[protocols] protocols Digest, Vol 10, Issue 1

Tue Feb 9 23:49:30 PST 2016

Hi,
I followed the protocol at given link
http://khmer-protocols.readthedocs.org/en/latest/mrnaseq/6-annotating-transcript-families.html

After running this command

annotate-seqs.py trinity-nematostella.renamed.fa nema.x.mouse.ortho
nema.x.mouse.homol

I got following output as below, Also pasted the first few lines from
each output file.
* I used the data given by the author I could not replicate the results can
you see why ??? *
(khmerEnv)q at dx4-biotek12:~/Software/Annotation$
./eel-pond-master/annotate-seqs.py trinity-nematostella.renamed.fa
nema.x.mouse.ortho nema.x.mouse.homol
Scanning sequences -- first pass to gather info
... 0
... 25000
... 50000
... 75000
... 100000
... 125000
... 150000
... 175000
... 200000
second pass: annotating
... x2 0
... x2 25000
... x2 50000
... x2 75000
... x2 100000
... x2 125000
... x2 150000
... x2 175000
... x2 200000
----
207533 sequences total
0 annotated / ortho
0 annotated / homol
0 annotated / tr
0 total annotated

annotated sequences in FASTA format: trinity-nematostella.renamed.fa.annot
annotation spreadsheet in: trinity-nematostella.renamed.fa.annot.csv
annotation spreadsheet with sequences (warning: LARGE):
trinity-nematostella.renamed.fa.annot.large.csv

*less*
*trinity-nematostella.renamed.fa.annot*>nema.id1.tr89018
1_of_1_in_tr89018 len=261 id=1 tr=89018
CAGCCTTTAGAAGGAAACAGTGGCAATATATAATTCTAGATGAAGCTCAGAATATCAAAAATTTTAAAAGTCAAAGGTGGCAGTTGCTGTTGAATTTTTCAAGTCAGAGGAGACTTTTGTTGACTGGAACACCTTTGCAGAACAATTTGATGGAGCTGTGGTCGCTTATGCATTTCCTCATGCCATCAATGTTTGCTTCTCATAAAGATTTTAGGGAGTGGTTTTCTAACCCTGTTACAGGGATGATTGAAGGGAATTCAG
>nema.id2.tr459575 1_of_1_in_tr459575 len=217 id=2 tr=459575
GCCAGTTGCAAACACGAATTTCAATCCATTAACATTTCATGAGTTGGAATCTCCACAGAAACTTTCTTTTCATCACGACCCCTGTTCCAAATGATTCCTTTCACACAAAACTGACCGGACAGGAAACAGAAAAAACAAGCAAGGGTCATGCAATAGACGACTTATTACCGGAAACCGCGATATTTAGCCAAGACATAAGTGCAAATTAAAACATCGA
>nema.id3.tr219232 1_of_1_in_tr219232 len=252 id=3 tr=219232

*less trinity-nematostella.renamed.fa.annot.csv*
sequence name,unique ID,Transcript family,ortholog,homology
score,homolog,family orthology,family homology,additional information
nema.id1.tr89018 1_of_1_in_tr89018 len=261 id=1 tr=89018,id1,tr89018
1_of_1_in_tr89018 len=261 id=1 tr=89018,,,,,,
nema.id2.tr459575 1_of_1_in_tr459575 len=217 id=2
tr=459575,id2,tr459575 1_of_1_in_tr459575 len=217 id=2 tr=459575,,,,,,
nema.id3.tr219232 1_of_1_in_tr219232 len=252 id=3
tr=219232,id3,tr219232 1_of_1_in_tr219232 len=252 id=3 tr=219232,,,,,,
nema.id4.tr355712 1_of_1_in_tr355712 len=226 id=4
tr=355712,id4,tr355712 1_of_1_in_tr355712 len=226 id=4 tr=355712,,,,,,
nema.id5.tr222444 1_of_1_in_tr222444 len=252 id=5
tr=222444,id5,tr222444 1_of_1_in_tr222444 len=252 id=5 tr=222444,,,,,,

*less trinity-nematostella.renamed.fa.annot.large.csv*
sequence name,unique ID,Transcript family,ortholog,homology
score,homolog,family orthology,family homology,additional
information,sequence
nema.id1.tr89018 1_of_1_in_tr89018 len=261 id=1 tr=89018,id1,tr89018
1_of_1_in_tr89018 len=261 id=1
tr=89018,,,,,,,CAGCCTTTAGAAGGAAACAGTGGCAATATATAATTCTAGATGAAGCTCAGAATATCAAAAATTTTAAAAGTCAAAGGTGGCAGTTGCTGTTGAATTTTTCAAGTCAGAGGAGACTTTTGTTGACTGGAACACCTTTGCAGAACAATTTGATGGAGCTGTGGTCGCTTATGCATTTCCTCATGCCATCAATGTTTGCTTCTCATAAAGATTTTAGGGAGTGGTTTTCTAACCCTGTTACAGGGATGATTGAAGGGAATTCAG

On Tue, Feb 9, 2016 at 10:00 PM, <protocols-request at lists.idyll.org> wrote:

