How Do i remove a specific character from a specific read in a fasta file?Increasing performance of clear...

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How Do i remove a specific character from a specific read in a fasta file?


Increasing performance of clear text file readsHow to prevent grep from excessive unnecessary memory usageRemove the Nth specified character from a lineRemoving a line from a file which has only specific characterhow to remove newline characters in fasta sequencesed + remove word from specific lineHow to search for a match, then a non-match on that line, but include context lines for matched line?how to fatch fasta sequences if header line match from another fileRemove n character after specific word






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0















An error occurred while processing read where a "+" symbol seems to hinder the sequence. This is the specif error that I got after i converted a multi line fasta to a single line fasta and used sed command to remove unwanted characters.



An error occurred processing read TTGTATGCAGCCCAAAAATACCTAAAATTTGGCTCGCGCGGAATGCTAATTCCACCGTTTACAGCCTCCCTTGGGTTGACGAGCCAAAAAAGTGGATCCTTCATGCATGTGTGCCCATGCTATCCTTTAATAGTAACCTTGTCGTTTATCTTAATACTCCTCCGACAACATAATAGTGATTTTACATGAAAAAGACGTGAGTCAACGTTGCGAATCCATTCCGTGACTGATTCGATCCTAGTTTCGTCGAGTTCTTCAATATCTATTTCGTGGCCACATGTTGAGCTATTTGTGACAAATTTGTCAAATTTGCGTCGCAGTCGGCCAGTCGAAACATATTTCGAGTAACTTTCGTGTTAAATATTTTCTCATTTTGATATTCATGCAGGTAGATCGAATCCCCAATATACCGTATAAAGTTATAGATCTACTCGGCTAACTCGGCTACGAATGTCAAAACCAAAGGTTAGAACACGATAGTTGTGCGAAATGGTCTCCTCAAAGAAAATTTCTAGATAATTACGTGCATGTACGTGTGAGCAGAAAACGTCATCAAAAATATCTAAATGTGAACATTGAATAGAGCTTTAAGCACTCGATACGAACAGTCATGGAAATGGAATCAAAACATCGAGCAACACATCTTTTTCATGTAGACCTTGGCTAAATTAAAGCATGATTAGATAGATCAAGAGGATTAAAAAAGATTGAACTACTTTAGTTAAACACAACATACATAATGTACATGTAACCAAACAACGGGACTTATGTTTCTCCCACATATTAGCGAAAGTGGAACTGTTAGCAACCAAACCATATGCAGAATTAGGCCCAAATCAGAGTTTCCACCTATACAACTTTCCAATGGGCCAAGTTGCAAGAGGGAAACACCCATGTGGGCACCAAACCTCCACAAAAGCAGCTCGTATGCGAGCTCTGCATGAACTTGGCCTAGCTCAGTGCAGCTAGCAAGCCAGCAGCGTAGGTCACTTCCATGTGGGTTCATATTCCCTGTACGTAGGGGCGACATATATGGAGCATGCTGCACCATGGACGAGGAGGATGGTGCTATAGCGAATTATGTGGCGGCATAGTGGGGGTGAGGGAGCAAGGCTGCACGAGTCGTTGTGGCTTGGCATGTCAGCCCCGACGTCGTGGGTGAAGGTTGATGCGGTTTCGCGAGGACTATGTGGTATGCATACGAGTGTGCGGTGGGGAAGGCTTTAGGTGGCCACACACATAGTGTTTTTATTGTGGCCACAGGCTTGAGGTAGAGAGTTTGTGATGTGGCAGGATGATAGGGTGGGATGAACGACCACCAACTCCCAAATAATTTTCCAATTAATAGCAAATATACAAAATTTCTTGCATACTCTCATTGTTTCAATGAATAATACTTCTTTTAAAAAAATCAGGCCAAGTAAAGTTTATCCAAGATGTTATATGAATATCTTATAAAAATATATTTCATGATCTTGTATCTAATGATACTACCTCCCGTCCAGATTCATAGGGTTGCGCGTATCCCTAGGTTGTAAATTTGAAAATTGATATAATATCGTTTGTATAATATAAAAAATATCATTAGAAAGAAAGTAGAACATACAAAGCTTTACTACATTGATATATATTTTTGTAATACGTATGTTGTTATCATTCTGGAATTTACGGCTTACAGTTTCTGTGTGAGTCTGTGGCCAGGACGAAAGTATTGATTTTTCATTTGCATGTTGATAACATTGAGATGGATTTTCTCCATCCTTACGTTATCTTCTCAATCTCTGCATCAGAGTTGGCTTTGGGCTCCTATACGGGAGGCGTCTGTTGGCCGTTTTAAGCGGAGCGGACAGGTGGCTCCGCATACCTTTTTTGGTGATCAGATTTGATGGGCTCGGCCCATTTACCGACCTGATGTTCTTATAGGATTTACCCTTACGAACAGCTGAGTCTTATCATCAGAAAATGATCAGCAGTTATCAATATGTTTAACTCCGTTGACCTAACGTATAGAAATATAAAATGGAATATTATATCGCGCTCTTTTGATCCTCAAAGGGCTTTTTTGGAAGGCCTATCCTCCGAGATCTAAGGCCGATCAATCGCGATCCCAGCAATCATTCCAGCCGCTGCGCATCCAGCAGAGACCTTCGAACCCTCCTCCGACGACCTGTCGGCCGCCGCCGGCGACTACCCTCCCTGGGTGATTTTCGACGAGCAGGAACGCCGCTATCGCCACAAGGAGGTCAATGATACCCCAGCCCGCTGACCCCAGGACGGTGGCGCACGCTCGCACCTCCACCGGCCACCCCGTCCAGTTTCCTTCCGCTTCGCCGCTCCCCGGCAGTTTCGTGTCTGGACCTCAGCGTCGACGACGGCTTGCTGGATGGGGTGGATATTATTTCCAGCGTCGTCGTGGCTCACGGCGATCCGTCCTCCTTACATATGATACTGTTACTGTACAAGTACGAGATCAACACGACCGACTATTTCGTCTACAATGCCGGCGACGGCGCCACGGCCGCCGTCGTTGTCGCTTCTCCCCTTGTTACATGGACGAGGAGGAACAGTCCCATGACAGACGGTACCGGTGACTATGAGTAGGAAACGCACTGGCATCCTGCGTCGCGGCGACGAGGAGTTGGTGGTGATGATGGACCTGAGGATGATGAACACTATTGCGTGCGATGATGATGGGTGGGGCAAAGCAGGTGGAAGGTGAGGTCGCGTACTCCGGTCGGGGAGTGGCAGTGGAAGGCCGAGGCGCTCCGGTCCGCCACGATGTGAGCAAAGGCGAGGTGACTTCGTACTGCTGGTGGTGGGTGTGGGAGACCGACCGGGTGATCCCCGTCGGCGACCGGTTCTTATACTGGGTAGACCTACACCGAGGCATCGTCTTCTCCGACGTGTCCGAAAGCCCCGATCTGAGGTTCGTGCCTCTGCCCGTGGAGCCTATCCTCCGTAGACGCGAGGACTGGGACCGGCCCAGTCGCGCCGCAGCCTGTGCGCCACGGCCGGCGGCGCGACTCTGAAGTTCGTCCACGTCTCACCTCGCTGCTGTTGCGAGCAATACGTAA

