Re: missing character when reading input file

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Re^2: missing character when reading input file by JediGorf (Initiate) on Sep 11, 2018 at 15:47 UTC
As an example: Input of first line: acggaccgcggcatttgccaatttgcgcgtcgtcgggggtcgccatgatgtttcgcttggcaggcttttttgctttggcactgctggtcgcgggaaagcc Output of first line: ACGGACCGCGGCATTTGCCAATTTGCGCGTCGTCGGGGGTCGCCATGATGTTTCGCTTGGCAGGCTTTTTTGCTTTGGCA So the sequence: ctgctggtcgcgggaaagcc is completely gone from my output. Interestingly, the output is 80 chars while the input is 100, so the missing chunk is exactly 20. Is Perl somehow limited to only 80 chars in a line of text?	[reply]
Re^3: missing character when reading input file by AnomalousMonk (Archbishop) on Sep 11, 2018 at 16:10 UTC
Still not a lot of info to do \| go on, but let me suggest you have "invisible" characters lurking in your input: `c:\@Work\Perl\monks>perl -wMstrict -MData::Dump -le "my $seq = qq{what is wrong with this\x0dline}; print $seq; dd $seq; " line is wrong with this "what is wrong with this\rline"` [download] Some kind of data dump (Data::Dumper, Data::Dump) might be informative. (`Data::Dumper` is core and so should already be installed.) Give a man a fish: `<%-{-{-{-<`	[reply] [d/l] [select]
Re^4: missing character when reading input file by Eily (Monsignor) on Sep 11, 2018 at 16:19 UTC
For this to work with Data::Dumper you need to set $Data::Dumper::Useqq = 1; Otherwise the \r isn't replaced by visible chars. `perl -MData::Dumper -E "print Dumper qq<a\rb>" b';R1 = 'a` [download] `perl -MData::Dumper -E "$Data::Dumper::Useqq = 1; print Dumper qq<a\rb +>" $VAR1 = "a\rb";` [download] One of the main reasons to prefer Data::Dump over Data::Dumper for debugging :) 80 chars really sounds like a display limit though, rather than an invisible char	[reply] [d/l] [select]
Re^3: missing character when reading input file by Eily (Monsignor) on Sep 11, 2018 at 15:59 UTC
Perl has no such limitations, so it comes from the way you display your output. I'm guessing this is on a terminal? If so, try forwarding it to a file instead	[reply]
Re^3: missing character when reading input file by AnomalousMonk (Archbishop) on Sep 11, 2018 at 19:28 UTC
Further to Eily's post: 80 chars really sounds like a display limit ... JediGorf: Is the truncation always at 80 characters? Give a man a fish: `<%-{-{-{-<`	[reply] [d/l]
Re^2: missing character when reading input file by JediGorf (Initiate) on Sep 11, 2018 at 15:53 UTC
With a space between the "lines" instead of a carriage return, is Perl not getting each "line" from: `while ($line = <$input>) { }`? Never mind. When I look at the original input file that I'm using, those are carriage returns at the ends of the lines.	[reply] [d/l]