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>    1. annotate-seqs.py Gives not hit (Guddu Khan)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 9 Feb 2016 17:54:05 +0200
> From: Guddu Khan <gudduport at gmail.com>
> Subject: [protocols] annotate-seqs.py Gives not hit
> To: protocols at lists.idyll.org
> Message-ID:
>         <
> CA+QNwoAXa7pnqj4_LosPJwPV+neZbwMXhtuy_XMjSeoY1T4mUg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
> I followed the protocol in given link
>
> http://khmer-protocols.readthedocs.org/en/latest/mrnaseq/6-annotating-transcript-families.html
>
> After running this command
>
> annotate-seqs.py trinity-nematostella.renamed.fa nema.x.mouse.ortho
> nema.x.mouse.homol
>
> I got following output as below, Also pasted the first few lines from
> each output file.
>
> (khmerEnv)q at dx4-biotek12:~/Software/Annotation$
> ./eel-pond-master/annotate-seqs.py trinity-nematostella.renamed.fa
> nema.x.mouse.ortho nema.x.mouse.homol
> Scanning sequences -- first pass to gather info
> ... 0
> ... 25000
> ... 50000
> ... 75000
> ... 100000
> ... 125000
> ... 150000
> ... 175000
> ... 200000
> second pass: annotating
> ... x2 0
> ... x2 25000
> ... x2 50000
> ... x2 75000
> ... x2 100000
> ... x2 125000
> ... x2 150000
> ... x2 175000
> ... x2 200000
> ----
> 207533 sequences total
> 0 annotated / ortho
> 0 annotated / homol
> 0 annotated / tr
> 0 total annotated
>
> annotated sequences in FASTA format: trinity-nematostella.renamed.fa.annot
> annotation spreadsheet in: trinity-nematostella.renamed.fa.annot.csv
> annotation spreadsheet with sequences (warning: LARGE):
> trinity-nematostella.renamed.fa.annot.large.csv
>
>
>
>
> *less*
> *trinity-nematostella.renamed.fa.annot*>nema.id1.tr89018
> 1_of_1_in_tr89018 len=261 id=1 tr=89018
>
> CAGCCTTTAGAAGGAAACAGTGGCAATATATAATTCTAGATGAAGCTCAGAATATCAAAAATTTTAAAAGTCAAAGGTGGCAGTTGCTGTTGAATTTTTCAAGTCAGAGGAGACTTTTGTTGACTGGAACACCTTTGCAGAACAATTTGATGGAGCTGTGGTCGCTTATGCATTTCCTCATGCCATCAATGTTTGCTTCTCATAAAGATTTTAGGGAGTGGTTTTCTAACCCTGTTACAGGGATGATTGAAGGGAATTCAG
> >nema.id2.tr459575 1_of_1_in_tr459575 len=217 id=2 tr=459575
>
> GCCAGTTGCAAACACGAATTTCAATCCATTAACATTTCATGAGTTGGAATCTCCACAGAAACTTTCTTTTCATCACGACCCCTGTTCCAAATGATTCCTTTCACACAAAACTGACCGGACAGGAAACAGAAAAAACAAGCAAGGGTCATGCAATAGACGACTTATTACCGGAAACCGCGATATTTAGCCAAGACATAAGTGCAAATTAAAACATCGA
> >nema.id3.tr219232 1_of_1_in_tr219232 len=252 id=3 tr=219232
>
>
>
> *less trinity-nematostella.renamed.fa.annot.csv*
> sequence name,unique ID,Transcript family,ortholog,homology
> score,homolog,family orthology,family homology,additional information
> nema.id1.tr89018 1_of_1_in_tr89018 len=261 id=1 tr=89018,id1,tr89018
> 1_of_1_in_tr89018 len=261 id=1 tr=89018,,,,,,
> nema.id2.tr459575 1_of_1_in_tr459575 len=217 id=2
> tr=459575,id2,tr459575 1_of_1_in_tr459575 len=217 id=2 tr=459575,,,,,,
> nema.id3.tr219232 1_of_1_in_tr219232 len=252 id=3
> tr=219232,id3,tr219232 1_of_1_in_tr219232 len=252 id=3 tr=219232,,,,,,
> nema.id4.tr355712 1_of_1_in_tr355712 len=226 id=4
> tr=355712,id4,tr355712 1_of_1_in_tr355712 len=226 id=4 tr=355712,,,,,,
> nema.id5.tr222444 1_of_1_in_tr222444 len=252 id=5
> tr=222444,id5,tr222444 1_of_1_in_tr222444 len=252 id=5 tr=222444,,,,,,
>
> *less trinity-nematostella.renamed.fa.annot.large.csv*
> sequence name,unique ID,Transcript family,ortholog,homology
> score,homolog,family orthology,family homology,additional
> information,sequence
> nema.id1.tr89018 1_of_1_in_tr89018 len=261 id=1 tr=89018,id1,tr89018
> 1_of_1_in_tr89018 len=261 id=1
>
> tr=89018,,,,,,,CAGCCTTTAGAAGGAAACAGTGGCAATATATAATTCTAGATGAAGCTCAGAATATCAAAAATTTTAAAAGTCAAAGGTGGCAGTTGCTGTTGAATTTTTCAAGTCAGAGGAGACTTTTGTTGACTGGAACACCTTTGCAGAACAATTTGATGGAGCTGTGGTCGCTTATGCATTTCCTCATGCCATCAATGTTTGCTTCTCATAAAGATTTTAGGGAGTGGTTTTCTAACCCTGTTACAGGGATGATTGAAGGGAATTCAG
>
>
>
>
> Regards
>
> Imran Khan
> Research Scholar,
> University of Porto
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