Mercurial > repos > mcharles > rapsosnp
comparison rapsodyn/extractseq.pl @ 10:0a6c1cfe4dc8 draft
Uploaded
author | mcharles |
---|---|
date | Mon, 19 Jan 2015 04:33:21 -0500 |
parents | 0e7c6fe60646 |
children |
comparison
equal
deleted
inserted
replaced
9:0e7c6fe60646 | 10:0a6c1cfe4dc8 |
---|---|
1 #!/usr/bin/perl | 1 #!/usr/bin/perl |
2 #V1.10 manage empty files | |
3 #V1.02 Trop de pb avec nbci blast+, changment du header des fasta | |
2 #V1.01 #Ajout d'un _ a la fin du nom pour eviter les problemes avec ncbi blast+ | 4 #V1.01 #Ajout d'un _ a la fin du nom pour eviter les problemes avec ncbi blast+ |
3 | 5 |
4 use strict; | 6 use strict; |
5 use warnings; | 7 use warnings; |
6 use Getopt::Long; | 8 use Getopt::Long; |
14 "input_assembly_file=s" => \$input_assembly_file, | 16 "input_assembly_file=s" => \$input_assembly_file, |
15 "window_length=i" => \$WINDOWS_LENGTH | 17 "window_length=i" => \$WINDOWS_LENGTH |
16 ) or die("Error in command line arguments\n"); | 18 ) or die("Error in command line arguments\n"); |
17 | 19 |
18 open(INV, $input_variant_file) or die ("Can't open $input_variant_file\n"); | 20 open(INV, $input_variant_file) or die ("Can't open $input_variant_file\n"); |
21 | |
22 if ( -z INV){ | |
23 print ">empty\nAAAAA"; | |
24 exit(0); | |
25 } | |
26 | |
19 open(INA, $input_assembly_file) or die ("Can't open $input_assembly_file\n"); | 27 open(INA, $input_assembly_file) or die ("Can't open $input_assembly_file\n"); |
20 | 28 |
21 my @variant_list; | 29 my @variant_list; |
22 | 30 |
23 | 31 |
87 else { | 95 else { |
88 $descriptor.="?_?"; | 96 $descriptor.="?_?"; |
89 } | 97 } |
90 $variant{"desc"}=$descriptor; | 98 $variant{"desc"}=$descriptor; |
91 | 99 |
92 print ">",$variant{"ref"},"_",$descriptor,"_","\n",$variant{"SEQ"},"\n"; | 100 #print ">",$variant{"ref"},"_",$descriptor,"_","\n",$variant{"SEQ"},"\n"; |
93 | 101 |
94 | 102 |
95 | 103 |
104 #V1.02 : changement du header | |
96 #print ">",$variant{"ref"},"_",$variant{"position"},"_",$variant{"depth"},"\n",$variant{"SEQ"},"\n"; | 105 #print ">",$variant{"ref"},"_",$variant{"position"},"_",$variant{"depth"},"\n",$variant{"SEQ"},"\n"; |
106 print ">",$variant{"ref"},"_",$variant{"position"},"_",$variant{"depth"},"\n",$variant{"SEQ"},"\n"; | |
97 | 107 |
98 push(@variant_list,\%variant); | 108 push(@variant_list,\%variant); |
99 } | 109 } |
100 } | 110 } |
101 close (INV); | 111 close (INV); |