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Top Forums Shell Programming and Scripting Count and search by sequence in multiple fasta file Post 302892115 by ahamed101 on Tuesday 11th of March 2014 05:03:50 AM
Old 03-11-2014
a bash approach
Code:
#!/bin/bash

query=query.txt
file_list=(*.txt)
declare -A pattern

printf "%-10s\t%-10s\t" "" "Sequence"
for file in ${file_list[@]}
do
  printf "%-10s\t" $file
  while read line
  do
    [[ "$line" =~ ">" ]] && continue
    ((pattern[$file,$line]+=1))
  done < $file
done
echo

while read line
do
  [[ "$line" =~ ">" ]] && printf "%-10s\t" ${line/>/} && continue
  printf "%-10s\t" $line
  for file in ${file_list[@]}
  do
    printf "%-10s\t" ${pattern[$file,$line]:-0}
  done
  echo
done < $query

 

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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)
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