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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_MULTI_QUERY(3)							 1						      MAXDB_MULTI_QUERY(3)

maxdb_multi_query - Performs a query on the database

       Procedural style

SYNOPSIS
bool maxdb_multi_query (resource $link, string $query) DESCRIPTION
Object oriented style bool maxdb::multi_query (string $query) The maxdb_multi_query(3) works like the function maxdb_query(3). Multiple queries are not yet supported. RETURN VALUES
Returns TRUE on success or FALSE on failure. 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(); } $query = "SELECT * FROM dual"; /* execute multi query */ if ($maxdb->multi_query($query)) { do { /* store first result set */ if ($result = $maxdb->store_result()) { while ($row = $result->fetch_row()) { printf("%s ", $row[0]); } $result->close(); } /* print divider */ if ($maxdb->more_results()) { printf("----------------- "); } } while ($maxdb->next_result()); } /* 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(); } $query = "SELECT * FROM dual"; /* execute multi query */ if (maxdb_multi_query($link, $query)) { do { /* store first result set */ if ($result = maxdb_store_result($link)) { while ($row = maxdb_fetch_row($result)) { printf("%s ", $row[0]); } maxdb_free_result($result); } /* print divider */ if (maxdb_more_results($link)) { printf("----------------- "); } } while (maxdb_next_result($link)); } /* close connection */ maxdb_close($link); ?> The above example will output something similar to: a SEE ALSO
maxdb_use_result(3), maxdb_store_result(3), maxdb_next_result(3), maxdb_more_results(3). PHP Documentation Group MAXDB_MULTI_QUERY(3)
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