The error occurred at buffer index 1612084529while processing file block at offset 81604378624 to 83751862272

File offset at error location is 83216463153

File dump around this offset:

1612084479 84 T

1612084480 71 G

1612084481 65 A

1612084482 65 A

1612084483 71 G

1612084484 84 T

1612084485 84 T

1612084486 67 C

1612084487 71 G

1612084488 84 T

1612084489 67 C

1612084490 67 C

1612084491 65 A

1612084492 67 C

1612084493 71 G

1612084494 84 T

1612084495 67 C

1612084496 84 T

1612084497 67 C

1612084498 65 A

1612084499 67 C

1612084500 67 C

1612084501 84 T

1612084502 67 C

1612084503 71 G

1612084504 67 C

1612084505 84 T

1612084506 71 G

1612084507 67 C

1612084508 84 T

1612084509 71 G

1612084510 84 T

1612084511 84 T

1612084512 71 G

1612084513 67 C

1612084514 71 G

1612084515 65 A

1612084516 71 G

1612084517 67 C

1612084518 65 A

1612084519 65 A

1612084520 84 T

1612084521 65 A

1612084522 67 C

1612084523 71 G

1612084524 84 T

1612084525 65 A

1612084526 65 A

1612084527 10

1612084528 43 +

1612084529 10 Error occurred at this position.

1612084530 62 >


So is there a way to remove all of this specific read or just tweek the "+" character out of this read?



Thanks
S






linux







share|improve this question









New contributor



sailajah vishwanathan is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.






















  • looks like a linefeed (10) followed by a + (43) and then another LF. can you show the sed command (and any other commands) you used to transform the input?

    – cas
    yesterday








  • 1





    also, while i am no expert in fasta files or bioinformatics, I have done some work in the field (as a programmer/sysadmin, not as a bio scientist) and i can't help but think you'd be better off manipulating such files using tools like bioperl or biopython than "rolling your own" with awk or sed. If you can't decide between perl or python, look here For what bioinformatics tasks is Biopython more adapted than Bioperl?

    – cas
    yesterday








  • 1





    BTW, if you haven't run across them before, both bioinformatics.stackexchange.com AND biostars.org are worth checking out.

    – cas
    yesterday













  • The sed command i used was sed -e '/^[^>]/s/[^ATGCatgc]//g' <input.fasta> <output.fasta>

    – sailajah vishwanathan
    yesterday











  • And for converting my fastq files into a single line fasta file i used a Python script

    – sailajah vishwanathan
    yesterday


















0















An error occurred while processing read where a "+" symbol seems to hinder the sequence. This is the specif error that I got after i converted a multi line fasta to a single line fasta and used sed command to remove unwanted characters.



