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common_scripts's Issues

gff2fasta.pl: help with a poorly formatted gff file

Hello,
I understand that you are not the original author of gff2fasta.pl (nor is it clear from the biostars page), but I was wondering if I could have some help modifying the script to be compatible with a gff file I was given that is oddly formatted.

Here are two entries from the file:

7000000037415267        .       gene    21339   22504   .       +       .       ID=7000003035155523;Function=polygalacturonase%2C%20putative;Name=PITG_19619
7000000037415267        .       mRNA    21339   22504   .       +       .       ID=7000003035155526;Parent=7000003035155523;Function=polygalacturonase%2C%20putative;Name=PITG_19619
7000000037415267        .       exon    21339   21714   .       +       .       ID=7000003035155526.exon2;Parent=7000003035155526
7000000037415267        .       CDS     21339   21714   .       +       0       ID=cds.7000003035155526;Parent=7000003035155526
7000000037415267        .       exon    21749   22170   .       +       .       ID=7000003035155526.exon3;Parent=7000003035155526
7000000037415267        .       CDS     21749   22170   .       +       2       ID=cds.7000003035155526;Parent=7000003035155526
7000000037415267        .       exon    22307   22504   .       +       .       ID=7000003035155526.exon4;Parent=7000003035155526
7000000037415267        .       CDS     22307   22504   .       +       0       ID=cds.7000003035155526;Parent=7000003035155526

7000000037414998        .       gene    679960  682584  .       +       .       ID=7000003035181604;Function=conserved%20hypothetical%20protein;Name=PITG_09139
7000000037414998        .       mRNA    679960  682584  .       +       .       ID=7000003035181607;Parent=7000003035181604;Function=conserved%20hypothetical%20protein;Name=PITG_09139
7000000037414998        .       five_prime_UTR  679960  680620  .       +       .       ID=7000003035181607.utr5p1;Parent=7000003035181607
7000000037414998        .       five_prime_UTR  680710  680802  .       +       .       ID=7000003035181607.utr5p2;Parent=7000003035181607
7000000037414998        .       five_prime_UTR  680907  680909  .       +       .       ID=7000003035181607.utr5p3;Parent=7000003035181607
7000000037414998        .       exon    679960  680620  .       +       .       ID=7000003035181607.exon1;Parent=7000003035181607
7000000037414998        .       exon    680710  680802  .       +       .       ID=7000003035181607.exon2;Parent=7000003035181607
7000000037414998        .       exon    680907  681227  .       +       .       ID=7000003035181607.exon3;Parent=7000003035181607
7000000037414998        .       CDS     680910  681227  .       +       0       ID=cds.7000003035181607;Parent=7000003035181607
7000000037414998        .       exon    681298  681489  .       +       .       ID=7000003035181607.exon4;Parent=7000003035181607
7000000037414998        .       CDS     681298  681489  .       +       0       ID=cds.7000003035181607;Parent=7000003035181607
7000000037414998        .       exon    681563  682584  .       +       .       ID=7000003035181607.exon5;Parent=7000003035181607
7000000037414998        .       CDS     681563  682174  .       +       0       ID=cds.7000003035181607;Parent=7000003035181607
7000000037414998        .       three_prime_UTR 682175  682584  .       +       .       ID=7000003035181607.utr3p1;Parent=7000003035181607

The gff2fasta.pl script is using, as entry/gene names, whatever string is behind "ID=" entry. As in, the genes output will be:

>7000003035155523
ATGCCTTTAGCGACGATCACTCTCCTCTTCTTCGCTAGCTTACCTCCCCAATCCACTCTT...
>7000003035181604
GGTGAACATGTTGTCTGTATTGTCTGTACTTGCCGACCATGAGCTCCTCGGTAGTGCACA...

And the output for mRNA, peptides, cds will be:

>7000003035155526
MPLATITLLFFASLPPQSTLHSAICFLPTQRPLKVQPAMKLVSSAFGVFALLAAFVSGST...
>7000003035181607
MSFSKSNLPPTLPVAIKKEREDPSSLSGSMSIPGSSSSIPRKDSIGWGADDFLGMISHTP...

Is there a way to name each line of the resulting fasta file to the string following "Name="? In these cases, that would be:

>PITG_19619
ATGCCTTTAGCGACGATCACTCTCCTCTTCTTCGCTAGCTTACCTCCCCAATCCACTCTT...
>PITG_19619
GGTGAACATGTTGTCTGTATTGTCTGTACTTGCCGACCATGAGCTCCTCGGTAGTGCACA...

and

>PITG_19619
MPLATITLLFFASLPPQSTLHSAICFLPTQRPLKVQPAMKLVSSAFGVFALLAAFVSGST...
>PITG_19619
MSFSKSNLPPTLPVAIKKEREDPSSLSGSMSIPGSSSSIPRKDSIGWGADDFLGMISHTP...

Much appreciated,
Mike

Confirm that use of BLAST's `-max_target_seqs` is intentional

Hi there,

This is a semi-automated message from a fellow bioinformatician. Through a GitHub search, I found that the following source files make use of BLAST's -max_target_seqs parameter:

Based on the recently published report, Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows, there is a strong chance that this parameter is misused in your repository.

If the use of this parameter was intentional, please feel free to ignore and close this issue but I would highly recommend to add a comment to your source code to notify others about this use case. If this is a duplicate issue, please accept my apologies for the redundancy as this simple automation is not smart enough to identify such issues.

Thank you!
-- Arman (armish/blast-patrol)

Extract exon sequence based on GFF3 end FASTA

Hi, after a hard search on the net I found this awesome script. It works nice. However, I need to extract all exon sequence from a genome based on GFF3 and FASTA. Please, found attached a GFF3 sample file.
From that file I need to extract these sequences:
>Eucgr.A00001.1.v2.0.exon.1
ACTGTGACA......
>Eucgr.A00001.1.v2.0.exon.2
ACTGTGACA......
>Eucgr.A00001.1.v2.0.exon.3
ACTGTGACA......
(...)
>Eucgr.A00001.1.v2.0.exon.12
ACTGTGACA......
(...)
Could you help me?
Thank you so much!

sample_GFF3_tsv.txt

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