Re^3: missing character when reading input file by poj (Abbot) on Sep 11, 2018 at 16:03 UTC
Is that the complete input file. If not how long is the last line ? poj	[reply]
Re^3: missing character when reading input file by AnomalousMonk (Archbishop) on Sep 12, 2018 at 00:05 UTC
When I look at the original input file ... those are carriage returns at the ends of the lines. Is it literally true that you are seeing "carriage return" (ASCII 0x0d) characters at the ends of your lines? If so, that may be a big part of your problem. On what sort of system do the files originate? Windows? On what sort of system are you processing the files? *nix? Line-ending delimiters are different on these two systems (and on others). Give a man a fish: `<%-{-{-{-<`	[reply] [d/l]
Re^2: missing character when reading input file by JediGorf (Initiate) on Sep 12, 2018 at 00:33 UTC
Input: >symbB.v1.2.017277.t1\|scaffold1325.1\|size176917\|3 acggaccgcggcatttgccaatttgcgcgtcgtcgggggtcgccatgatgtttcgcttggcaggcttttttgctttggcactgctggtcgcgggaaagcc caagggtggcaaaggtgcaaaaggagaacaagaccccttctctgagcttagccgcctcgcagacaatttgaaagatgctaaagaacagccggagaaggcc aagaatgctctgaacatgatggatccagaaagtttaggcgattctatggccaacatgatggtgatggcaatggataaggaccaggatggtgtgttgtcag aggaggagattgccaccatggtacaatcgggagagacggagaacaaaggcaaagcagaggagatgtttgaacagatggatgaagatggcgatggagaggt aaccagagacgaagcgaaggtgtacttttcaaaactaggaaacaccttgcaaggcctttcaaaaatgatgggtggttcaaaatcagagttgtgattggga gaatcgctctgtcaaccgcctgcggtggtgcggttggaaggttgagcttgaaaggtgcgaagcgtctctccattggtgtccgagatagcctgagatagcc tgagatatttaggtgatactgtatcttcttgggttttcggatgcaaatttttgacaacagatcagaaatccatccgaatatcccggccgccagggcaaaa atcatagagtttccctgtgcagaagctgcaagttttgagtttttctcattccattggggcctgaatttcaagaaaatcgtatagtctta Output: ACGGACCGCGGCATTTGCCAATTTGCGCGTCGTCGGGGGTCGCCATGATGTTTCGCTTGGCAGGCTTTTTTGCTTTGGCACTGCTGGTCGCGGGAAAGCC CAAGGGTGGCAAAGGTGCAAAAGGAGAACAAGACCCCTTCTCTGAGCTTAGCCGCCTCGCAGACAATTTGAAAGATGCTAAAGAACAGCCGGAGAAGGCC AAGAATGCTCTGAACATGATGGATCCAGAAAGTTTAGGCGATTCTATGGCCAACATGATGGTGATGGCAATGGATAAGGACCAGGATGGTGTGTTGTCAG AGGAGGAGATTGCCACCATGGTACAATCGGGAGAGACGGAGAACAAAGGCAAAGCAGAGGAGATGTTTGAACAGATGGATGAAGATGGCGATGGAGAGGT AACCAGAGACGAAGCGAAGGTGTACTTTTCAAAACTAGGAAACACCTTGCAAGGCCTTTCAAAAATGATGGGTGGTTCAAAATCAGAGTTGTGATTGGGA GAATCGCTCTGTCAACCGCCTGCGGTGGTGCGGTTGGAAGGTTGAGCTTGAAAGGTGCGAAGCGTCTCTCCATTGGTGTCCGAGATAGCCTGAGATAGCC TGAGATATTTAGGTGATACTGTATCTTCTTGGGTTTTCGGATGCAAATTTTTGACAACAGATCAGAAATCCATCCGAATATCCCGGCCGCCAGGGCAAAA ATCATAGAGTTTCCCTGTGCAGAAGCTGCAAGTTTTGAGTTTTTCTCATTCCATTGGGGCCTGAATTTCAAGAAAATCGTATAGTCTTA