An error occurred processing read TTGTATGCAGCCCAAAAATACCTAAAATTTGGCTCGCGCGGAATGCTAATTCCACCGTTTACAGCCTCCCTTGGGTTGACGAGCCAAAAAAGTGGATCCTTCATGCATGTGTGCCCATGCTATCCTTTAATAGTAACCTTGTCGTTTATCTTAATACTCCTCCGACAACATAATAGTGATTTTACATGAAAAAGACGTGAGTCAACGTTGCGAATCCATTCCGTGACTGATTCGATCCTAGTTTCGTCGAGTTCTTCAATATCTATTTCGTGGCCACATGTTGAGCTATTTGTGACAAATTTGTCAAATTTGCGTCGCAGTCGGCCAGTCGAAACATATTTCGAGTAACTTTCGTGTTAAATATTTTCTCATTTTGATATTCATGCAGGTAGATCGAATCCCCAATATACCGTATAAAGTTATAGATCTACTCGGCTAACTCGGCTACGAATGTCAAAACCAAAGGTTAGAACACGATAGTTGTGCGAAATGGTCTCCTCAAAGAAAATTTCTAGATAATTACGTGCATGTACGTGTGAGCAGAAAACGTCATCAAAAATATCTAAATGTGAACATTGAATAGAGCTTTAAGCACTCGATACGAACAGTCATGGAAATGGAATCAAAACATCGAGCAACACATCTTTTTCATGTAGACCTTGGCTAAATTAAAGCATGATTAGATAGATCAAGAGGATTAAAAAAGATTGAACTACTTTAGTTAAACACAACATACATAATGTACATGTAACCAAACAACGGGACTTATGTTTCTCCCACATATTAGCGAAAGTGGAACTGTTAGCAACCAAACCATATGCAGAATTAGGCCCAAATCAGAGTTTCCACCTATACAACTTTCCAATGGGCCAAGTTGCAAGAGGGAAACACCCATGTGGGCACCAAACCTCCACAAAAGCAGCTCGTATGCGAGCTCTGCATGAACTTGGCCTAGCTCAGTGCAGCTAGCAAGCCAGCAGCGTAGGTCACTTCCATGTGGGTTCATATTCCCTGTACGTAGGGGCGACATATATGGAGCATGCTGCACCATGGACGAGGAGGATGGTGCTATAGCGAATTATGTGGCGGCATAGTGGGGGTGAGGGAGCAAGGCTGCACGAGTCGTTGTGGCTTGGCATGTCAGCCCCGACGTCGTGGGTGAAGGTTGATGCGGTTTCGCGAGGACTATGTGGTATGCATACGAGTGTGCGGTGGGGAAGGCTTTAGGTGGCCACACACATAGTGTTTTTATTGTGGCCACAGGCTTGAGGTAGAGAGTTTGTGATGTGGCAGGATGATAGGGTGGGATGAACGACCACCAACTCCCAAATAATTTTCCAATTAATAGCAAATATACAAAATTTCTTGCATACTCTCATTGTTTCAATGAATAATACTTCTTTTAAAAAAATCAGGCCAAGTAAAGTTTATCCAAGATGTTATATGAATATCTTATAAAAATATATTTCATGATCTTGTATCTAATGATACTACCTCCCGTCCAGATTCATAGGGTTGCGCGTATCCCTAGGTTGTAAATTTGAAAATTGATATAATATCGTTTGTATAATATAAAAAATATCATTAGAAAGAAAGTAGAACATACAAAGCTTTACTACATTGATATATATTTTTGTAATACGTATGTTGTTATCATTCTGGAATTTACGGCTTACAGTTTCTGTGTGAGTCTGTGGCCAGGACGAAAGTATTGATTTTTCATTTGCATGTTGATAACATTGAGATGGATTTTCTCCATCCTTACGTTATCTTCTCAATCTCTGCATCAGAGTTGGCTTTGGGCTCCTATACGGGAGGCGTCTGTTGGCCGTTTTAAGCGGAGCGGACAGGTGGCTCCGCATACCTTTTTTGGTGATCAGATTTGATGGGCTCGGCCCATTTACCGACCTGATGTTCTTATAGGATTTACCCTTACGAACAGCTGAGTCTTATCATCAGAAAATGATCAGCAGTTATCAATATGTTTAACTCCGTTGACCTAACGTATAGAAATATAAAATGGAATATTATATCGCGCTCTTTTGATCCTCAAAGGGCTTTTTTGGAAGGCCTATCCTCCGAGATCTAAGGCCGATCAATCGCGATCCCAGCAATCATTCCAGCCGCTGCGCATCCAGCAGAGACCTTCGAACCCTCCTCCGACGACCTGTCGGCCGCCGCCGGCGACTACCCTCCCTGGGTGATTTTCGACGAGCAGGAACGCCGCTATCGCCACAAGGAGGTCAATGATACCCCAGCCCGCTGACCCCAGGACGGTGGCGCACGCTCGCACCTCCACCGGCCACCCCGTCCAGTTTCCTTCCGCTTCGCCGCTCCCCGGCAGTTTCGTGTCTGGACCTCAGCGTCGACGACGGCTTGCTGGATGGGGTGGATATTATTTCCAGCGTCGTCGTGGCTCACGGCGATCCGTCCTCCTTACATATGATACTGTTACTGTACAAGTACGAGATCAACACGACCGACTATTTCGTCTACAATGCCGGCGACGGCGCCACGGCCGCCGTCGTTGTCGCTTCTCCCCTTGTTACATGGACGAGGAGGAACAGTCCCATGACAGACGGTACCGGTGACTATGAGTAGGAAACGCACTGGCATCCTGCGTCGCGGCGACGAGGAGTTGGTGGTGATGATGGACCTGAGGATGATGAACACTATTGCGTGCGATGATGATGGGTGGGGCAAAGCAGGTGGAAGGTGAGGTCGCGTACTCCGGTCGGGGAGTGGCAGTGGAAGGCCGAGGCGCTCCGGTCCGCCACGATGTGAGCAAAGGCGAGGTGACTTCGTACTGCTGGTGGTGGGTGTGGGAGACCGACCGGGTGATCCCCGTCGGCGACCGGTTCTTATACTGGGTAGACCTACACCGAGGCATCGTCTTCTCCGACGTGTCCGAAAGCCCCGATCTGAGGTTCGTGCCTCTGCCCGTGGAGCCTATCCTCCGTAGACGCGAGGACTGGGACCGGCCCAGTCGCGCCGCAGCCTGTGCGCCACGGCCGGCGGCGCGACTCTGAAGTTCGTCCACGTCTCACCTCGCTGCTGTTGCGAGCAATACGTAA

