If you want to extract Sbjct: lines, and print them out, the following should work fine: 

#!/usr/bin/perl -w
use strict;

while (<>) {
    print if /^Sbjct:\s*\d+\D+\d+$/;
}

[download]
After running this code for your sample input data i get: 
Sbjct: 38348818 AGGCATAAACCACATCCAGCCACCTCCTTCTGATCAGCAGCAAAGCTGACGTTT
+TGATCT 38348759
Sbjct: 38348758 CCATCTGTCTGATTCTTGTGTCTACTTCTCAGTTTACAACTCCAGTGGGAAAGA
+AAGAGC 38348699
Sbjct: 38348698 TTTATTTACAGACCCATAAAAATCCCATCAGTGTCGTCCCCTGCTGAGAGGCCA
+TGTGAG 38348639
Sbjct: 94217254 CAAGAAACTATATAGGTATACACTTACGACTTCACAAAACCTATACTTAATATA
+GTAAAT 94217195
Sbjct: 94217194 CTAAGTAAACATGTATTACTCAAAGTAATATATTTAGAATTATGTATTAGTATA
+AGATCA 94217135
Sbjct: 94217134 GAATTGAATTTAAGTTGTTGGTGACATCTGCATCATTTCATAGGATTAGAACTT
+ACTCAA 94217075
Sbjct: 94217074 AATAATGTAAATCTTTAAAAATATAAATTAGAATGACAAGTGGGAATCATAAAT
+TAAACG 94217015

[download]

Hope that helps,
Luke

In reply to Re^3: Parsing a file by 1Nf3
in thread Parsing a file by cowboyrocks

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