CGGACCGCGGCATTTGCCAATTTGCGCGTCGTCGGGGGTCGCCATGATGTTTCGCTTGGCAGGCTTTTTTGCTTTGGCACTGCTGGTCGCGGGAAAGCC CAAGGGTGGCAAAGGTGCAAAAGGAGAACAAGACCCCTTCTCTGAGCTTAGCCGCCTCGCAGACAATTTGAAAGATGCTAAAGAACAGCCGGAGAAGGCC AAGAATGCTCTGAACATGATGGATCCAGAAAGTTTAGGCGATTCTATGGCCAACATGATGGTGATGGCAATGGATAAGGACCAGGATGGTGTGTTGTCAG AGGAGGAGATTGCCACCATGGTACAATCGGGAGAGACGGAGAACAAAGGCAAAGCAGAGGAGATGTTTGAACAGATGGATGAAGATGGCGATGGAGAGGT AACCAGAGACGAAGCGAAGGTGTACTTTTCAAAACTAGGAAACACCTTGCAAGGCCTTTCAAAAATGATGGGTGGTTCAAAATCAGAGTTGTGATTGGGA GAATCGCTCTGTCAACCGCCTGCGGTGGTGCGGTTGGAAGGTTGAGCTTGAAAGGTGCGAAGCGTCTCTCCATTGGTGTCCGAGATAGCCTGAGATAGCC TGAGATATTTAGGTGATACTGTATCTTCTTGGGTTTTCGGATGCAAATTTTTGACAACAGATCAGAAATCCATCCGAATATCCCGGCCGCCAGGGCAAAA ATCATAGAGTTTCCCTGTGCAGAAGCTGCAAGTTTTGAGTTTTTCTCATTCCATTGGGGCCTGAATTTCAAGAAAATCGTATAGTCTTA GGACCGCGGCATTTGCCAATTTGCGCGTCGTCGGGGGTCGCCATGATGTTTCGCTTGGCAGGCTTTTTTGCTTTGGCACTGCTGGTCGCGGGAAAGCC CAAGGGTGGCAAAGGTGCAAAAGGAGAACAAGACCCCTTCTCTGAGCTTAGCCGCCTCGCAGACAATTTGAAAGATGCTAAAGAACAGCCGGAGAAGGCC AAGAATGCTCTGAACATGATGGATCCAGAAAGTTTAGGCGATTCTATGGCCAACATGATGGTGATGGCAATGGATAAGGACCAGGATGGTGTGTTGTCAG AGGAGGAGATTGCCACCATGGTACAATCGGGAGAGACGGAGAACAAAGGCAAAGCAGAGGAGATGTTTGAACAGATGGATGAAGATGGCGATGGAGAGGT AACCAGAGACGAAGCGAAGGTGTACTTTTCAAAACTAGGAAACACCTTGCAAGGCCTTTCAAAAATGATGGGTGGTTCAAAATCAGAGTTGTGATTGGGA GAATCGCTCTGTCAACCGCCTGCGGTGGTGCGGTTGGAAGGTTGAGCTTGAAAGGTGCGAAGCGTCTCTCCATTGGTGTCCGAGATAGCCTGAGATAGCC TGAGATATTTAGGTGATACTGTATCTTCTTGGGTTTTCGGATGCAAATTTTTGACAACAGATCAGAAATCCATCCGAATATCCCGGCCGCCAGGGCAAAA ATCATAGAGTTTCCCTGTGCAGAAGCTGCAAGTTTTGAGTTTTTCTCATTCCATTGGGGCCTGAATTTCAAGAAAATCGTATAGTCTTA `open ($input, $ARGV[0]) or die ("Could not open input file $ARGV[0].\n +"); open ($output, '>output.txt') or die ("Could not open input file outpu +t.txt.\n"); while ($line = <$input>) { chomp($line); unless ($line =~ m/>/) { $line = uc($line); $seq .= $line; } } $orf1 = $seq; $orf2 = substr($seq, 1); $orf3 = substr($seq, 2);` [download] OK, so the problem is a little different than what I thought earlier. What I'm trying to get is for $seq to be a continuous string of letters, but as you can see, when I use substr it deletes characters on the first line like it should but doesn't shift the other lines (i.e. the GCC on the first line should connect right to the CAA that begins the second line of the output without any spaces or newlines). I'm guessing this is some sort of newline issue? But I used chomp, so I'm confused.	[reply] [d/l]
Re^3: missing character when reading input file by JediGorf (Initiate) on Sep 12, 2018 at 00:47 UTC
Added this `$line =~ s/\r//;` and it fixed the issue. Newlines/carriage returns can be a huge pain.	[reply] [d/l]