The error occurred at buffer index 1612084529while processing file block at offset 81604378624 to 83751862272

File offset at error location is 83216463153

File dump around this offset:

1612084479 84 T

1612084480 71 G

1612084481 65 A

1612084482 65 A

1612084483 71 G

1612084484 84 T

1612084485 84 T

1612084486 67 C

1612084487 71 G

1612084488 84 T

1612084489 67 C

1612084490 67 C

1612084491 65 A

1612084492 67 C

1612084493 71 G

1612084494 84 T

1612084495 67 C

1612084496 84 T

1612084497 67 C

1612084498 65 A

1612084499 67 C

1612084500 67 C

1612084501 84 T

1612084502 67 C

1612084503 71 G

1612084504 67 C

1612084505 84 T

1612084506 71 G

1612084507 67 C

1612084508 84 T

1612084509 71 G

1612084510 84 T

1612084511 84 T

1612084512 71 G

1612084513 67 C

1612084514 71 G

1612084515 65 A

1612084516 71 G

1612084517 67 C

1612084518 65 A

1612084519 65 A

1612084520 84 T

1612084521 65 A

1612084522 67 C

1612084523 71 G

1612084524 84 T

1612084525 65 A

1612084526 65 A

1612084527 10

1612084528 43 +

1612084529 10 Error occurred at this position.

1612084530 62 >


So is there a way to remove all of this specific read or just tweek the "+" character out of this read?



Thanks
S






linux







share|improve this question









New contributor



sailajah vishwanathan is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.






















  • looks like a linefeed (10) followed by a + (43) and then another LF. can you show the sed command (and any other commands) you used to transform the input?

    – cas
    yesterday








  • 1





    also, while i am no expert in fasta files or bioinformatics, I have done some work in the field (as a programmer/sysadmin, not as a bio scientist) and i can't help but think you'd be better off manipulating such files using tools like bioperl or biopython than "rolling your own" with awk or sed. If you can't decide between perl or python, look here For what bioinformatics tasks is Biopython more adapted than Bioperl?

    – cas
    yesterday








  • 1





    BTW, if you haven't run across them before, both bioinformatics.stackexchange.com AND biostars.org are worth checking out.

    – cas
    yesterday













  • The sed command i used was sed -e '/^[^>]/s/[^ATGCatgc]//g' <input.fasta> <output.fasta>

    – sailajah vishwanathan
    yesterday











  • And for converting my fastq files into a single line fasta file i used a Python script

    – sailajah vishwanathan
    yesterday














0












0








0








An error occurred while processing read where a "+" symbol seems to hinder the sequence. This is the specif error that I got after i converted a multi line fasta to a single line fasta and used sed command to remove unwanted characters.



