Please advice how can we search for a string say (abc) in multiple files and to get total occurrence of that searched string. (Need number of records that exits in period of time).
File look like this (read as filename.yyyymmdd)
a.20100101
b.20100108
c.20100115
d.20100122
e.20100129... (2 Replies)
Hi.. I have a seperate chromosome sequences and i wanted to parse some regions of chromosome based on start site and end site.. how can i achieve this?
For Example Chr 1 is in following format
I need regions from 2 - 10 should give me AATTCCAAA
and in a similar way 15- 25 should give... (8 Replies)
Hey,
I've been trying to break a massive fasta formatted file into files containing each gene separately. Could anyone help me? I've tried to use the following code but i've recieved errors every time:
for i in *.rtf.out
do
awk '/^>/{f=++d".fasta"} {print > $i.out}' $i
done (1 Reply)
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)
I have fasta files with multiple sequences in each. I need to change the sequence name headers from:
>accD:_59176-60699
ATGGAAAAGTGGAGGATTTATTCGTTTCAGAAGGAGTTCGAACGCA
>atpA_(reverse_strand):_showing_revcomp_of_10525-12048
ATGGTAACCATTCAAGCCGACGAAATTAGTAATCTTATCCGGGAAC... (2 Replies)
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)
Hi,
I want to search only duplicate sequence number in file e.g
4757610
4757610
should display only duplicate sequence number in file.
file contain is:
4757610 6zE:EXPNL ORDER_PRIORITY='30600022004757610' ORDER_IDENTIFIER='4257771056' MM_ASK_VOLUME='273' MM_ASK_PRICE='1033.0000' m='GBX'... (5 Replies)
Hi,
I have a fasta file with multiple sequences. How can i get only unique sequences from the file.
For example
my_file.fasta
>seq1
TCTCAAAGAAAGCTGTGCTGCATACTGTACAAAACTTTGTCTGGAGAGATGGAGAATCTCATTGACTTTACAGGTGTGGACGGTCTTCAGAGATGGCTCAAGCTAACATTCCCTGACACACCTATAGGGAAAGAGCTAAC
>seq2... (3 Replies)
I could calculate the length of entire fasta sequences by following command,
awk '/^>/{if (l!="") print l; print; l=0; next}{l+=length($0)}END{print l}' unique.fasta
But, I need to calculate the length of a particular fasta sequence specified/listed in another txt file. The results to to be... (14 Replies)
I have to mine the following sequence pattern from a large fasta file namely gene.fasta (contains multiple fasta sequences) along with the flanking sequences of 5 bases at starting position and ending position,
AAGCZ-N16-AAGCZ
Z represents A, C or G (Except T)
N16 represents any of the four... (3 Replies)
Discussion started by: dineshkumarsrk
3 Replies
LEARN ABOUT PHP
maxdb_fetch_field_direct
MAXDB_FETCH_FIELD_DIRECT(3) 1 MAXDB_FETCH_FIELD_DIRECT(3)maxdb_fetch_field_direct - Fetch meta-data for a single field
Procedural style
SYNOPSIS
mixed maxdb_fetch_field_direct (resource $result, int $fieldnr)
DESCRIPTION
Object oriented style
mixed maxdb_result::fetch_field_direct (int $fieldnr)
maxdb_fetch_field_direct(3) returns an resource which contains field definition information from specified resultset. The value of fieldnr
must be in the range from 0 to number of fields - 1.
RETURN VALUES
Returns an resource which contains field definition information or FALSE if no field information for specified fieldnr is available.
Object attributes
+-----------+---------------------------------------------------+
|Attribute | |
| | |
| | Description |
| | |
+-----------+---------------------------------------------------+
| name | |
| | |
| | The name of the column |
| | |
|max_length | |
| | |
| | The maximum width of the field for the result |
| | set. |
| | |
| type | |
| | |
| | The data type used for this field |
| | |
| decimals | |
| | |
| | The number of decimals used (for integer fields) |
| | |
+-----------+---------------------------------------------------+
EXAMPLES
Example #1
Object oriented style
<?php
$maxdb = new maxdb("localhost", "MONA", "RED", "DEMODB");
/* check connection */
if (maxdb_connect_errno()) {
printf("Connect failed: %s
", maxdb_connect_error());
exit();
}
$query = "SELECT name, cno from hotel.customer ORDER BY name";
if ($result = $maxdb->query($query)) {
/* Get field information for column 'SurfaceArea' */
$finfo = $result->fetch_field_direct(1);
printf("Name: %s
", $finfo->name);
printf("Table: %s
", $finfo->table);
printf("max. Len: %d
", $finfo->max_length);
printf("Flags: %d
", $finfo->flags);
printf("Type: %d
", $finfo->type);
$result->close();
}
/* close connection */
$maxdb->close();
?>
Example #2
Procedural style
<?php
$link = maxdb_connect("localhost", "MONA", "RED", "DEMODB");
/* check connection */
if (maxdb_connect_errno()) {
printf("Connect failed: %s
", maxdb_connect_error());
exit();
}
$query = "SELECT name, cno from hotel.customer ORDER BY name";
if ($result = maxdb_query($link, $query)) {
/* Get field information for column 'cno' */
$finfo = maxdb_fetch_field_direct($result, 1);
printf("Name: %s
", $finfo->name);
printf("Table: %s
", $finfo->table);
printf("max. Len: %d
", $finfo->max_length);
printf("Flags: %d
", $finfo->flags);
printf("Type: %d
", $finfo->type);
maxdb_free_result($result);
}
/* close connection */
maxdb_close($link);
?>
The above example will output something similar to:
Name: CNO
Table:
max. Len: 4
Flags: -1
Type: 0
SEE ALSO maxdb_num_fields(3), maxdb_fetch_field(3), maxdb_fetch_fields(3).
PHP Documentation Group MAXDB_FETCH_FIELD_DIRECT(3)