I'm using a php script, and I need to use blastp to recover some data. This works fine when I run it in command prompt.
我使用的是php脚本，我需要使用blastp来恢复一些数据。当我在命令提示符中运行它时，它运行良好。
blastp -query test_query.fa -db notas.fa -task blastp -outfmt "7 qseqid qseq sseqid sseq evalue bitscore" -out musica1.fa
But it doesn't work in my script. This is my script:
但它在我的脚本中不起作用。这是我的脚本:
$blastp = "C:/wamp/www/SiMiLa/blastp.exe";
$texto = "'7 qseqid qseq sseqid sseq evalue bitscore'";
$cmd = $blastp." -query test_query.fa -db notas.fa -task blastp -outfmt '$texto' -out musica1.fa 2>&1";
$result = shell_exec($cmd);
print_r ($result);
When I run it, I get the following error:
当我运行它时，我得到如下错误:
USAGE blastp [-h] [-help] [-import_search_strategy filename] [-export_search_strategy filename] [-task task_name] [-db database_name] [-dbsize num_letters] [-gilist filename] [-seqidlist filename] [-negative_gilist filename] [-entrez_query entrez_query] [-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm] [-subject subject_input_file] [-subject_loc range] [-query input_file] [-out output_file] [-evalue evalue] [-word_size int_value] [-gapopen open_penalty] [-gapextend extend_penalty] [-qcov_hsp_perc float_value] [-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value] [-xdrop_gap_final float_value] [-searchsp int_value] [-sum_stats bool_value] [-seg SEG_options] [-soft_masking soft_masking] [-matrix matrix_name] [-threshold float_value] [-culling_limit int_value] [-best_hit_overhang float_value] [-best_hit_score_edge float_value] [-window_size int_value] [-lcase_masking] [-query_loc range] [-parse_deflines] [-outfmt format] [-show_gis] [-num_descriptions int_value] [-num_alignments int_value] [-line_length line_length] [-html] [-max_target_seqs num_sequences] [-num_threads int_value] [-ungapped] [-remote] [-comp_based_stats compo] [-use_sw_tback] [-version] DESCRIPTION Protein-Protein BLAST 2.2.31+ Use '-help' to print detailed descriptions of command line arguments ======================================================================== Error: Too many positional arguments (1), the offending value: qseqid
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Can someone help me?
有人能帮助我吗?
1 个解决方案
#1
0
I solved it by changing my script to:
我把剧本改成:
$blastp = "C:/wamp/www/SiMiLa/blastp.exe";
$texto = "7 qseqid qseq sseqid sseq evalue bitscore";
$cmd = $blastp." -query test_query.fa -db notas.fa -task blastp -outfmt \"7 qseqid qseq sseqid sseq evalue bitscore\" -out musica1.fa 2>&1";
$result = shell_exec($cmd);
print_r ($result);
#1
0
I solved it by changing my script to:
我把剧本改成:
$blastp = "C:/wamp/www/SiMiLa/blastp.exe";
$texto = "7 qseqid qseq sseqid sseq evalue bitscore";
$cmd = $blastp." -query test_query.fa -db notas.fa -task blastp -outfmt \"7 qseqid qseq sseqid sseq evalue bitscore\" -out musica1.fa 2>&1";
$result = shell_exec($cmd);
print_r ($result);