An error occurred processing read TTGTATGCAGCCCAAAAATACCTAAAATTTGGCTCGCGCGGAATGCTAATTCCACCGTTTACAGCCTCCCTTGGGTTGACGAGCCAAAAAAGTGGATCCTTCATGCATGTGTGCCCATGCTATCCTTTAATAGTAACCTTGTCGTTTATCTTAATACTCCTCCGACAACATAATAGTGATTTTACATGAAAAAGACGTGAGTCAACGTTGCGAATCCATTCCGTGACTGATTCGATCCTAGTTTCGTCGAGTTCTTCAATATCTATTTCGTGGCCACATGTTGAGCTATTTGTGACAAATTTGTCAAATTTGCGTCGCAGTCGGCCAGTCGAAACATATTTCGAGTAACTTTCGTGTTAAATATTTTCTCATTTTGATATTCATGCAGGTAGATCGAATCCCCAATATACCGTATAAAGTTATAGATCTACTCGGCTAACTCGGCTACGAATGTCAAAACCAAAGGTTAGAACACGATAGTTGTGCGAAATGGTCTCCTCAAAGAAAATTTCTAGATAATTACGTGCATGTACGTGTGAGCAGAAAACGTCATCAAAAATATCTAAATGTGAACATTGAATAGAGCTTTAAGCACTCGATACGAACAGTCATGGAAATGGAATCAAAACATCGAGCAACACATCTTTTTCATGTAGACCTTGGCTAAATTAAAGCATGATTAGATAGATCAAGAGGATTAAAAAAGATTGAACTACTTTAGTTAAACACAACATACATAATGTACATGTAACCAAACAACGGGACTTATGTTTCTCCCACATATTAGCGAAAGTGGAACTGTTAGCAACCAAACCATATGCAGAATTAGGCCCAAATCAGAGTTTCCACCTATACAACTTTCCAATGGGCCAAGTTGCAAGAGGGAAACACCCATGTGGGCACCAAACCTCCACAAAAGCAGCTCGTATGCGAGCTCTGCATGAACTTGGCCTAGCTCAGTGCAGCTAGCAAGCCAGCAGCGTAGGTCACTTCCATGTGGGTTCATATTCCCTGTACGTAGGGGCGACATATATGGAGCATGCTGCACCATGGACGAGGAGGATGGTGCTATAGCGAATTATGTGGCGGCATAGTGGGGGTGAGGGAGCAAGGCTGCACGAGTCGTTGTGGCTTGGCATGTCAGCCCCGACGTCGTGGGTGAAGGTTGATGCGGTTTCGCGAGGACTATGTGGTATGCATACGAGTGTGCGGTGGGGAAGGCTTTAGGTGGCCACACACATAGTGTTTTTATTGTGGCCACAGGCTTGAGGTAGAGAGTTTGTGATGTGGCAGGATGATAGGGTGGGATGAACGACCACCAACTCCCAAATAATTTTCCAATTAATAGCAAATATACAAAATTTCTTGCATACTCTCATTGTTTCAATGAATAATACTTCTTTTAAAAAAATCAGGCCAAGTAAAGTTTATCCAAGATGTTATATGAATATCTTATAAAAATATATTTCATGATCTTGTATCTAATGATACTACCTCCCGTCCAGATTCATAGGGTTGCGCGTATCCCTAGGTTGTAAATTTGAAAATTGATATAATATCGTTTGTATAATATAAAAAATATCATTAGAAAGAAAGTAGAACATACAAAGCTTTACTACATTGATATATATTTTTGTAATACGTATGTTGTTATCATTCTGGAATTTACGGCTTACAGTTTCTGTGTGAGTCTGTGGCCAGGACGAAAGTATTGATTTTTCATTTGCATGTTGATAACATTGAGATGGATTTTCTCCATCCTTACGTTATCTTCTCAATCTCTGCATCAGAGTTGGCTTTGGGCTCCTATACGGGAGGCGTCTGTTGGCCGTTTTAAGCGGAGCGGACAGGTGGCTCCGCATACCTTTTTTGGTGATCAGATTTGATGGGCTCGGCCCATTTACCGACCTGATGTTCTTATAGGATTTACCCTTACGAACAGCTGAGTCTTATCATCAGAAAATGATCAGCAGTTATCAATATGTTTAACTCCGTTGACCTAACGTATAGAAATATAAAATGGAATATTATATCGCGCTCTTTTGATCCTCAAAGGGCTTTTTTGGAAGGCCTATCCTCCGAGATCTAAGGCCGATCAATCGCGATCCCAGCAATCATTCCAGCCGCTGCGCATCCAGCAGAGACCTTCGAACCCTCCTCCGACGACCTGTCGGCCGCCGCCGGCGACTACCCTCCCTGGGTGATTTTCGACGAGCAGGAACGCCGCTATCGCCACAAGGAGGTCAATGATACCCCAGCCCGCTGACCCCAGGACGGTGGCGCACGCTCGCACCTCCACCGGCCACCCCGTCCAGTTTCCTTCCGCTTCGCCGCTCCCCGGCAGTTTCGTGTCTGGACCTCAGCGTCGACGACGGCTTGCTGGATGGGGTGGATATTATTTCCAGCGTCGTCGTGGCTCACGGCGATCCGTCCTCCTTACATATGATACTGTTACTGTACAAGTACGAGATCAACACGACCGACTATTTCGTCTACAATGCCGGCGACGGCGCCACGGCCGCCGTCGTTGTCGCTTCTCCCCTTGTTACATGGACGAGGAGGAACAGTCCCATGACAGACGGTACCGGTGACTATGAGTAGGAAACGCACTGGCATCCTGCGTCGCGGCGACGAGGAGTTGGTGGTGATGATGGACCTGAGGATGATGAACACTATTGCGTGCGATGATGATGGGTGGGGCAAAGCAGGTGGAAGGTGAGGTCGCGTACTCCGGTCGGGGAGTGGCAGTGGAAGGCCGAGGCGCTCCGGTCCGCCACGATGTGAGCAAAGGCGAGGTGACTTCGTACTGCTGGTGGTGGGTGTGGGAGACCGACCGGGTGATCCCCGTCGGCGACCGGTTCTTATACTGGGTAGACCTACACCGAGGCATCGTCTTCTCCGACGTGTCCGAAAGCCCCGATCTGAGGTTCGTGCCTCTGCCCGTGGAGCCTATCCTCCGTAGACGCGAGGACTGGGACCGGCCCAGTCGCGCCGCAGCCTGTGCGCCACGGCCGGCGGCGCGACTCTGAAGTTCGTCCACGTCTCACCTCGCTGCTGTTGCGAGCAATACGTAA

