Re^13: how to read input from a file, one section at a time?

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Re^14: how to read input from a file, one section at a time? by davi54 (Sexton) on Apr 02, 2019 at 17:40 UTC
Hi Poj, Can I get your email ID if that's okay with you? I can send you the complete script and you can help me with my struggle.	[reply]
Re^15: how to read input from a file, one section at a time? by poj (Abbot) on Apr 02, 2019 at 17:43 UTC
You can post code on you scratchpad davi54's scratchpad	[reply]
Re^15: how to read input from a file, one section at a time? by davi54 (Sexton) on Apr 02, 2019 at 17:54 UTC
I posted the test file and the script in the scratchpad. Again thanks for everything Poj. I really appreciate your effort.	[reply]
Re^16: how to read input from a file, one section at a time? by poj (Abbot) on Apr 02, 2019 at 18:05 UTC
I suspect the problem is trailing whitespace (carriage returns, line feeds, spaces etc) on your sequences `# Remove comment line(s) $para =~ s/^\s#.//mg; # Trim trailing white space $para =~ s/\s+$//; # add this ..` [download] poj	[reply] [d/l]
Re^17: how to read input from a file, one section at a time? by davi54 (Sexton) on Apr 02, 2019 at 18:38 UTC
Re^18: how to read input from a file, one section at a time? by poj (Abbot) on Apr 02, 2019 at 19:20 UTC
Some notes below your chosen depth have not been shown here
Re^14: how to read input from a file, one section at a time? by davi54 (Sexton) on Apr 02, 2019 at 16:38 UTC
Hi Poj, When I made the modifications that you suggested, for some reason, it mucked up the entire script. It started giving me errors like: Use of uninitialized value $lowest in printf at poj_repeat.pl line 60, <$PROTFILE> chunk 2. Use of uninitialized value $lowest in numeric eq (==) at poj_repeat.pl line 61, <$PROTFILE> chunk 2. Use of uninitialized value in numeric eq (==) at poj_repeat.pl line 61, <$PROTFILE> chunk 2. Can you help me with this? Use of uninitialized value in concatenation (.) or string at poj_repeat.pl line 62, <$PROTFILE> chunk 2. Missing argument in printf at poj_repeat.pl line 67, <$PROTFILE> chunk 2. Missing argument in printf at poj_repeat.pl line 67, <$PROTFILE> chunk 2	[reply]
Re^15: how to read input from a file, one section at a time? by poj (Abbot) on Apr 02, 2019 at 17:21 UTC
Did you remove or comment out the original line ? `#next FASTA_RECORD if $fasta_seen{ $para }++;` [download] poj	[reply] [d/l]
Re^16: how to read input from a file, one section at a time? by davi54 (Sexton) on Apr 02, 2019 at 17:36 UTC
However, now the script has stopped giving me the duplicate information. I have a test file where I have put the same sequence twice. It was giving me the duplicate print message earlier, but not anymore after fixing the semicolon issue.	[reply]
Re^15: how to read input from a file, one section at a time? by davi54 (Sexton) on Apr 02, 2019 at 17:30 UTC
Hi, Yes, I did. I actually forgot to put a semicolon. Lol. Nevermind.	[reply]


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