaagccatcttggatatgagggttcgtcggcctcttcagccaagg-cccccagcagaacatccagctgatcg
>P39PT-784 Freq 2... (2 Replies)
Discussion started by: Xterra
2 Replies
8. UNIX for Dummies Questions & Answers
I would like to extract all entries containing the following patterns: ccccta & ccccccccc from the following infile:
>P39PT-1224_Freq_900
cccctacgacggcattggtaatggctcccgcaagccatctctcttcagccaagg
>P39PT-784_Freq_2
cccctacgacggcattggtaatggcacccgcaagccatctctcttccccccccc
>P39PT-678_Freq_5... (4 Replies)
Discussion started by: Xterra
4 Replies
9. UNIX for Beginners Questions & Answers
I have two fasta files as shown below,
File:1
>Contig_1:90600-91187
AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGAACAGGAATTGATGACGGTC
>Contig_98:35323-35886
GACGAAGCGCTCGCCAAGGCCGAAGAAGAAGGCCTGGATCTGGTCGAAATCCAGCCGCAG
>Contig_24:26615-28387... (11 Replies)
Discussion started by: dineshkumarsrk
11 Replies
10. UNIX for Beginners Questions & Answers
I have 5 sequences in a fasta file namely gene1.fasta as follows,
gene1.fasta
>1256
ATGTAGC
>GEP
TAGAG
>GTY578
ATGCATA
>67_iga
ATGCTGA
>90_ld
ATGCTG
I need to rename the gene1.fasta file based on the sequence position specified in list.txt as follows,
list.txt
position1=org5... (5 Replies)
Discussion started by: dineshkumarsrk
5 Replies
LEARN ABOUT PHP
headers_sent
HEADERS_SENT(3) 1 HEADERS_SENT(3)
headers_sent - Checks if or where headers have been sent
SYNOPSIS
bool headers_sent ([string &$file], [int &$line])
DESCRIPTION
Checks if or where headers have been sent.
You can't add any more header lines using the header(3) function once the header block has already been sent. Using this function you can
at least prevent getting HTTP header related error messages. Another option is to use Output Buffering.
PARAMETERS
o $file
- If the optional $file and $line parameters are set, headers_sent(3) will put the PHP source file name and line number where out-
put started in the $file and $line variables.
o $line
- The line number where the output started.
RETURN VALUES
headers_sent(3) will return FALSE if no HTTP headers have already been sent or TRUE otherwise.
EXAMPLES
Example #1
Examples using headers_sent(3)
<?php
// If no headers are sent, send one
if (!headers_sent()) {
header('Location: http://www.example.com/');
exit;
}
// An example using the optional file and line parameters, as of PHP 4.3.0
// Note that $filename and $linenum are passed in for later use.
// Do not assign them values beforehand.
if (!headers_sent($filename, $linenum)) {
header('Location: http://www.example.com/');
exit;
// You would most likely trigger an error here.
} else {
echo "Headers already sent in $filename on line $linenum
" .
"Cannot redirect, for now please click this <a " .
"href="http://www.example.com">link</a> instead
";
exit;
}
?>
NOTES
Note
Headers will only be accessible and output when a SAPI that supports them is in use.
SEE ALSO
ob_start(3), trigger_error(3), headers_list(3), header(3) for a more detailed discussion of the matters involved. .
PHP Documentation Group HEADERS_SENT(3)