The error occurred at buffer index 1612084529while processing file block at offset 81604378624 to 83751862272

File offset at error location is 83216463153

File dump around this offset:

1612084479 84 T

1612084480 71 G

1612084481 65 A

1612084482 65 A

1612084483 71 G

1612084484 84 T

1612084485 84 T

1612084486 67 C

1612084487 71 G

1612084488 84 T

1612084489 67 C

1612084490 67 C

1612084491 65 A

1612084492 67 C

1612084493 71 G

1612084494 84 T

1612084495 67 C

1612084496 84 T

1612084497 67 C

1612084498 65 A

1612084499 67 C

1612084500 67 C

1612084501 84 T

1612084502 67 C

1612084503 71 G

1612084504 67 C

1612084505 84 T

1612084506 71 G

1612084507 67 C

1612084508 84 T

1612084509 71 G

1612084510 84 T

1612084511 84 T

1612084512 71 G

1612084513 67 C

1612084514 71 G

1612084515 65 A

1612084516 71 G

1612084517 67 C

1612084518 65 A

1612084519 65 A

1612084520 84 T

1612084521 65 A

1612084522 67 C

1612084523 71 G

1612084524 84 T

1612084525 65 A

1612084526 65 A

1612084527 10

1612084528 43 +

1612084529 10 Error occurred at this position.

1612084530 62 >


So is there a way to remove all of this specific read or just tweek the "+" character out of this read?



Thanks
S






linux







share|improve this question









New contributor



sailajah vishwanathan is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.











An error occurred while processing read where a "+" symbol seems to hinder the sequence. This is the specif error that I got after i converted a multi line fasta to a single line fasta and used sed command to remove unwanted characters.



