在PHP中执行外部BLAST程序 [英] Execute an external BLAST program in PHP
问题描述
我想用PHP而不是Linux控制台文本终端执行blastx搜索应用程序.
I want to execute a blastx search application in PHP instead of Linux console text terminal.
实际的命令行参数将是(请参见Referer的定义 ):
The actual command line arguments would be (see definition of refer):
./blastx -query $input -db ${Sbjct}_db -evalue 0.0001 -outfmt 6 -out /path/to/output.tsv
这是我的PHP部分代码.
Here's my PHP partial code.
exec('
/path/to/blastx
-query /path/to/PAO1.fasta
-db /path/to/VFDB_setB_pro
-evalue 0.0001
-outfmt 6
-out /path/to/output.tsv
');
但是,当我在PHP程序中调用exec()
函数时,没有任何反应.
However, when I call exec()
function in PHP program there is nothing happened.
我也尝试了另一种方法.它返回错误代码1.这是我的php exec()
内容:
I also tried another method. It return error code 1. Here is my php exec()
content:
exec('sh /path/to/myscript.sh', $output, $return_var);
我错过了哪些重要步骤? 是否有其他方法可以执行外部程序?
What vital steps I missed out? Is there any alternative method to execute external programs?
任何建议将不胜感激.
推荐答案
中断线是问题,请尝试
<?php
exec('\
/path/to/blastx \
-query /path/to/PAO1.fasta \
-db /path/to/VFDB_setB_pro \
-evalue 0.0001 \
outfmt 6 \
-out /path/to/output.tsv \
');
编辑
我显示了过程,因为我无法进行跟踪
I show the process since I cann't do tracking
1-输入数据
cat seq.fa #NUCLEOTIDES
cat seq.fa #NUCLEOTIDES
>seq_1
GGCAGCCTAACACATGCAAGTCGAACGGTAACAGGAAGCAGCTTGCTGCTTTGCT
GACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGAT
AACTACTGGAAACGGTAGCTAATACCGCATAATGTCGCAAGACCAAAGAGGGGGA
cat database.fa#蛋白质
cat database.fa #PROTEINS
>KDG85104.1 hypothetical protein AE17_03267, partial [Escherichia coli UCI 58]
PVVIPLHQAVSQTLLTRPPLVSKAASCFLLPFDLHVLGLPPAFNLSHDQTLQFKSLMLKELNFVMNYVFTLETWYSFFVL
RR
>EUM99718.1 hypothetical protein L347_09473, partial [Enterobacter sp. MGH 1]
VVIPLHQAVSQTLLTRPPLVSEAASCFLLPFDLHVLGLPPAFNLSHDQTLQFKSLMLNELNFVMNYVFTR
>CSD41531.1 Uncharacterised protein [Vibrio cholerae]
MADHPLRPARDRRLGEPLPHQLANPTWAYPVAQGPKVPCFALARLCGISHRFQWLSPSTGQFPRHYSPVRRSPPKEQVPL
CCRSTCMC
2-格式化数据库
makeblastdb -in database.fa -dbtype prot -out database
3- bash脚本
cat myscript.sh
cat myscript.sh
path_to_blast/blastx -query path_to_query/seq.fa -db path_to_db/database -evalue 0.0001 -outfmt 6
4- php脚本
cat blast.php
cat blast.php
<?php
exec('sh myscript.sh', $output, $return_var);
print_r($output);
echo "$return_var\n";
5-运行它,
php blast.php
你得到
Array
(
[0] => seq_1 KDG85104.1 100.00 38 0 0 118 5 1 38 1e-24 77.0
[1] => seq_1 EUM99718.1 97.30 37 1 0 115 5 1 37 2e-23 73.6
[2] => seq_1 CSD41531.1 70.59 51 15 0 162 10 38 88 1e-22 72.0
)
0
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