Dear all, I have a file, where i have to extract specific lines from the file. 
# ----- prediction on sequence number 1 (length = 105, name = seq_01) 
+--
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
seq_01    CHECKED    gene    28503    30196    0.89    +    .    g1
seq_01    CHECKED    transcript    28503    30196    0.89    +    .   
+ g1.t1
seq_01    CHECKED    start_codon    28503    28505    .    +    0    t
+ranscript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtcgtccctccccactctcatctttctccaccc
# atcgctgcggtcctcgccgacccttttgtgccggaagtagggaccgg]
# protein sequence = [MTASAFVLGTVAFLHNRLRRSRPRQASTAHR
# GTETPLLRSDKENLTTVLDATILVHSLGQKTNLALGATSSSLDLQKTNLAL
# VAALTPGIVFPLPSPFVATGLCLQKTNLALGATSSSLDL]
# end gene g1
###
# start gene g2
seq_01    CHECKED    gene    77978    79779    0.44    +    .    g2
seq_01    CHECKED    transcript    77978    79779    0.44    +    .   
+ g2.t1
seq_01    CHECKED    start_codon    77978    77980    .    +    0    t
+ranscript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgccgtcctcgtcaaagcagctggcgatgcc
# tcggcccctccttctgcaaaccgccctgccgcccgcctcggctcctccgaa
# gccgagcagcctacgcaggggccgcagatgctcgcgggagggaatatcgg]
# protein sequence =[MPLDSSSTPTSNPAPSHSSTAYLLFERLHIAEQ
# CCPGQGIRHGKWSPGSSEAPT]
# end gene g2
###
#
# ----- prediction on sequence number 2 (length = 710, name = seq_02) 
+-----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 2 on both strands
# start gene g3
seq_02    CHECKED    gene    150    2800    0.31    +    .    g3
seq_02    CHECKED    transcript    150    2800    0.31    +    .    g3
+.t1
seq_02    CHECKED    intron    1    149    0.75    +    .    transcrip
+t_id "g3.t1"; gene_id "g3";
# coding sequence = [agctgccctcctcggggccagccttctcttaactc
# tttgagaccttcaatcctgaggcgtgagacgcagtctggaggagcagctc]
# protein sequence = [LRRETQSGGAALCSLFDPPPTPTACAHANSP]
# end gene g3
###
#
# ----- prediction on sequence number 3 (length = 713, name = seq_03) 
+-----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 3 on both strands
# start gene g4 ....
[as same as above]......so on and on...

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From this file, i need to extract sequences to 2 different files like: 
FILE 1:
>seq_01 g1
atgtcgtccctccccactctcatctttctccacccatcgctgcggtcctcgccgacccttttgtgccgga
+agtagggaccgg
>seq_01 g2
atgccgtcctcgtcaaagcagctggcgatgcctcggcccctccttctgcaaaccgccctgccgcccgcct
+cggctcctccgaagccgagcagcctacgcaggggccgcagatgctcgcgggagggaatatcgg
>seq_02 g3
agctgccctcctcggggccagccttctcttaactctttgagaccttcaatcctgaggcgtgagacgcagt
+ctggaggagcagctc
>seq_03 g4
......so on...

FILE 2:
>seq_01 g1
MTASAFVLGTVAFLHNRLRRSRPRQASTAHRGTETPLLRSDKENLTTVLDATILVHSLGQKTNLALGATS
+SSLDLQKTNLALVAALTPGIVFPLPSPFVATGLCLQKTNLALGATSSSLDL
>seq_01 g2
MPLDSSSTPTSNPAPSHSSTAYLLFERLHIAEQCCPGQGIRHGKWSPGSSEAPT
>seq_02 g3
LRRETQSGGAALCSLFDPPPTPTACAHANSP
>seq_03 g4
......so on...

[download]
The code i have written so far to obtain this is: 
#!/usr/bin/perl
open(FH,$ARGV[0]);
open(OUT1,">file1.txt");
open(OUT2,">file2.txt");
@array=<FH>;
$str=join("",@array);
@list=split("###",$str);
foreach $line(@list){
    $line=~m/(# coding sequence = [.*\])(# protein sequence = [.*\])/;
  print OUT1 "$1";
  print OUT2 "$2";
}

[download]
I am not getting any answer for this program. havent found how to print the headers too. How can i do it? please advice or give suggestions. thank you. :)

In reply to extraction of sequences by patric

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