An error occurred processing read TTGTATGCAGCCCAAAAATACCTAAAATTTGGCTCGCGCGGAATGCTAATTCCACCGTTTACAGCCTCCCTTGGGTTGACGAGCCAAAAAAGTGGATCCTTCATGCATGTGTGCCCATGCTATCCTTTAATAGTAACCTTGTCGTTTATCTTAATACTCCTCCGACAACATAATAGTGATTTTACATGAAAAAGACGTGAGTCAACGTTGCGAATCCATTCCGTGACTGATTCGATCCTAGTTTCGTCGAGTTCTTCAATATCTATTTCGTGGCCACATGTTGAGCTATTTGTGACAAATTTGTCAAATTTGCGTCGCAGTCGGCCAGTCGAAACATATTTCGAGTAACTTTCGTGTTAAATATTTTCTCATTTTGATATTCATGCAGGTAGATCGAATCCCCAATATACCGTATAAAGTTATAGATCTACTCGGCTAACTCGGCTACGAATGTCAAAACCAAAGGTTAGAACACGATAGTTGTGCGAAATGGTCTCCTCAAAGAAAATTTCTAGATAATTACGTGCATGTACGTGTGAGCAGAAAACGTCATCAAAAATATCTAAATGTGAACATTGAATAGAGCTTTAAGCACTCGATACGAACAGTCATGGAAATGGAATCAAAACATCGAGCAACACATCTTTTTCATGTAGACCTTGGCTAAATTAAAGCATGATTAGATAGATCAAGAGGATTAAAAAAGATTGAACTACTTTAGTTAAACACAACATACATAATGTACATGTAACCAAACAACGGGACTTATGTTTCTCCCACATATTAGCGAAAGTGGAACTGTTAGCAACCAAACCATATGCAGAATTAGGCCCAAATCAGAGTTTCCACCTATACAACTTTCCAATGGGCCAAGTTGCAAGAGGGAAACACCCATGTGGGCACCAAACCTCCACAAAAGCAGCTCGTATGCGAGCTCTGCATGAACTTGGCCTAGCTCAGTGCAGCTAGCAAGCCAGCAGCGTAGGTCACTTCCATGTGGGTTCATATTCCCTGTACGTAGGGGCGACATATATGGAGCATGCTGCACCATGGACGAGGAGGATGGTGCTATAGCGAATTATGTGGCGGCATAGTGGGGGTGAGGGAGCAAGGCTGCACGAGTCGTTGTGGCTTGGCATGTCAGCCCCGACGTCGTGGGTGAAGGTTGATGCGGTTTCGCGAGGACTATGTGGTATGCATACGAGTGTGCGGTGGGGAAGGCTTTAGGTGGCCACACACATAGTGTTTTTATTGTGGCCACAGGCTTGAGGTAGAGAGTTTGTGATGTGGCAGGATGATAGGGTGGGATGAACGACCACCAACTCCCAAATAATTTTCCAATTAATAGCAAATATACAAAATTTCTTGCATACTCTCATTGTTTCAATGAATAATACTTCTTTTAAAAAAATCAGGCCAAGTAAAGTTTATCCAAGATGTTATATGAATATCTTATAAAAATATATTTCATGATCTTGTATCTAATGATACTACCTCCCGTCCAGATTCATAGGGTTGCGCGTATCCCTAGGTTGTAAATTTGAAAATTGATATAATATCGTTTGTATAATATAAAAAATATCATTAGAAAGAAAGTAGAACATACAAAGCTTTACTACATTGATATATATTTTTGTAATACGTATGTTGTTATCATTCTGGAATTTACGGCTTACAGTTTCTGTGTGAGTCTGTGGCCAGGACGAAAGTATTGATTTTTCATTTGCATGTTGATAACATTGAGATGGATTTTCTCCATCCTTACGTTATCTTCTCAATCTCTGCATCAGAGTTGGCTTTGGGCTCCTATACGGGAGGCGTCTGTTGGCCGTTTTAAGCGGAGCGGACAGGTGGCTCCGCATACCTTTTTTGGTGATCAGATTTGATGGGCTCGGCCCATTTACCGACCTGATGTTCTTATAGGATTTACCCTTACGAACAGCTGAGTCTTATCATCAGAAAATGATCAGCAGTTATCAATATGTTTAACTCCGTTGACCTAACGTATAGAAATATAAAATGGAATATTATATCGCGCTCTTTTGATCCTCAAAGGGCTTTTTTGGAAGGCCTATCCTCCGAGATCTAAGGCCGATCAATCGCGATCCCAGCAATCATTCCAGCCGCTGCGCATCCAGCAGAGACCTTCGAACCCTCCTCCGACGACCTGTCGGCCGCCGCCGGCGACTACCCTCCCTGGGTGATTTTCGACGAGCAGGAACGCCGCTATCGCCACAAGGAGGTCAATGATACCCCAGCCCGCTGACCCCAGGACGGTGGCGCACGCTCGCACCTCCACCGGCCACCCCGTCCAGTTTCCTTCCGCTTCGCCGCTCCCCGGCAGTTTCGTGTCTGGACCTCAGCGTCGACGACGGCTTGCTGGATGGGGTGGATATTATTTCCAGCGTCGTCGTGGCTCACGGCGATCCGTCCTCCTTACATATGATACTGTTACTGTACAAGTACGAGATCAACACGACCGACTATTTCGTCTACAATGCCGGCGACGGCGCCACGGCCGCCGTCGTTGTCGCTTCTCCCCTTGTTACATGGACGAGGAGGAACAGTCCCATGACAGACGGTACCGGTGACTATGAGTAGGAAACGCACTGGCATCCTGCGTCGCGGCGACGAGGAGTTGGTGGTGATGATGGACCTGAGGATGATGAACACTATTGCGTGCGATGATGATGGGTGGGGCAAAGCAGGTGGAAGGTGAGGTCGCGTACTCCGGTCGGGGAGTGGCAGTGGAAGGCCGAGGCGCTCCGGTCCGCCACGATGTGAGCAAAGGCGAGGTGACTTCGTACTGCTGGTGGTGGGTGTGGGAGACCGACCGGGTGATCCCCGTCGGCGACCGGTTCTTATACTGGGTAGACCTACACCGAGGCATCGTCTTCTCCGACGTGTCCGAAAGCCCCGATCTGAGGTTCGTGCCTCTGCCCGTGGAGCCTATCCTCCGTAGACGCGAGGACTGGGACCGGCCCAGTCGCGCCGCAGCCTGTGCGCCACGGCCGGCGGCGCGACTCTGAAGTTCGTCCACGTCTCACCTCGCTGCTGTTGCGAGCAATACGTAA

The error occurred at buffer index 1612084529while processing file block at offset 81604378624 to 83751862272

File offset at error location is 83216463153

File dump around this offset:

1612084479 84 T

1612084480 71 G

1612084481 65 A

1612084482 65 A

1612084483 71 G

1612084484 84 T

1612084485 84 T

1612084486 67 C

1612084487 71 G

1612084488 84 T

1612084489 67 C

1612084490 67 C

1612084491 65 A

1612084492 67 C

1612084493 71 G

1612084494 84 T

1612084495 67 C

1612084496 84 T

1612084497 67 C

1612084498 65 A

1612084499 67 C

1612084500 67 C

1612084501 84 T

1612084502 67 C

1612084503 71 G

1612084504 67 C

1612084505 84 T

1612084506 71 G

1612084507 67 C

1612084508 84 T

1612084509 71 G

1612084510 84 T

1612084511 84 T

1612084512 71 G

1612084513 67 C

1612084514 71 G

1612084515 65 A

1612084516 71 G

1612084517 67 C

1612084518 65 A

1612084519 65 A

1612084520 84 T

1612084521 65 A

1612084522 67 C

1612084523 71 G

1612084524 84 T

1612084525 65 A

1612084526 65 A

1612084527 10

1612084528 43 +

1612084529 10 Error occurred at this position.

1612084530 62 >


So is there a way to remove all of this specific read or just tweek the "+" character out of this read?



Thanks
S






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edited yesterday









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asked yesterday









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  • looks like a linefeed (10) followed by a + (43) and then another LF. can you show the sed command (and any other commands) you used to transform the input?

    – cas
    yesterday








  • 1





    also, while i am no expert in fasta files or bioinformatics, I have done some work in the field (as a programmer/sysadmin, not as a bio scientist) and i can't help but think you'd be better off manipulating such files using tools like bioperl or biopython than "rolling your own" with awk or sed. If you can't decide between perl or python, look here For what bioinformatics tasks is Biopython more adapted than Bioperl?

    – cas
    yesterday








  • 1





    BTW, if you haven't run across them before, both bioinformatics.stackexchange.com AND biostars.org are worth checking out.

    – cas
    yesterday













  • The sed command i used was sed -e '/^[^>]/s/[^ATGCatgc]//g' <input.fasta> <output.fasta>

    – sailajah vishwanathan
    yesterday











  • And for converting my fastq files into a single line fasta file i used a Python script

    – sailajah vishwanathan
    yesterday



















  • looks like a linefeed (10) followed by a + (43) and then another LF. can you show the sed command (and any other commands) you used to transform the input?

    – cas
    yesterday








  • 1





    also, while i am no expert in fasta files or bioinformatics, I have done some work in the field (as a programmer/sysadmin, not as a bio scientist) and i can't help but think you'd be better off manipulating such files using tools like bioperl or biopython than "rolling your own" with awk or sed. If you can't decide between perl or python, look here For what bioinformatics tasks is Biopython more adapted than Bioperl?

    – cas
    yesterday








  • 1





    BTW, if you haven't run across them before, both bioinformatics.stackexchange.com AND biostars.org are worth checking out.

    – cas
    yesterday













  • The sed command i used was sed -e '/^[^>]/s/[^ATGCatgc]//g' <input.fasta> <output.fasta>

    – sailajah vishwanathan
    yesterday











  • And for converting my fastq files into a single line fasta file i used a Python script

    – sailajah vishwanathan
    yesterday

















looks like a linefeed (10) followed by a + (43) and then another LF. can you show the sed command (and any other commands) you used to transform the input?

– cas
yesterday







looks like a linefeed (10) followed by a + (43) and then another LF. can you show the sed command (and any other commands) you used to transform the input?

– cas
yesterday






1




1





also, while i am no expert in fasta files or bioinformatics, I have done some work in the field (as a programmer/sysadmin, not as a bio scientist) and i can't help but think you'd be better off manipulating such files using tools like bioperl or biopython than "rolling your own" with awk or sed. If you can't decide between perl or python, look here For what bioinformatics tasks is Biopython more adapted than Bioperl?

– cas
yesterday







also, while i am no expert in fasta files or bioinformatics, I have done some work in the field (as a programmer/sysadmin, not as a bio scientist) and i can't help but think you'd be better off manipulating such files using tools like bioperl or biopython than "rolling your own" with awk or sed. If you can't decide between perl or python, look here For what bioinformatics tasks is Biopython more adapted than Bioperl?

– cas
yesterday






1




1





BTW, if you haven't run across them before, both bioinformatics.stackexchange.com AND biostars.org are worth checking out.

– cas
yesterday







BTW, if you haven't run across them before, both bioinformatics.stackexchange.com AND biostars.org are worth checking out.

– cas
yesterday















The sed command i used was sed -e '/^[^>]/s/[^ATGCatgc]//g' <input.fasta> <output.fasta>

– sailajah vishwanathan
yesterday





The sed command i used was sed -e '/^[^>]/s/[^ATGCatgc]//g' <input.fasta> <output.fasta>

– sailajah vishwanathan
yesterday













And for converting my fastq files into a single line fasta file i used a Python script

– sailajah vishwanathan
yesterday





And for converting my fastq files into a single line fasta file i used a Python script

– sailajah vishwanathan
yesterday










0






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